1 |
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2003-06-25 16:12 mmeineke |
2 |
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|
3 |
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* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
4 |
< |
to Harmonic bonds in the DUFF frc file |
5 |
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|
6 |
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fixed constraints. |
7 |
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|
8 |
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2003-06-25 16:11 mmeineke |
9 |
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|
10 |
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* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
11 |
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the DUFF frc file |
12 |
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|
13 |
< |
2003-06-24 17:51 gezelter |
14 |
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|
15 |
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* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
16 |
< |
|
17 |
< |
2003-06-24 14:57 mmeineke |
18 |
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|
19 |
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* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
20 |
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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 |
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* libmdtools/Integrator.cpp: Doing some work to debug the |
26 |
< |
constraint code. |
27 |
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|
28 |
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2003-06-20 15:50 gezelter |
29 |
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|
30 |
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* libmdtools/Integrator.hpp: NPT fix |
31 |
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|
32 |
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2003-06-20 15:29 mmeineke |
33 |
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|
34 |
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* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
35 |
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libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
36 |
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libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
37 |
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libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
38 |
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libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
39 |
< |
integrator and NVT seem to be working now. |
40 |
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|
41 |
< |
2003-06-20 11:49 gezelter |
42 |
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|
43 |
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* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
44 |
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|
45 |
< |
2003-06-19 17:02 mmeineke |
46 |
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|
47 |
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* forceFields/DUFF.frc, forceFields/LJFF.frc, |
48 |
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forceFields/LJ_FF.frc, forceFields/Makefile, |
49 |
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forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
50 |
< |
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
51 |
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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 |
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|
58 |
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* 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 |
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|
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, |
1 |
> |
2004-05-07 16:36 gezelter |
2 |
> |
|
3 |
> |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
4 |
> |
for fortran group-based switching function |
5 |
> |
|
6 |
> |
2004-05-07 16:35 gezelter |
7 |
> |
|
8 |
> |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
9 |
> |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
10 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
11 |
> |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
12 |
> |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
13 |
> |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
14 |
> |
simulation_module.F90: Many changes to get group-based cutoffs to |
15 |
> |
work |
16 |
> |
|
17 |
> |
2004-05-01 13:52 tim |
18 |
> |
|
19 |
> |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
20 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
21 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
22 |
> |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
23 |
> |
libmdtools/fortranWrapDefines.hpp, |
24 |
> |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
25 |
> |
|
26 |
> |
2004-04-29 11:03 tim |
27 |
> |
|
28 |
> |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
29 |
> |
calc_charge_charge when using molecular cutoff |
30 |
> |
|
31 |
> |
2004-04-28 21:11 tim |
32 |
> |
|
33 |
> |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
34 |
> |
unmatched c/fortran interface |
35 |
> |
|
36 |
> |
2004-04-28 18:09 tim |
37 |
> |
|
38 |
> |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
39 |
> |
keep the previous position of cantilever in SMD |
40 |
> |
|
41 |
> |
2004-04-28 17:34 tim |
42 |
> |
|
43 |
> |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
44 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
45 |
> |
in Molecule.cpp which initialize massRatio before creat the array. |
46 |
> |
fix two bugs in ZconsVisitor |
47 |
> |
|
48 |
> |
2004-04-28 17:06 gezelter |
49 |
> |
|
50 |
> |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
51 |
> |
Adding molecular cutoffs |
52 |
> |
|
53 |
> |
2004-04-28 16:39 gezelter |
54 |
> |
|
55 |
> |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
56 |
> |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
57 |
> |
molecular cutoffs |
58 |
> |
|
59 |
> |
2004-04-28 16:39 gezelter |
60 |
> |
|
61 |
> |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
62 |
> |
Globals |
63 |
> |
|
64 |
> |
2004-04-27 11:26 tim |
65 |
> |
|
66 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
67 |
> |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
68 |
> |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
69 |
> |
molecule and massRation into atom class |
70 |
> |
|
71 |
> |
2004-04-26 16:16 mmeineke |
72 |
> |
|
73 |
> |
* libBASS/Globals.cpp: modified the defaults for the system init |
74 |
> |
time and system init state. |
75 |
> |
|
76 |
> |
2004-04-26 09:29 gezelter |
77 |
> |
|
78 |
> |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
79 |
> |
calc_charge_charge.F90 |
80 |
> |
|
81 |
> |
2004-04-23 23:31 tim |
82 |
> |
|
83 |
> |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
84 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
85 |
> |
reaction field correction to charge-charge interaction |
86 |
> |
|
87 |
> |
2004-04-22 16:33 tim |
88 |
> |
|
89 |
> |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
90 |
> |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
91 |
> |
calculation of pressure tensor |
92 |
> |
|
93 |
> |
2004-04-22 09:55 tim |
94 |
> |
|
95 |
> |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
96 |
> |
another bug in InitFromFile. MPI verion of OOPSE is working again |
97 |
> |
|
98 |
> |
2004-04-21 22:29 tim |
99 |
> |
|
100 |
> |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
101 |
> |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
102 |
> |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
103 |
> |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
104 |
> |
DumpWriter |
105 |
> |
|
106 |
> |
2004-04-21 00:32 tim |
107 |
> |
|
108 |
> |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
109 |
> |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
110 |
> |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
111 |
> |
useless files |
112 |
> |
|
113 |
> |
2004-04-20 11:56 tim |
114 |
> |
|
115 |
> |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
116 |
> |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
117 |
> |
velocitize at thermo |
118 |
> |
|
119 |
> |
2004-04-20 00:39 tim |
120 |
> |
|
121 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
122 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
123 |
> |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
124 |
> |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
125 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
126 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
127 |
> |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
128 |
> |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
129 |
> |
|
130 |
> |
2004-04-19 17:13 gezelter |
131 |
> |
|
132 |
> |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
133 |
> |
Thermo.cpp: Fixed a charge bug |
134 |
> |
|
135 |
> |
2004-04-19 15:54 tim |
136 |
> |
|
137 |
> |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
138 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
139 |
> |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
140 |
> |
a bug in CompositeVisitor which cause the double counting problem |
141 |
> |
|
142 |
> |
2004-04-19 12:44 tim |
143 |
> |
|
144 |
> |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
145 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
146 |
> |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
147 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
148 |
> |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
149 |
> |
Dump2XYZ is almost working except atoms in rigidbody are double |
150 |
> |
counted |
151 |
> |
|
152 |
> |
2004-04-18 22:52 tim |
153 |
> |
|
154 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
155 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
156 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
157 |
> |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
158 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
159 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
160 |
> |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
161 |
> |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
162 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
163 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
164 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
165 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
166 |
> |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
167 |
> |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
168 |
> |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
169 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
170 |
> |
implement of quickLate using visitor and composite pattern |
171 |
> |
|
172 |
> |
2004-04-15 17:15 tim |
173 |
> |
|
174 |
> |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
175 |
> |
exclude list |
176 |
> |
|
177 |
> |
2004-04-15 11:18 tim |
178 |
> |
|
179 |
> |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
180 |
> |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
181 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
182 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
183 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
184 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
185 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
186 |
> |
whole bunch of bugs :-) |
187 |
> |
|
188 |
> |
2004-04-14 12:20 chrisfen |
189 |
> |
|
190 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
191 |
> |
|
192 |
> |
2004-04-14 11:32 gezelter |
193 |
> |
|
194 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
195 |
> |
|
196 |
> |
2004-04-14 10:37 tim |
197 |
> |
|
198 |
> |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
199 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
200 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
201 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
202 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
203 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
204 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
205 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
206 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
207 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
208 |
> |
Change DumpWriter and InitFromFile |
209 |
> |
|
210 |
> |
2004-04-13 11:26 gezelter |
211 |
> |
|
212 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
213 |
> |
molecules can keep track of their own IntegrableObjects (and |
214 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
215 |
> |
RigidBodies (which was done incorrectly before). |
216 |
> |
|
217 |
> |
2004-04-13 11:25 gezelter |
218 |
> |
|
219 |
> |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
220 |
> |
(will back out momentarily) |
221 |
> |
|
222 |
> |
2004-04-13 10:10 gezelter |
223 |
> |
|
224 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
225 |
> |
Those were old. |
226 |
> |
|
227 |
> |
2004-04-13 10:09 gezelter |
228 |
> |
|
229 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
230 |
> |
to add IntegrableObjects |
231 |
> |
|
232 |
> |
2004-04-12 16:02 gezelter |
233 |
> |
|
234 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
235 |
> |
|
236 |
> |
2004-04-12 15:32 gezelter |
237 |
> |
|
238 |
> |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
239 |
> |
test run |
240 |
> |
|
241 |
> |
2004-04-12 15:32 gezelter |
242 |
> |
|
243 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
244 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
245 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
246 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
247 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
248 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
249 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
250 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
251 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
252 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
253 |
> |
(Somewhat extensive) |
254 |
> |
|
255 |
> |
2004-04-12 15:31 gezelter |
256 |
> |
|
257 |
> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
258 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
259 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
260 |
> |
Changes for RigidBody dynamics |
261 |
> |
|
262 |
> |
2004-03-17 09:22 tim |
263 |
> |
|
264 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
265 |
> |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
266 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
267 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
268 |
> |
does not sound a good choice, next commit will seperate SMD and |
269 |
> |
ZConstraint |
270 |
> |
|
271 |
> |
2004-03-16 14:22 tim |
272 |
> |
|
273 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
274 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
275 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
276 |
> |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
277 |
> |
now can support sequential moving. Refactorying is needed to |
278 |
> |
support SMD in ZConstraint |
279 |
> |
|
280 |
> |
2004-03-02 15:32 tim |
281 |
> |
|
282 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
283 |
> |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
284 |
> |
support large file |
285 |
> |
|
286 |
> |
2004-03-01 16:17 tim |
287 |
> |
|
288 |
> |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
289 |
> |
|
290 |
> |
2004-03-01 15:01 tim |
291 |
> |
|
292 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
293 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
294 |
> |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
295 |
> |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
296 |
> |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
297 |
> |
program which can be used to replace atom type for zconstraint into |
298 |
> |
OOPSE |
299 |
> |
|
300 |
> |
2004-02-24 11:36 tim |
301 |
> |
|
302 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
303 |
> |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
304 |
> |
message] |
305 |
> |
|
306 |
> |
2004-02-24 10:49 tim |
307 |
> |
|
308 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
309 |
> |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
310 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
311 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
312 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
313 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
314 |
> |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
315 |
> |
|
316 |
> |
2004-02-24 10:44 tim |
317 |
> |
|
318 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
319 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
320 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
321 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
322 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
323 |
> |
compose to implement Minimizer both versions are working |
324 |
> |
|
325 |
> |
2004-02-17 14:23 tim |
326 |
> |
|
327 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
328 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
329 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
330 |
> |
libmdtools/MinimizerParameterSet.hpp, |
331 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
332 |
> |
to remove the constraint force along bond direction |
333 |
> |
|
334 |
> |
2004-02-10 16:33 tim |
335 |
> |
|
336 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
337 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
338 |
> |
single version of energy minimization is working. |
339 |
> |
|
340 |
> |
2004-02-09 15:38 mmeineke |
341 |
> |
|
342 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
343 |
> |
the massive memory overusage by OOPSE |
344 |
> |
|
345 |
> |
2004-02-09 09:48 chrisfen |
346 |
> |
|
347 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
348 |
> |
hardwired LJ_rcut |
349 |
> |
|
350 |
> |
2004-02-06 19:14 tim |
351 |
> |
|
352 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
353 |
> |
message] |
354 |
> |
|
355 |
> |
2004-02-06 16:37 tim |
356 |
> |
|
357 |
> |
* ChangeLog, libBASS/Globals.cpp, |
358 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
359 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
360 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
361 |
> |
energy minimization for argon is working, need to add constraint |
362 |
> |
|
363 |
> |
2004-02-06 14:05 tim |
364 |
> |
|
365 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
366 |
> |
one more file into Makefile.in |
367 |
> |
|
368 |
> |
2004-02-06 13:58 tim |
369 |
> |
|
370 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
371 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
372 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
373 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
374 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
375 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
376 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
377 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
378 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
379 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
380 |
> |
some lines into global.cpp to make it work with energy minimization |
381 |
> |
|
382 |
> |
2004-02-04 17:26 tim |
383 |
> |
|
384 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
385 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
386 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
387 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
388 |
> |
Single version of conjugate gradient with golden search linesearch |
389 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
390 |
> |
|
391 |
> |
2004-02-03 17:54 tim |
392 |
> |
|
393 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
394 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
395 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
396 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
397 |
> |
|
398 |
> |
2004-02-03 15:47 tim |
399 |
> |
|
400 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
401 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
402 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
403 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
404 |
> |
SteepestDescent.hpp: [no log message] |
405 |
> |
|
406 |
> |
2004-02-03 15:43 tim |
407 |
> |
|
408 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
409 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
410 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
411 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
412 |
> |
constraint class |
413 |
> |
|
414 |
> |
2004-02-03 12:10 tim |
415 |
> |
|
416 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
417 |
> |
|
418 |
> |
2004-02-03 10:21 tim |
419 |
> |
|
420 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
421 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
422 |
> |
|
423 |
> |
2004-02-02 15:29 tim |
424 |
> |
|
425 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
426 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
427 |
> |
Adding GoldenSection and Brent LineSearch Method |
428 |
> |
|
429 |
> |
2004-01-30 16:47 tim |
430 |
> |
|
431 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
432 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
433 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
434 |
> |
MinimizerBase instead of a functor to do line seach |
435 |
> |
|
436 |
> |
2004-01-30 10:00 chrisfen |
437 |
> |
|
438 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
439 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
440 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
441 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
442 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
443 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
444 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
445 |
> |
has a working WATER.cpp forcefield and parser. This involved |
446 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
447 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
448 |
> |
This will be removed on the next commit... |
449 |
> |
|
450 |
> |
2004-01-29 18:00 gezelter |
451 |
> |
|
452 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
453 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
454 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
455 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
456 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
457 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
458 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
459 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
460 |
> |
member list fixes for rigid bodies |
461 |
> |
|
462 |
> |
2004-01-29 16:44 tim |
463 |
> |
|
464 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
465 |
> |
MinimizerParameterSet class. |
466 |
> |
|
467 |
> |
2004-01-28 17:44 tim |
468 |
> |
|
469 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
470 |
> |
NLModel0 and NLModel1 |
471 |
> |
|
472 |
> |
2004-01-28 15:40 tim |
473 |
> |
|
474 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
475 |
> |
of NLModel |
476 |
> |
|
477 |
> |
2004-01-27 15:34 gezelter |
478 |
> |
|
479 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
480 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
481 |
> |
|
482 |
> |
2004-01-27 15:34 gezelter |
483 |
> |
|
484 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
485 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
486 |
> |
stuff |
487 |
> |
|
488 |
> |
2004-01-27 14:39 gezelter |
489 |
> |
|
490 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
491 |
> |
|
492 |
> |
2004-01-27 14:39 gezelter |
493 |
> |
|
494 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
495 |
> |
|
496 |
> |
2004-01-27 14:38 gezelter |
497 |
> |
|
498 |
> |
* samples/argon/argon.bass: Longer run time to test argon |
499 |
> |
|
500 |
> |
2004-01-27 14:38 gezelter |
501 |
> |
|
502 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
503 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
504 |
> |
morning |
505 |
> |
|
506 |
> |
2004-01-27 14:37 gezelter |
507 |
> |
|
508 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
509 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
510 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
511 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
512 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
513 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
514 |
> |
do new rigidBody scheme |
515 |
> |
|
516 |
> |
2004-01-27 14:15 tim |
517 |
> |
|
518 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
519 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
520 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
521 |
> |
constraint for Nonlinear Optimization Model |
522 |
> |
|
523 |
> |
2004-01-26 17:01 gezelter |
524 |
> |
|
525 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
526 |
> |
Euler angles for orientation instead of unit vectors required |
527 |
> |
changes in MoLocator |
528 |
> |
|
529 |
> |
2004-01-26 16:53 gezelter |
530 |
> |
|
531 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
532 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
533 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
534 |
> |
euler angles |
535 |
> |
|
536 |
> |
2004-01-26 16:52 gezelter |
537 |
> |
|
538 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
539 |
> |
|
540 |
> |
2004-01-26 16:45 gezelter |
541 |
> |
|
542 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
543 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
544 |
> |
the ability to set orientation using a unit vector |
545 |
> |
|
546 |
> |
2004-01-26 16:26 gezelter |
547 |
> |
|
548 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
549 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
550 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
551 |
> |
ability to set orientation using a unit vector |
552 |
> |
|
553 |
> |
2004-01-26 13:52 gezelter |
554 |
> |
|
555 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
556 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
557 |
> |
|
558 |
> |
2004-01-22 12:34 chrisfen |
559 |
> |
|
560 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
561 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
562 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
563 |
> |
|
564 |
> |
2004-01-21 17:16 tim |
565 |
> |
|
566 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
567 |
> |
NLOPModel.hpp: constraint class in energy minimization |
568 |
> |
|
569 |
> |
2004-01-20 15:34 tim |
570 |
> |
|
571 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
572 |
> |
|
573 |
> |
2004-01-20 15:32 tim |
574 |
> |
|
575 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
576 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
577 |
> |
|
578 |
> |
2004-01-19 16:17 gezelter |
579 |
> |
|
580 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
581 |
> |
more user-friendly |
582 |
> |
|
583 |
> |
2004-01-19 13:51 chrisfen |
584 |
> |
|
585 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
586 |
> |
|
587 |
> |
2004-01-19 13:36 tim |
588 |
> |
|
589 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
590 |
> |
time, status time, thermal time and reset time are not divisible by |
591 |
> |
dt |
592 |
> |
|
593 |
> |
2004-01-19 11:10 gezelter |
594 |
> |
|
595 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
596 |
> |
won't complain |
597 |
> |
|
598 |
> |
2004-01-19 11:10 gezelter |
599 |
> |
|
600 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
601 |
> |
|
602 |
> |
2004-01-19 11:09 gezelter |
603 |
> |
|
604 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
605 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
606 |
> |
in mpiSimulation.cpp |
607 |
> |
|
608 |
> |
2004-01-19 11:08 gezelter |
609 |
> |
|
610 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
611 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
612 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
613 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
614 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
615 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
616 |
> |
|
617 |
> |
2004-01-16 16:55 tim |
618 |
> |
|
619 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
620 |
> |
eor file |
621 |
> |
|
622 |
> |
2004-01-16 16:51 mmeineke |
623 |
> |
|
624 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
625 |
> |
write eor files |
626 |
> |
|
627 |
> |
2004-01-16 10:01 mmeineke |
628 |
> |
|
629 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
630 |
> |
initialization of the AtomStruct |
631 |
> |
|
632 |
> |
2004-01-15 16:57 chuckv |
633 |
> |
|
634 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
635 |
> |
|
636 |
> |
2004-01-15 10:51 gezelter |
637 |
> |
|
638 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
639 |
> |
|
640 |
> |
2004-01-15 09:22 gezelter |
641 |
> |
|
642 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
643 |
> |
|
644 |
> |
2004-01-14 23:33 gezelter |
645 |
> |
|
646 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
647 |
> |
|
648 |
> |
2004-01-14 20:14 gezelter |
649 |
> |
|
650 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
651 |
> |
notifyCutoffs.F90: More work for adding charges |
652 |
> |
|
653 |
> |
2004-01-14 17:41 gezelter |
654 |
> |
|
655 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
656 |
> |
src/Makefile.in: autoconf fixes |
657 |
> |
|
658 |
> |
2004-01-14 11:28 mmeineke |
659 |
> |
|
660 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
661 |
> |
|
662 |
> |
2004-01-14 10:48 gezelter |
663 |
> |
|
664 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
665 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
666 |
> |
changes for icc8 |
667 |
> |
|
668 |
> |
2004-01-13 18:01 gezelter |
669 |
> |
|
670 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
671 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
672 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
673 |
> |
Changes for adding direct charge-charge interactions (with |
674 |
> |
switching function) |
675 |
> |
|
676 |
> |
2004-01-13 17:34 gezelter |
677 |
> |
|
678 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
679 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
680 |
> |
direct charge-charge interactions |
681 |
> |
|
682 |
> |
2004-01-13 17:11 tim |
683 |
> |
|
684 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
685 |
> |
|
686 |
> |
2004-01-13 16:22 tim |
687 |
> |
|
688 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
689 |
> |
|
690 |
> |
2004-01-13 15:35 tim |
691 |
> |
|
692 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
693 |
> |
eor file whenever it is used instead of rewinding it |
694 |
> |
|
695 |
> |
2004-01-13 15:04 tim |
696 |
> |
|
697 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
698 |
> |
of writeFrame |
699 |
> |
|
700 |
> |
2004-01-13 10:46 tim |
701 |
> |
|
702 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
703 |
> |
Merge the code of writeFinal and writeDump; |
704 |
> |
Adding sortingIndex into DumpWriter; |
705 |
> |
Fix a bug of writing last frame twice in integrator |
706 |
> |
|
707 |
> |
2004-01-12 17:54 tim |
708 |
> |
|
709 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
710 |
> |
a bug in copying string |
711 |
> |
|
712 |
> |
2004-01-12 15:37 tim |
713 |
> |
|
714 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
715 |
> |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
716 |
> |
master nodes |
717 |
> |
|
718 |
> |
2004-01-10 04:46 tim |
719 |
> |
|
720 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
721 |
> |
roll it back fix a bug of copying string to a pointer Still have |
722 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
723 |
> |
|
724 |
> |
2004-01-09 21:15 tim |
725 |
> |
|
726 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
727 |
> |
|
728 |
> |
2004-01-09 15:29 gezelter |
729 |
> |
|
730 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
731 |
> |
|
732 |
> |
2004-01-08 17:25 chuckv |
733 |
> |
|
734 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
735 |
> |
|
736 |
> |
2004-01-08 13:59 gezelter |
737 |
> |
|
738 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
739 |
> |
case |
740 |
> |
|
741 |
> |
2004-01-08 13:13 mmeineke |
742 |
> |
|
743 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
744 |
> |
state bug. |
745 |
> |
|
746 |
> |
2004-01-08 13:05 gezelter |
747 |
> |
|
748 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
749 |
> |
|
750 |
> |
2004-01-08 12:57 mmeineke |
751 |
> |
|
752 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
753 |
> |
exstended state bug |
754 |
> |
|
755 |
> |
2004-01-08 12:40 gezelter |
756 |
> |
|
757 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
758 |
> |
|
759 |
> |
2004-01-08 10:44 mmeineke |
760 |
> |
|
761 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
762 |
> |
XS state info flag |
763 |
> |
|
764 |
> |
2004-01-07 14:26 tim |
765 |
> |
|
766 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
767 |
> |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
768 |
> |
sending message from master node to itself in DumpWriter.cpp and |
769 |
> |
InitializeFromFile.cpp |
770 |
> |
|
771 |
> |
2004-01-06 14:49 chuckv |
772 |
> |
|
773 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
774 |
> |
performance fixes in the dipole dipole and reaction field code |
775 |
> |
|
776 |
> |
2004-01-06 13:54 chuckv |
777 |
> |
|
778 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
779 |
> |
little more sane |
780 |
> |
|
781 |
> |
2004-01-05 17:49 chuckv |
782 |
> |
|
783 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
784 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
785 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
786 |
> |
performance by reducing spurious function calls |
787 |
> |
|
788 |
> |
2004-01-05 17:18 chuckv |
789 |
> |
|
790 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
791 |
> |
|
792 |
> |
2004-01-05 17:18 chuckv |
793 |
> |
|
794 |
> |
* configure, ac-tools/configure.in: mpich mucking |
795 |
> |
|
796 |
> |
2004-01-05 17:12 chuckv |
797 |
> |
|
798 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
799 |
> |
|
800 |
> |
2004-01-05 16:00 chuckv |
801 |
> |
|
802 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
803 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
804 |
> |
lookup |
805 |
> |
|
806 |
> |
2003-12-29 14:56 chuckv |
807 |
> |
|
808 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
809 |
> |
third-party directory for code not written by us. Also added |
810 |
> |
Mersenne Twister random number generator code. This will eventually |
811 |
> |
replace sprng as the random number generator used by OOPSE. |
812 |
> |
|
813 |
> |
2003-12-22 16:26 chuckv |
814 |
> |
|
815 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
816 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
817 |
> |
Fixes to profile code. |
818 |
> |
|
819 |
> |
2003-12-19 15:36 mmeineke |
820 |
> |
|
821 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
822 |
> |
timing.F90, timing.f90: More profiling fixes. |
823 |
> |
|
824 |
> |
2003-12-19 15:19 chuckv |
825 |
> |
|
826 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
827 |
> |
|
828 |
> |
2003-12-19 15:17 chuckv |
829 |
> |
|
830 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
831 |
> |
|
832 |
> |
2003-12-19 13:53 mmeineke |
833 |
> |
|
834 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
835 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
836 |
> |
the code |
837 |
> |
|
838 |
> |
2003-12-19 12:25 mmeineke |
839 |
> |
|
840 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
841 |
> |
some profiling routines |
842 |
> |
|
843 |
> |
2003-12-19 10:12 mmeineke |
844 |
> |
|
845 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
846 |
> |
and GofRomega |
847 |
> |
|
848 |
> |
additional work on randomBilayer |
849 |
> |
|
850 |
> |
2003-12-19 10:12 mmeineke |
851 |
> |
|
852 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
853 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
854 |
> |
GofRomega |
855 |
> |
|
856 |
> |
2003-12-18 16:47 mmeineke |
857 |
> |
|
858 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
859 |
> |
some profile functionality |
860 |
> |
|
861 |
> |
2003-12-18 15:46 chuckv |
862 |
> |
|
863 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
864 |
> |
Added functions for simple profiling in fortran. |
865 |
> |
|
866 |
> |
2003-12-17 15:13 chuckv |
867 |
> |
|
868 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
869 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
870 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
871 |
> |
zeros the array between scatters so half of the sum was being lost. |
872 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
873 |
> |
nlocal. |
874 |
> |
|
875 |
> |
2003-12-16 15:49 mmeineke |
876 |
> |
|
877 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
878 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
879 |
> |
gofRomega. both need to be debugged and tested. |
880 |
> |
|
881 |
> |
2003-12-12 10:42 gezelter |
882 |
> |
|
883 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
884 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
885 |
> |
gradients (to do minimizations) |
886 |
> |
|
887 |
> |
2003-12-12 10:33 mmeineke |
888 |
> |
|
889 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
890 |
> |
header |
891 |
> |
|
892 |
> |
2003-12-10 11:52 mmeineke |
893 |
> |
|
894 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
895 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
896 |
> |
randomBilayer to the build. Also move the random bilayer builder |
897 |
> |
from bilayerSys to randomBilayer |
898 |
> |
|
899 |
> |
2003-11-25 10:44 mmeineke |
900 |
> |
|
901 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
902 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
903 |
> |
TB3 in DUFF.frc |
904 |
> |
|
905 |
> |
2003-11-21 15:09 mmeineke |
906 |
> |
|
907 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
908 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
909 |
> |
message in SimInfo. Added a more informative error message in |
910 |
> |
InitializeFromFile |
911 |
> |
|
912 |
> |
2003-11-21 15:07 mmeineke |
913 |
> |
|
914 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
915 |
> |
ing in the GofR,CosTheta |
916 |
> |
|
917 |
> |
2003-11-21 14:31 chrisfen |
918 |
> |
|
919 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
920 |
> |
a bug in SimInfo ordering of radii |
921 |
> |
|
922 |
> |
2003-11-11 12:20 mmeineke |
923 |
> |
|
924 |
> |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
925 |
> |
a min function. |
926 |
> |
|
927 |
> |
2003-11-10 16:50 mmeineke |
928 |
> |
|
929 |
> |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
930 |
> |
reordered the rcut/ecr/boxSize initialization |
931 |
> |
|
932 |
> |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
933 |
> |
now exit when it runs into rcut or ecr. |
934 |
> |
|
935 |
> |
2003-11-07 16:46 chuckv |
936 |
> |
|
937 |
> |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
938 |
> |
oopseMPI_module.F90: Added support for compiling fortran without |
939 |
> |
use of mpich modules. We use mpif.h instead.: |
940 |
> |
|
941 |
> |
2003-11-07 12:09 mmeineke |
942 |
> |
|
943 |
> |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
944 |
> |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
945 |
> |
the atom loop in the NPT family of integrators. |
946 |
> |
|
947 |
> |
2003-11-06 17:01 mmeineke |
948 |
> |
|
949 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
950 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
951 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
952 |
> |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
953 |
> |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
954 |
> |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
955 |
> |
* useIntiTime => useInitialTime |
956 |
> |
|
957 |
> |
2003-11-06 14:24 mmeineke |
958 |
> |
|
959 |
> |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
960 |
> |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
961 |
> |
parse_tree.h: fixed the includes in the Make.dep |
962 |
> |
|
963 |
> |
2003-11-06 14:11 mmeineke |
964 |
> |
|
965 |
> |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
966 |
> |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
967 |
> |
new-templateless branch to the main trunk. |
968 |
> |
|
969 |
> |
bug Fixes include: * fixed the switching function from ortho to |
970 |
> |
non-ortho box. !!!!! THis was responsible for all of the |
971 |
> |
sudden deaths we saw. * some formating in the string when we |
972 |
> |
write out the extended system state. * added NPT.cpp to the |
973 |
> |
makefile.in |
974 |
> |
|
975 |
> |
2003-11-06 13:20 mmeineke |
976 |
> |
|
977 |
> |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
978 |
> |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
979 |
> |
bug. The box was not switching between orthorhombic and |
980 |
> |
non-orthorhombic wrapping correctly. we added a fabs() to |
981 |
> |
the check.which should fix it. |
982 |
> |
|
983 |
> |
2003-11-05 14:16 mmeineke |
984 |
> |
|
985 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
986 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
987 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
988 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
989 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
990 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
991 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
992 |
> |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
993 |
> |
some work on trying to find the compression bug |
994 |
> |
|
995 |
> |
2003-11-03 17:07 mmeineke |
996 |
> |
|
997 |
> |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
998 |
> |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
999 |
> |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1000 |
> |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1001 |
> |
most of standard template library from OOPSE. |
1002 |
> |
|
1003 |
> |
2003-10-31 16:06 mmeineke |
1004 |
> |
|
1005 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1006 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1007 |
> |
SimSetup.cpp: started work on template removal. |
1008 |
> |
|
1009 |
> |
2003-10-31 13:28 mmeineke |
1010 |
> |
|
1011 |
> |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1012 |
> |
added template stuff to the Maikefile template |
1013 |
> |
|
1014 |
> |
little changes to some printf format statements |
1015 |
> |
|
1016 |
> |
2003-10-31 13:28 mmeineke |
1017 |
> |
|
1018 |
> |
* libBASS/Makefile.in: added template stuff to the Maikefile |
1019 |
> |
template |
1020 |
> |
|
1021 |
> |
2003-10-30 13:59 gezelter |
1022 |
> |
|
1023 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1024 |
> |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1025 |
> |
rList problems |
1026 |
> |
|
1027 |
> |
2003-10-30 09:11 gezelter |
1028 |
> |
|
1029 |
> |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1030 |
> |
queried before q0 was allocated. |
1031 |
> |
|
1032 |
> |
2003-10-29 15:41 mmeineke |
1033 |
> |
|
1034 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1035 |
> |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1036 |
> |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1037 |
> |
in bass.l |
1038 |
> |
|
1039 |
> |
fixed a little bug in the first time step, regarding the setting of |
1040 |
> |
ecr and est in fortran |
1041 |
> |
|
1042 |
> |
2003-10-29 15:40 mmeineke |
1043 |
> |
|
1044 |
> |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1045 |
> |
|
1046 |
> |
2003-10-29 12:55 mmeineke |
1047 |
> |
|
1048 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1049 |
> |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1050 |
> |
rcut is setup, as well as additional debugging comments. |
1051 |
> |
|
1052 |
> |
2003-10-29 09:28 gezelter |
1053 |
> |
|
1054 |
> |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1055 |
> |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1056 |
> |
templates |
1057 |
> |
|
1058 |
> |
2003-10-28 22:16 gezelter |
1059 |
> |
|
1060 |
> |
* src/Makefile.in: Refixed broken makefile |
1061 |
> |
|
1062 |
> |
2003-10-28 22:06 gezelter |
1063 |
> |
|
1064 |
> |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1065 |
> |
fixes |
1066 |
> |
|
1067 |
> |
2003-10-28 19:19 tim |
1068 |
> |
|
1069 |
> |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1070 |
> |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1071 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1072 |
> |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1073 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1074 |
> |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1075 |
> |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1076 |
> |
file. |
1077 |
> |
|
1078 |
> |
2003-10-28 17:25 mmeineke |
1079 |
> |
|
1080 |
> |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1081 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1082 |
> |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1083 |
> |
how c calls fortran. All function pointers and fortran calls are |
1084 |
> |
rigidly typecast now. |
1085 |
> |
|
1086 |
> |
2003-10-28 15:42 gezelter |
1087 |
> |
|
1088 |
> |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1089 |
> |
Portability fixes |
1090 |
> |
|
1091 |
> |
2003-10-28 15:09 gezelter |
1092 |
> |
|
1093 |
> |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1094 |
> |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1095 |
> |
src/Makefile.in: Compatibility fixes |
1096 |
> |
|
1097 |
> |
2003-10-28 12:08 mmeineke |
1098 |
> |
|
1099 |
> |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1100 |
> |
started work on template removal |
1101 |
> |
|
1102 |
> |
2003-10-28 12:04 gezelter |
1103 |
> |
|
1104 |
> |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1105 |
> |
trying to understand extern "C" stuff for pointers |
1106 |
> |
|
1107 |
> |
2003-10-28 11:20 gezelter |
1108 |
> |
|
1109 |
> |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1110 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1111 |
> |
|
1112 |
> |
2003-10-28 11:03 gezelter |
1113 |
> |
|
1114 |
> |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1115 |
> |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1116 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1117 |
> |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1118 |
> |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1119 |
> |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1120 |
> |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1121 |
> |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1122 |
> |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1123 |
> |
more portable c header stuff Also, mod file fixes and portability |
1124 |
> |
changes Some fortran changes will need to be reversed. |
1125 |
> |
|
1126 |
> |
2003-10-28 11:03 gezelter |
1127 |
> |
|
1128 |
> |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1129 |
> |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1130 |
> |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1131 |
> |
portable c header stuff Also, mod file fixes and portability |
1132 |
> |
changes |
1133 |
> |
|
1134 |
> |
2003-10-28 11:02 gezelter |
1135 |
> |
|
1136 |
> |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1137 |
> |
stuff |
1138 |
> |
|
1139 |
> |
2003-10-27 18:00 gezelter |
1140 |
> |
|
1141 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1142 |
> |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1143 |
> |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1144 |
> |
|
1145 |
> |
2003-10-27 17:08 mmeineke |
1146 |
> |
|
1147 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1148 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1149 |
> |
added routines for the sysbuilder to work with simSetup |
1150 |
> |
|
1151 |
> |
remved the QuickBass routines, and had all parsing go through |
1152 |
> |
SimSetup. LatticeBilayer is in complete working order now. |
1153 |
> |
|
1154 |
> |
2003-10-27 17:07 mmeineke |
1155 |
> |
|
1156 |
> |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1157 |
> |
routines for the sysbuilder to work with simSetup |
1158 |
> |
|
1159 |
> |
2003-10-27 11:20 gezelter |
1160 |
> |
|
1161 |
> |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1162 |
> |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1163 |
> |
|
1164 |
> |
2003-10-24 17:17 mmeineke |
1165 |
> |
|
1166 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1167 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1168 |
> |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1169 |
> |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1170 |
> |
overhauled latticeBilayer into its own program. Removed sysBuild |
1171 |
> |
from the Makefile |
1172 |
> |
|
1173 |
> |
2003-10-24 12:36 gezelter |
1174 |
> |
|
1175 |
> |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1176 |
> |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1177 |
> |
builder |
1178 |
> |
|
1179 |
> |
2003-10-24 12:35 gezelter |
1180 |
> |
|
1181 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1182 |
> |
merge problem |
1183 |
> |
|
1184 |
> |
2003-10-23 14:57 mmeineke |
1185 |
> |
|
1186 |
> |
* samples/metals/Makefile.in: added eam ForceField files to the |
1187 |
> |
init |
1188 |
> |
|
1189 |
> |
fixed an eam mpi parmeter setup bug |
1190 |
> |
|
1191 |
> |
added the init file to the makefile |
1192 |
> |
|
1193 |
> |
2003-10-23 14:57 mmeineke |
1194 |
> |
|
1195 |
> |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1196 |
> |
to the init |
1197 |
> |
|
1198 |
> |
fixed an eam mpi parmeter setup bug |
1199 |
> |
|
1200 |
> |
2003-10-23 14:57 mmeineke |
1201 |
> |
|
1202 |
> |
* forceFields/Makefile.in: added eam ForceField files to the init |
1203 |
> |
|
1204 |
> |
2003-10-22 16:17 mmeineke |
1205 |
> |
|
1206 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1207 |
> |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1208 |
> |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1209 |
> |
no box skew allowed. |
1210 |
> |
|
1211 |
> |
2003-10-21 14:33 mmeineke |
1212 |
> |
|
1213 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1214 |
> |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1215 |
> |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1216 |
> |
* useInitTime = false: sets the origin time to 0.0 regardless |
1217 |
> |
of the time stamp in the .init file * default=> useInitTime = |
1218 |
> |
true; |
1219 |
> |
|
1220 |
> |
2003-10-17 16:19 mmeineke |
1221 |
> |
|
1222 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1223 |
> |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1224 |
> |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1225 |
> |
to the build list for both configure and configure.in |
1226 |
> |
|
1227 |
> |
fixed a number of bugs in the staticProps code. gofr is now |
1228 |
> |
working. |
1229 |
> |
|
1230 |
> |
2003-10-17 16:18 mmeineke |
1231 |
> |
|
1232 |
> |
* ac-tools/configure.in: added the staticProps directory to the |
1233 |
> |
build list for both configure and configure.in |
1234 |
> |
|
1235 |
> |
2003-10-17 16:17 mmeineke |
1236 |
> |
|
1237 |
> |
* configure: added the staticProps directory to the build list |
1238 |
> |
|
1239 |
> |
2003-10-16 14:16 mmeineke |
1240 |
> |
|
1241 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1242 |
> |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1243 |
> |
use linked lists instead of a vector. |
1244 |
> |
|
1245 |
> |
Fixed the makefile to build DumpReader.cpp |
1246 |
> |
|
1247 |
> |
Removed a comment output in Exclude.cpp |
1248 |
> |
|
1249 |
> |
Modified DumpWriter and Integrator to write an eor file every time |
1250 |
> |
a frame is written. This lets the .eor file represent the last |
1251 |
> |
written frame of a simulation. |
1252 |
> |
|
1253 |
> |
2003-10-10 12:10 mmeineke |
1254 |
> |
|
1255 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1256 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1257 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1258 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1259 |
> |
over to staticProps |
1260 |
> |
|
1261 |
> |
2003-10-09 17:09 mmeineke |
1262 |
> |
|
1263 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1264 |
> |
a position where it will compile and run first runs. |
1265 |
> |
|
1266 |
> |
2003-10-04 13:46 chuckv |
1267 |
> |
|
1268 |
> |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1269 |
> |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1270 |
> |
|
1271 |
> |
2003-10-04 13:08 chuckv |
1272 |
> |
|
1273 |
> |
* samples/metals/init_au.in: added Au init file for eam. |
1274 |
> |
|
1275 |
> |
2003-10-03 17:11 mmeineke |
1276 |
> |
|
1277 |
> |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1278 |
> |
entahlpy from the statwriter and thermo. |
1279 |
> |
|
1280 |
> |
2003-10-03 17:02 mmeineke |
1281 |
> |
|
1282 |
> |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1283 |
> |
statements in simError |
1284 |
> |
|
1285 |
> |
added a function to get the maxCutoff |
1286 |
> |
|
1287 |
> |
2003-10-03 17:01 mmeineke |
1288 |
> |
|
1289 |
> |
* libBASS/simError.c: changed the formating ogf the error |
1290 |
> |
statements in simError |
1291 |
> |
|
1292 |
> |
2003-09-30 11:00 mmeineke |
1293 |
> |
|
1294 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1295 |
> |
f90Flags so they are no longer overwritten by the compiler. |
1296 |
> |
|
1297 |
> |
2003-09-29 17:06 mmeineke |
1298 |
> |
|
1299 |
> |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1300 |
> |
for conifig.in |
1301 |
> |
|
1302 |
> |
fixed wrappers to extern "C" |
1303 |
> |
|
1304 |
> |
2003-09-29 17:06 mmeineke |
1305 |
> |
|
1306 |
> |
* ac-tools/configure.in: added mpif90 mod check back same for |
1307 |
> |
conifig.in |
1308 |
> |
|
1309 |
> |
2003-09-29 17:05 mmeineke |
1310 |
> |
|
1311 |
> |
* configure: added mpif90 mod check back |
1312 |
> |
|
1313 |
> |
2003-09-29 16:16 mmeineke |
1314 |
> |
|
1315 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1316 |
> |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1317 |
> |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1318 |
> |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1319 |
> |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1320 |
> |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1321 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1322 |
> |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1323 |
> |
found with SUN's SUNWspro.s1s7 |
1324 |
> |
|
1325 |
> |
2003-09-29 12:38 mmeineke |
1326 |
> |
|
1327 |
> |
* libmdtools/GenericData.hpp: light change in syntax. no |
1328 |
> |
signifigant change. |
1329 |
> |
|
1330 |
> |
2003-09-25 16:17 mmeineke |
1331 |
> |
|
1332 |
> |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1333 |
> |
additional remarks from icc -w3 (extra verbose output) |
1334 |
> |
|
1335 |
> |
2003-09-25 14:27 mmeineke |
1336 |
> |
|
1337 |
> |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1338 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1339 |
> |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1340 |
> |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1341 |
> |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1342 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1343 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1344 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1345 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1346 |
> |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1347 |
> |
gcc -Wall and g++ -Wall |
1348 |
> |
|
1349 |
> |
2003-09-25 13:54 gezelter |
1350 |
> |
|
1351 |
> |
* configure, ac-tools/configure.in: fixed a bug in configure |
1352 |
> |
|
1353 |
> |
2003-09-25 11:42 gezelter |
1354 |
> |
|
1355 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1356 |
> |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1357 |
> |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1358 |
> |
fixes for configure |
1359 |
> |
|
1360 |
> |
2003-09-24 14:34 mmeineke |
1361 |
> |
|
1362 |
> |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1363 |
> |
that it is called before the first Statistics are written. |
1364 |
> |
|
1365 |
> |
2003-09-23 15:36 gezelter |
1366 |
> |
|
1367 |
> |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1368 |
> |
bunch of Make.dep files to CVS |
1369 |
> |
|
1370 |
> |
2003-09-23 15:34 mmeineke |
1371 |
> |
|
1372 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1373 |
> |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1374 |
> |
|
1375 |
> |
Some small syntax cleaning in NPTfm and SimSetup |
1376 |
> |
|
1377 |
> |
2003-09-22 18:07 tim |
1378 |
> |
|
1379 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1380 |
> |
SimInfo.hpp: fix bug in calculating maxCutoff |
1381 |
> |
|
1382 |
> |
2003-09-22 16:23 mmeineke |
1383 |
> |
|
1384 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1385 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1386 |
> |
Converted NPTf to work with the NPT base class. |
1387 |
> |
|
1388 |
> |
Removed NPTfm and NPTim from cvs |
1389 |
> |
|
1390 |
> |
2003-09-19 15:00 mmeineke |
1391 |
> |
|
1392 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1393 |
> |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1394 |
> |
class. NPTi is up to date. NPTf is not. |
1395 |
> |
|
1396 |
> |
2003-09-19 11:03 mmeineke |
1397 |
> |
|
1398 |
> |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1399 |
> |
makefile |
1400 |
> |
|
1401 |
> |
2003-09-19 11:01 gezelter |
1402 |
> |
|
1403 |
> |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1404 |
> |
|
1405 |
> |
2003-09-19 11:01 gezelter |
1406 |
> |
|
1407 |
> |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1408 |
> |
(nearly) conserved quantities for both NPTi and NPTf |
1409 |
> |
|
1410 |
> |
2003-09-19 10:20 mmeineke |
1411 |
> |
|
1412 |
> |
* utils/Makefile.in: fixed a typo in the makefile. |
1413 |
> |
|
1414 |
> |
2003-09-19 09:55 gezelter |
1415 |
> |
|
1416 |
> |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1417 |
> |
samples/water/ssd.bass: [no log message] |
1418 |
> |
|
1419 |
> |
2003-09-19 09:22 tim |
1420 |
> |
|
1421 |
> |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1422 |
> |
|
1423 |
> |
2003-09-17 09:22 mmeineke |
1424 |
> |
|
1425 |
> |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1426 |
> |
work with constraints. |
1427 |
> |
|
1428 |
> |
2003-09-16 15:02 tim |
1429 |
> |
|
1430 |
> |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1431 |
> |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1432 |
> |
|
1433 |
> |
fixed conserved quantity in NPT (Still some small bug) |
1434 |
> |
|
1435 |
> |
NPTi appears very stable. |
1436 |
> |
|
1437 |
> |
2003-09-15 11:52 tim |
1438 |
> |
|
1439 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1440 |
> |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1441 |
> |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1442 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1443 |
> |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1444 |
> |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1445 |
> |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1446 |
> |
statWriter fix bug of vector wrapping at NPTi |
1447 |
> |
|
1448 |
> |
2003-09-12 11:20 gezelter |
1449 |
> |
|
1450 |
> |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1451 |
> |
Makefile.in |
1452 |
> |
|
1453 |
> |
2003-09-12 11:20 gezelter |
1454 |
> |
|
1455 |
> |
* ChangeLog: Entered changes for configure into ChangeLog |
1456 |
> |
|
1457 |
> |
2003-09-09 15:35 mmeineke |
1458 |
> |
|
1459 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1460 |
> |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1461 |
> |
|
1462 |
> |
added two new NPT integrators, they still need work. |
1463 |
> |
|
1464 |
> |
2003-09-09 15:34 mmeineke |
1465 |
> |
|
1466 |
> |
* ChangeLog: updated the ChangeLog |
1467 |
> |
|
1468 |
> |
2003-09-05 17:45 gezelter |
1469 |
> |
|
1470 |
> |
* libmdtools/Make.dep: dependency on config.h |
1471 |
> |
|
1472 |
> |
2003-09-05 17:36 gezelter |
1473 |
> |
|
1474 |
> |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1475 |
> |
|
1476 |
> |
2003-09-05 16:29 gezelter |
1477 |
> |
|
1478 |
> |
* samples/metals/Makefile.in: New Makefile for metals sample |
1479 |
> |
|
1480 |
> |
2003-09-05 16:27 gezelter |
1481 |
> |
|
1482 |
> |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1483 |
> |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1484 |
> |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1485 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1486 |
> |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1487 |
> |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1488 |
> |
libmdtools/Makefile, libmdtools/Makefile.in, |
1489 |
> |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1490 |
> |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1491 |
> |
libmdtools/fortranWrappers.cpp, |
1492 |
> |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1493 |
> |
libmdtools/simulation_module.F90, samples/Makefile, |
1494 |
> |
samples/Makefile.in, samples/alkane/Makefile, |
1495 |
> |
samples/alkane/Makefile.in, samples/argon/Makefile, |
1496 |
> |
samples/argon/Makefile.in, samples/argon/argon.bass, |
1497 |
> |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1498 |
> |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1499 |
> |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1500 |
> |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1501 |
> |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1502 |
> |
autoconf / configure method of configuring OOPSE |
1503 |
> |
|
1504 |
> |
2003-09-04 16:48 mmeineke |
1505 |
> |
|
1506 |
> |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1507 |
> |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
1508 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
1509 |
> |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
1510 |
> |
added resetTime to the Global namespace. |
1511 |
> |
|
1512 |
> |
added ability to reset the integrators in the NVT and NPT family. |
1513 |
> |
|
1514 |
> |
2003-09-04 16:48 mmeineke |
1515 |
> |
|
1516 |
> |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
1517 |
> |
namespace. |
1518 |
> |
|
1519 |
> |
2003-09-02 09:30 tim |
1520 |
> |
|
1521 |
> |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
1522 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
1523 |
> |
PolicyByMass |
1524 |
> |
|
1525 |
> |
2003-08-28 16:09 tim |
1526 |
> |
|
1527 |
> |
* ChangeLog, libmdtools/GenericData.cpp, |
1528 |
> |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1529 |
> |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1530 |
> |
|
1531 |
> |
2003-08-27 14:23 tim |
1532 |
> |
|
1533 |
> |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1534 |
> |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
1535 |
> |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
1536 |
> |
turn on the optimization flag, it causes a seg fault |
1537 |
> |
|
1538 |
> |
2003-08-27 11:25 gezelter |
1539 |
> |
|
1540 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
1541 |
> |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
1542 |
> |
stress tensor parallel bug. |
1543 |
> |
|
1544 |
> |
2003-08-27 11:16 tim |
1545 |
> |
|
1546 |
> |
* ChangeLog, libmdtools/DUFF.cpp, |
1547 |
> |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
1548 |
> |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
1549 |
> |
molMembershipList use global index instead of local index |
1550 |
> |
|
1551 |
> |
2003-08-26 15:37 tim |
1552 |
> |
|
1553 |
> |
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
1554 |
> |
mpiSimulation.cpp: set default force substraction policy to |
1555 |
> |
PolicyByMass |
1556 |
> |
|
1557 |
> |
2003-08-26 15:29 tim |
1558 |
> |
|
1559 |
> |
* libmdtools/Integrator.cpp: [no log message] |
1560 |
> |
|
1561 |
> |
2003-08-26 15:13 mmeineke |
1562 |
> |
|
1563 |
> |
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
1564 |
> |
Statwriter and Dumpwriter to handle files larger than 2 gb. |
1565 |
> |
|
1566 |
> |
commented out some print statements in Zconstraint |
1567 |
> |
|
1568 |
> |
hard coding some system init into bilayer.sys |
1569 |
> |
|
1570 |
> |
2003-08-26 15:12 mmeineke |
1571 |
> |
|
1572 |
> |
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
1573 |
> |
added define statemewnt to Statwriter and Dumpwriter to handle |
1574 |
> |
files larger than 2 gb. |
1575 |
> |
|
1576 |
> |
commented out some print statements in Zconstraint |
1577 |
> |
|
1578 |
> |
2003-08-26 15:02 tim |
1579 |
> |
|
1580 |
> |
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
1581 |
> |
and check the seed which is specified by user at least contains 9 |
1582 |
> |
digits |
1583 |
> |
|
1584 |
> |
2003-08-26 13:32 mmeineke |
1585 |
> |
|
1586 |
> |
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
1587 |
> |
|
1588 |
> |
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
1589 |
> |
constucted in MPI. (The MPI struct had 6 doubles declared versus |
1590 |
> |
the actual 11) |
1591 |
> |
|
1592 |
> |
2003-08-26 13:30 mmeineke |
1593 |
> |
|
1594 |
> |
* Makefile: changed the Makefiel a litle. |
1595 |
> |
|
1596 |
> |
2003-08-25 17:17 gezelter |
1597 |
> |
|
1598 |
> |
* utils/sysbuilder/Makefile: More FreeBSD fixes |
1599 |
> |
|
1600 |
> |
2003-08-25 16:51 gezelter |
1601 |
> |
|
1602 |
> |
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
1603 |
> |
libmdtools/Makefile, src/Makefile: [no log message] |
1604 |
> |
|
1605 |
> |
2003-08-22 15:04 mmeineke |
1606 |
> |
|
1607 |
> |
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
1608 |
> |
frequency of output dumps. |
1609 |
> |
|
1610 |
> |
2003-08-20 17:23 tim |
1611 |
> |
|
1612 |
> |
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
1613 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1614 |
> |
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
1615 |
> |
if he does not specify any value for seed, oopse will take the |
1616 |
> |
value of seconds of system time as seed |
1617 |
> |
|
1618 |
> |
2003-08-20 14:42 mmeineke |
1619 |
> |
|
1620 |
> |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1621 |
> |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
1622 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
1623 |
> |
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
1624 |
> |
|
1625 |
> |
added some bug fixes for setting the random number generator seed |
1626 |
> |
value. |
1627 |
> |
|
1628 |
> |
fixed a bug where ghostbend atom b was not being set. ( recent bug |
1629 |
> |
from SimState conversion) |
1630 |
> |
|
1631 |
> |
2003-08-20 14:41 mmeineke |
1632 |
> |
|
1633 |
> |
* libBASS/Globals.hpp: updated the Changelog. |
1634 |
> |
|
1635 |
> |
added some bug fixes for setting the random number generator seed |
1636 |
> |
value. |
1637 |
> |
|
1638 |
> |
2003-08-20 14:41 mmeineke |
1639 |
> |
|
1640 |
> |
* ChangeLog: updated the Changelog. |
1641 |
> |
|
1642 |
> |
2003-08-20 14:11 tim |
1643 |
> |
|
1644 |
> |
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
1645 |
> |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
1646 |
> |
bend class |
1647 |
> |
|
1648 |
> |
2003-08-20 10:13 mmeineke |
1649 |
> |
|
1650 |
> |
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
1651 |
> |
make links. added -f to ln -s. |
1652 |
> |
|
1653 |
> |
2003-08-20 09:50 tim |
1654 |
> |
|
1655 |
> |
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
1656 |
> |
|
1657 |
> |
2003-08-20 09:34 tim |
1658 |
> |
|
1659 |
> |
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
1660 |
> |
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
1661 |
> |
printing |
1662 |
> |
|
1663 |
> |
2003-08-18 15:59 chuckv |
1664 |
> |
|
1665 |
> |
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1666 |
> |
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
1667 |
> |
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
1668 |
> |
Nanobuilder still broke. |
1669 |
> |
|
1670 |
> |
2003-08-15 14:24 tim |
1671 |
> |
|
1672 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1673 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
1674 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
1675 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
1676 |
> |
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
1677 |
> |
Method |
1678 |
> |
|
1679 |
> |
2003-08-14 11:16 tim |
1680 |
> |
|
1681 |
> |
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
1682 |
> |
with average force substraction strategy |
1683 |
> |
|
1684 |
> |
2003-08-13 16:20 chuckv |
1685 |
> |
|
1686 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
1687 |
> |
profiling code -DPROFILE. |
1688 |
> |
|
1689 |
> |
2003-08-13 14:21 tim |
1690 |
> |
|
1691 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1692 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1693 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
1694 |
> |
potential & z-contraint method |
1695 |
> |
|
1696 |
> |
2003-08-12 16:44 mmeineke |
1697 |
> |
|
1698 |
> |
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
1699 |
> |
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1700 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
1701 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
1702 |
> |
annoying bug in Directional Atom, where mu was getting written to |
1703 |
> |
pseudorandom memory location. |
1704 |
> |
|
1705 |
> |
2003-08-12 14:56 tim |
1706 |
> |
|
1707 |
> |
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
1708 |
> |
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
1709 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
1710 |
> |
libmdtools/SimSetup.cpp: debugging globals |
1711 |
> |
|
1712 |
> |
2003-08-12 13:40 gezelter |
1713 |
> |
|
1714 |
> |
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
1715 |
> |
and new atypes in LJFF |
1716 |
> |
|
1717 |
> |
2003-08-12 13:15 gezelter |
1718 |
> |
|
1719 |
> |
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
1720 |
> |
stuff... |
1721 |
> |
|
1722 |
> |
2003-08-12 13:14 chuckv |
1723 |
> |
|
1724 |
> |
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
1725 |
> |
|
1726 |
> |
2003-08-12 13:04 chuckv |
1727 |
> |
|
1728 |
> |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
1729 |
> |
Missed del of files before. |
1730 |
> |
|
1731 |
> |
2003-08-12 13:03 chuckv |
1732 |
> |
|
1733 |
> |
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
1734 |
> |
message] |
1735 |
> |
|
1736 |
> |
2003-08-12 13:01 chuckv |
1737 |
> |
|
1738 |
> |
* utils/sysbuilder/Makefile: commit makefile |
1739 |
> |
|
1740 |
> |
2003-08-12 12:51 tim |
1741 |
> |
|
1742 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1743 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1744 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
1745 |
> |
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
1746 |
> |
harmonical potential to z-constraint method |
1747 |
> |
|
1748 |
> |
2003-08-11 17:31 chuckv |
1749 |
> |
|
1750 |
> |
* utils/Makefile: Changed makefile to only build quicklate. |
1751 |
> |
|
1752 |
> |
2003-08-11 17:25 chuckv |
1753 |
> |
|
1754 |
> |
* ac-tools/configure.in: added utils/sysbuilder to be built. |
1755 |
> |
|
1756 |
> |
2003-08-11 17:12 chuckv |
1757 |
> |
|
1758 |
> |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1759 |
> |
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
1760 |
> |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
1761 |
> |
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
1762 |
> |
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
1763 |
> |
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
1764 |
> |
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
1765 |
> |
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
1766 |
> |
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
1767 |
> |
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
1768 |
> |
with new atom allocation in libmdtools. |
1769 |
> |
|
1770 |
> |
2003-08-11 14:41 tim |
1771 |
> |
|
1772 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
1773 |
> |
moving zconstraint molecules to specified positions |
1774 |
> |
|
1775 |
> |
2003-08-11 14:39 tim |
1776 |
> |
|
1777 |
> |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
1778 |
> |
|
1779 |
> |
2003-08-11 14:38 mmeineke |
1780 |
> |
|
1781 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
1782 |
> |
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
1783 |
> |
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
1784 |
> |
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
1785 |
> |
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
1786 |
> |
libBASS/node_list.h, libBASS/parse_interface.h, |
1787 |
> |
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
1788 |
> |
into the BASS language syntax. |
1789 |
> |
|
1790 |
> |
2003-08-11 13:29 mmeineke |
1791 |
> |
|
1792 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
1793 |
> |
degrees of freedom to account for zConstreints |
1794 |
> |
|
1795 |
> |
2003-08-08 16:22 chuckv |
1796 |
> |
|
1797 |
> |
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
1798 |
> |
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1799 |
> |
samples/metals/Au.bass: EAM works...... Neighbor list also |
1800 |
> |
works..... |
1801 |
> |
|
1802 |
> |
2003-08-08 12:48 mmeineke |
1803 |
> |
|
1804 |
> |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1805 |
> |
instance of Atom::setZ and Atom::getZ in ZConstaint. |
1806 |
> |
|
1807 |
> |
2003-08-07 16:47 mmeineke |
1808 |
> |
|
1809 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
1810 |
> |
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
1811 |
> |
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
1812 |
> |
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
1813 |
> |
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
1814 |
> |
configuration from SimState rather than arrays from Atom |
1815 |
> |
|
1816 |
> |
2003-08-06 19:47 chuckv |
1817 |
> |
|
1818 |
> |
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
1819 |
> |
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
1820 |
> |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
1821 |
> |
samples/metals/Au.bass: Bug fixes for eam... |
1822 |
> |
|
1823 |
> |
2003-08-01 11:18 tim |
1824 |
> |
|
1825 |
> |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
1826 |
> |
Z-Constraint |
1827 |
> |
|
1828 |
> |
2003-07-31 14:59 tim |
1829 |
> |
|
1830 |
> |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1831 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1832 |
> |
libmdtools/ZConstraint.cpp: add index range checking into |
1833 |
> |
ZConstraint |
1834 |
> |
|
1835 |
> |
2003-07-31 10:38 tim |
1836 |
> |
|
1837 |
> |
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
1838 |
> |
to the globals |
1839 |
> |
|
1840 |
> |
2003-07-31 10:35 tim |
1841 |
> |
|
1842 |
> |
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
1843 |
> |
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
1844 |
> |
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1845 |
> |
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
1846 |
> |
Added Z constraint. |
1847 |
> |
|
1848 |
> |
2003-07-30 16:17 chuckv |
1849 |
> |
|
1850 |
> |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
1851 |
> |
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
1852 |
> |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
1853 |
> |
samples/metals/Au.bass: More bug fixes for eam. |
1854 |
> |
|
1855 |
> |
2003-07-29 11:32 mmeineke |
1856 |
> |
|
1857 |
> |
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1858 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1859 |
> |
working on the props code |
1860 |
> |
|
1861 |
> |
2003-07-29 11:32 mmeineke |
1862 |
> |
|
1863 |
> |
* libBASS/Globals.cpp: [no log message] |
1864 |
> |
|
1865 |
> |
2003-07-25 15:05 chuckv |
1866 |
> |
|
1867 |
> |
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
1868 |
> |
metals |
1869 |
> |
|
1870 |
> |
2003-07-25 15:00 chuckv |
1871 |
> |
|
1872 |
> |
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
1873 |
> |
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
1874 |
> |
|
1875 |
> |
2003-07-24 16:22 chuckv |
1876 |
> |
|
1877 |
> |
* ac-tools/configure.in: Changed configure to look for both upper |
1878 |
> |
and lower cass .mod files |
1879 |
> |
|
1880 |
> |
2003-07-24 14:57 chuckv |
1881 |
> |
|
1882 |
> |
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
1883 |
> |
eam and do_forces. |
1884 |
> |
|
1885 |
> |
2003-07-23 17:13 chuckv |
1886 |
> |
|
1887 |
> |
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
1888 |
> |
force_globals.F90, simulation_module.F90, status_module.F90: |
1889 |
> |
Finished most code for eam.... |
1890 |
> |
|
1891 |
> |
2003-07-22 16:49 mmeineke |
1892 |
> |
|
1893 |
> |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
1894 |
> |
function to the DumpReader. It should now save the start of each |
1895 |
> |
frame in a vector. |
1896 |
> |
|
1897 |
> |
2003-07-22 15:05 mmeineke |
1898 |
> |
|
1899 |
> |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
1900 |
> |
to read dump files |
1901 |
> |
|
1902 |
> |
2003-07-22 14:54 tim |
1903 |
> |
|
1904 |
> |
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
1905 |
> |
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
1906 |
> |
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
1907 |
> |
message] |
1908 |
> |
|
1909 |
> |
2003-07-22 11:41 mmeineke |
1910 |
> |
|
1911 |
> |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
1912 |
> |
SimSetup.cpp: Fixed a current time initialization bug in |
1913 |
> |
InitFromFile. |
1914 |
> |
|
1915 |
> |
2003-07-21 16:27 mmeineke |
1916 |
> |
|
1917 |
> |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
1918 |
> |
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
1919 |
> |
friends to accomadate random file access |
1920 |
> |
|
1921 |
> |
2003-07-21 11:23 mmeineke |
1922 |
> |
|
1923 |
> |
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
1924 |
> |
one sets it. |
1925 |
> |
|
1926 |
> |
2003-07-21 11:23 mmeineke |
1927 |
> |
|
1928 |
> |
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
1929 |
> |
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
1930 |
> |
from the time specified in the init file. |
1931 |
> |
|
1932 |
> |
2003-07-17 16:49 gezelter |
1933 |
> |
|
1934 |
> |
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
1935 |
> |
DumpReader.cpp: Started work on a DumpReader |
1936 |
> |
|
1937 |
> |
2003-07-17 15:38 gezelter |
1938 |
> |
|
1939 |
> |
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
1940 |
> |
|
1941 |
> |
2003-07-17 15:32 gezelter |
1942 |
> |
|
1943 |
> |
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
1944 |
> |
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
1945 |
> |
Changes for SSD/E |
1946 |
> |
|
1947 |
> |
2003-07-17 14:38 mmeineke |
1948 |
> |
|
1949 |
> |
* libmdtools/do_Forces.F90: commented out an eam line |
1950 |
> |
|
1951 |
> |
2003-07-17 14:32 chuckv |
1952 |
> |
|
1953 |
> |
* libmdtools/atype_module.F90: fixed spelling issue |
1954 |
> |
|
1955 |
> |
2003-07-17 14:29 chuckv |
1956 |
> |
|
1957 |
> |
* libmdtools/: fInfo.c, status_module.F90: added info module |
1958 |
> |
|
1959 |
> |
2003-07-17 14:25 chuckv |
1960 |
> |
|
1961 |
> |
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
1962 |
> |
atype_module.F90, calc_eam.F90, do_Forces.F90, |
1963 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1964 |
> |
mpiSimulation_module.F90: Added massive changes for eam.... |
1965 |
> |
|
1966 |
> |
2003-07-16 16:49 chuckv |
1967 |
> |
|
1968 |
> |
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
1969 |
> |
|
1970 |
> |
2003-07-16 16:30 mmeineke |
1971 |
> |
|
1972 |
> |
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
1973 |
> |
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1974 |
> |
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
1975 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1976 |
> |
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
1977 |
> |
wrappers.F90: Changed how cutoffs were handled from C. Now |
1978 |
> |
notifyCutoffs in Fortran notifies those who need the information of |
1979 |
> |
any changes to cutoffs. |
1980 |
> |
|
1981 |
> |
2003-07-16 12:35 gezelter |
1982 |
> |
|
1983 |
> |
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
1984 |
> |
quickLate is now somewhat more intelligent about periodic |
1985 |
> |
boundaries and wrapping. |
1986 |
> |
|
1987 |
> |
2003-07-16 11:40 chuckv |
1988 |
> |
|
1989 |
> |
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
1990 |
> |
|
1991 |
> |
2003-07-16 10:34 mmeineke |
1992 |
> |
|
1993 |
> |
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
1994 |
> |
rebuilds on BoB |
1995 |
> |
|
1996 |
> |
2003-07-15 21:11 gezelter |
1997 |
> |
|
1998 |
> |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
1999 |
> |
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
2000 |
> |
fixes for box changes |
2001 |
> |
|
2002 |
> |
2003-07-15 17:29 mmeineke |
2003 |
> |
|
2004 |
> |
* libmdtools/simulation_module.F90: removed some debugging print |
2005 |
> |
statements. |
2006 |
> |
|
2007 |
> |
2003-07-15 17:22 mmeineke |
2008 |
> |
|
2009 |
> |
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
2010 |
> |
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
2011 |
> |
do_forces. Rrf was not being used in the neighborlist correctly. |
2012 |
> |
rcut was conssistently being set lowere than Rrf causing the dipole |
2013 |
> |
cutoff region to be to small. Also led to the removal of the taper |
2014 |
> |
region to buffer the dipole cutoff. |
2015 |
> |
|
2016 |
> |
2003-07-15 16:34 mmeineke |
2017 |
> |
|
2018 |
> |
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
2019 |
> |
fixing ssd bug |
2020 |
> |
|
2021 |
> |
2003-07-15 14:56 gezelter |
2022 |
> |
|
2023 |
> |
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
2024 |
> |
for the NPT ensembles |
2025 |
> |
|
2026 |
> |
2003-07-15 13:52 mmeineke |
2027 |
> |
|
2028 |
> |
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
2029 |
> |
simSetup |
2030 |
> |
|
2031 |
> |
2003-07-15 12:57 mmeineke |
2032 |
> |
|
2033 |
> |
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
2034 |
> |
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
2035 |
> |
fixed some bugs, Changed entry_plug to info where appropriate |
2036 |
> |
|
2037 |
> |
2003-07-15 12:25 chuckv |
2038 |
> |
|
2039 |
> |
* utils/sysBuild.ggo: added more command line arguments |
2040 |
> |
|
2041 |
> |
2003-07-15 12:11 gezelter |
2042 |
> |
|
2043 |
> |
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
2044 |
> |
Fixing force field line |
2045 |
> |
|
2046 |
> |
2003-07-15 12:10 gezelter |
2047 |
> |
|
2048 |
> |
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
2049 |
> |
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
2050 |
> |
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
2051 |
> |
tensor |
2052 |
> |
|
2053 |
> |
2003-07-15 10:50 gezelter |
2054 |
> |
|
2055 |
> |
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
2056 |
> |
|
2057 |
> |
2003-07-15 10:42 gezelter |
2058 |
> |
|
2059 |
> |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
2060 |
> |
removed old outdated code |
2061 |
> |
|
2062 |
> |
2003-07-15 09:45 gezelter |
2063 |
> |
|
2064 |
> |
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
2065 |
> |
|
2066 |
> |
2003-07-15 09:28 gezelter |
2067 |
> |
|
2068 |
> |
* libmdtools/Molecule.cpp: removing get_vx |
2069 |
> |
|
2070 |
> |
2003-07-14 22:28 gezelter |
2071 |
> |
|
2072 |
> |
* libmdtools/NPTfm.cpp: Added NPTfm |
2073 |
> |
|
2074 |
> |
2003-07-14 22:27 gezelter |
2075 |
> |
|
2076 |
> |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
2077 |
> |
Bugfix in NPTim, fixes for NPTfm |
2078 |
> |
|
2079 |
> |
2003-07-14 22:08 gezelter |
2080 |
> |
|
2081 |
> |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
2082 |
> |
Checking in changes for NPTim |
2083 |
> |
|
2084 |
> |
2003-07-14 18:06 gezelter |
2085 |
> |
|
2086 |
> |
* utils/Makefile: Broken SysBuilder |
2087 |
> |
|
2088 |
> |
2003-07-14 18:06 gezelter |
2089 |
> |
|
2090 |
> |
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2091 |
> |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2092 |
> |
for samples |
2093 |
> |
|
2094 |
> |
2003-07-14 18:06 gezelter |
2095 |
> |
|
2096 |
> |
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
2097 |
> |
debugging write statements |
2098 |
> |
|
2099 |
> |
2003-07-14 17:38 gezelter |
2100 |
> |
|
2101 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
2102 |
> |
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
2103 |
> |
|
2104 |
> |
2003-07-14 16:48 mmeineke |
2105 |
> |
|
2106 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
2107 |
> |
and set routines to Atom and DirectionalAtom |
2108 |
> |
|
2109 |
> |
2003-07-14 16:35 chuckv |
2110 |
> |
|
2111 |
> |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
2112 |
> |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
2113 |
> |
that takes different cmd line arguments. |
2114 |
> |
|
2115 |
> |
2003-07-14 16:28 mmeineke |
2116 |
> |
|
2117 |
> |
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
2118 |
> |
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
2119 |
> |
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
2120 |
> |
were not being updated |
2121 |
> |
|
2122 |
> |
2003-07-14 10:04 gezelter |
2123 |
> |
|
2124 |
> |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
2125 |
> |
NPTim |
2126 |
> |
|
2127 |
> |
2003-07-14 09:55 mmeineke |
2128 |
> |
|
2129 |
> |
* forceFields/DUFF.frc: Switched the bond in the force field back |
2130 |
> |
to constrained, to preserve energy |
2131 |
> |
|
2132 |
> |
2003-07-11 17:34 mmeineke |
2133 |
> |
|
2134 |
> |
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
2135 |
> |
Integrator.hpp: working on som integrator bugs |
2136 |
> |
|
2137 |
> |
2003-07-11 10:26 gezelter |
2138 |
> |
|
2139 |
> |
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
2140 |
> |
to worry about all the strtok() calls in our code |
2141 |
> |
|
2142 |
> |
2003-07-11 09:49 gezelter |
2143 |
> |
|
2144 |
> |
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
2145 |
> |
|
2146 |
> |
2003-07-10 20:15 gezelter |
2147 |
> |
|
2148 |
> |
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
2149 |
> |
eor. |
2150 |
> |
|
2151 |
> |
2003-07-10 17:15 mmeineke |
2152 |
> |
|
2153 |
> |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
2154 |
> |
SimInfo.cpp, Thermo.cpp: fixed some bugs |
2155 |
> |
|
2156 |
> |
2003-07-10 14:53 chuckv |
2157 |
> |
|
2158 |
> |
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
2159 |
> |
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
2160 |
> |
nanoBuilder and a general Lattice builder. |
2161 |
> |
|
2162 |
> |
2003-07-10 12:10 gezelter |
2163 |
> |
|
2164 |
> |
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
2165 |
> |
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
2166 |
> |
|
2167 |
> |
2003-07-09 17:14 mmeineke |
2168 |
> |
|
2169 |
> |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
2170 |
> |
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
2171 |
> |
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
2172 |
> |
caclulation of HmatInverse. |
2173 |
> |
|
2174 |
> |
2003-07-09 10:34 mmeineke |
2175 |
> |
|
2176 |
> |
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
2177 |
> |
|
2178 |
> |
2003-07-09 10:33 mmeineke |
2179 |
> |
|
2180 |
> |
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
2181 |
> |
|
2182 |
> |
2003-07-09 08:56 gezelter |
2183 |
> |
|
2184 |
> |
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
2185 |
> |
|
2186 |
> |
2003-07-09 08:56 gezelter |
2187 |
> |
|
2188 |
> |
* libBASS/Globals.cpp: Removed Qmass |
2189 |
> |
|
2190 |
> |
2003-07-08 21:15 gezelter |
2191 |
> |
|
2192 |
> |
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
2193 |
> |
and NPTi |
2194 |
> |
|
2195 |
> |
2003-07-08 20:41 gezelter |
2196 |
> |
|
2197 |
> |
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
2198 |
> |
|
2199 |
> |
2003-07-08 16:10 gezelter |
2200 |
> |
|
2201 |
> |
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
2202 |
> |
|
2203 |
> |
2003-07-08 16:06 gezelter |
2204 |
> |
|
2205 |
> |
* libmdtools/NPTi.cpp: fixed box scaling |
2206 |
> |
|
2207 |
> |
2003-07-08 15:56 gezelter |
2208 |
> |
|
2209 |
> |
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
2210 |
> |
SimInfo.hpp, Thermo.cpp: NPTi |
2211 |
> |
|
2212 |
> |
2003-07-03 14:41 mmeineke |
2213 |
> |
|
2214 |
> |
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
2215 |
> |
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
2216 |
> |
scripts in the makefiles |
2217 |
> |
|
2218 |
> |
2003-07-02 16:26 mmeineke |
2219 |
> |
|
2220 |
> |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2221 |
> |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2222 |
> |
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
2223 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2224 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2225 |
> |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
2226 |
> |
utils/Makefile: fixed the bugs introduced by switching the periodic |
2227 |
> |
box to a matrix |
2228 |
> |
|
2229 |
> |
2003-07-01 17:39 gezelter |
2230 |
> |
|
2231 |
> |
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
2232 |
> |
|
2233 |
> |
2003-07-01 17:29 gezelter |
2234 |
> |
|
2235 |
> |
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
2236 |
> |
|
2237 |
> |
2003-07-01 16:33 mmeineke |
2238 |
> |
|
2239 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
2240 |
> |
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
2241 |
> |
the box matrix to everything. |
2242 |
> |
|
2243 |
> |
2003-06-30 17:03 mmeineke |
2244 |
> |
|
2245 |
> |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2246 |
> |
src/oopse.cpp: |
2247 |
> |
Updated the ChangeLog, and Converted most of the SImInfo to use |
2248 |
> |
non-Isotropic boxes. wrapVector needs to be finished. |
2249 |
> |
|
2250 |
> |
2003-06-25 16:12 mmeineke |
2251 |
> |
|
2252 |
> |
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
2253 |
> |
to Harmonic bonds in the DUFF frc file |
2254 |
> |
|
2255 |
> |
fixed constraints. |
2256 |
> |
|
2257 |
> |
2003-06-25 16:11 mmeineke |
2258 |
> |
|
2259 |
> |
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
2260 |
> |
the DUFF frc file |
2261 |
> |
|
2262 |
> |
2003-06-24 17:51 gezelter |
2263 |
> |
|
2264 |
> |
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
2265 |
> |
|
2266 |
> |
2003-06-24 14:57 mmeineke |
2267 |
> |
|
2268 |
> |
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
2269 |
> |
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
2270 |
> |
the DUFF forcefield and BondExtensions.cpp |
2271 |
> |
|
2272 |
> |
2003-06-23 16:24 mmeineke |
2273 |
> |
|
2274 |
> |
* libmdtools/Integrator.cpp: Doing some work to debug the |
2275 |
> |
constraint code. |
2276 |
> |
|
2277 |
> |
2003-06-20 15:50 gezelter |
2278 |
> |
|
2279 |
> |
* libmdtools/Integrator.hpp: NPT fix |
2280 |
> |
|
2281 |
> |
2003-06-20 15:29 mmeineke |
2282 |
> |
|
2283 |
> |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
2284 |
> |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
2285 |
> |
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
2286 |
> |
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
2287 |
> |
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
2288 |
> |
integrator and NVT seem to be working now. |
2289 |
> |
|
2290 |
> |
2003-06-20 11:49 gezelter |
2291 |
> |
|
2292 |
> |
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
2293 |
> |
|
2294 |
> |
2003-06-19 17:02 mmeineke |
2295 |
> |
|
2296 |
> |
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
2297 |
> |
forceFields/LJ_FF.frc, forceFields/Makefile, |
2298 |
> |
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
2299 |
> |
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
2300 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
2301 |
> |
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
2302 |
> |
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
2303 |
> |
forcefield names. |
2304 |
> |
|
2305 |
> |
2003-06-19 14:21 mmeineke |
2306 |
> |
|
2307 |
> |
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
2308 |
> |
finished the basics of the integrator and SimSetup.cpp |
2309 |
> |
|
2310 |
> |
2003-06-19 14:11 mmeineke |
2311 |
> |
|
2312 |
> |
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
2313 |
> |
up / get it to work with the new Integrator. |
2314 |
> |
|
2315 |
> |
2003-06-18 17:20 mmeineke |
2316 |
> |
|
2317 |
> |
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
2318 |
> |
output times. |
2319 |
> |
|
2320 |
> |
2003-06-17 16:56 mmeineke |
2321 |
> |
|
2322 |
> |
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
2323 |
> |
fro the ghost Bend in TraPPE_Ex |
2324 |
> |
|
2325 |
> |
some work on the integrator. ( incomplete) |
2326 |
> |
|
2327 |
> |
2003-06-17 16:55 mmeineke |
2328 |
> |
|
2329 |
> |
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
2330 |
> |
Bend in TraPPE_Ex |
2331 |
> |
|
2332 |
> |
2003-06-04 16:06 mmeineke |
2333 |
> |
|
2334 |
> |
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
2335 |
> |
constrainB to the Symplectic integrator |
2336 |
> |
|
2337 |
> |
2003-05-30 16:32 mmeineke |
2338 |
> |
|
2339 |
> |
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
2340 |
> |
the basic integrator. |
2341 |
> |
|
2342 |
> |
bilayerSys.cpp altered for building tb3. |
2343 |
> |
|
2344 |
> |
2003-05-30 16:31 mmeineke |
2345 |
> |
|
2346 |
> |
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
2347 |
> |
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
2348 |
> |
modifiying Symplectic to become the basic integrator. |
2349 |
> |
|
2350 |
> |
2003-05-30 15:19 mmeineke |
2351 |
> |
|
2352 |
> |
* libmdtools/Integrator.hpp: added some member variables for |
2353 |
> |
position, velocity, etc. |
2354 |
> |
|
2355 |
> |
2003-05-30 14:07 mmeineke |
2356 |
> |
|
2357 |
> |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
2358 |
> |
is now derived from Integrator |
2359 |
> |
|
2360 |
> |
2003-05-20 11:44 mmeineke |
2361 |
> |
|
2362 |
> |
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
2363 |
> |
|
2364 |
> |
2003-05-17 11:57 mmeineke |
2365 |
> |
|
2366 |
> |
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
2367 |
> |
working |
2368 |
> |
|
2369 |
> |
2003-05-16 16:37 mmeineke |
2370 |
> |
|
2371 |
> |
* utils/bilayerSys.cpp: still working on the bilayer code |
2372 |
> |
|
2373 |
> |
2003-05-16 09:28 mmeineke |
2374 |
> |
|
2375 |
> |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
2376 |
> |
work to overhaul sysbuild. |
2377 |
> |
|
2378 |
> |
2003-05-13 16:23 mmeineke |
2379 |
> |
|
2380 |
> |
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
2381 |
> |
|
2382 |
> |
2003-05-13 15:47 mmeineke |
2383 |
> |
|
2384 |
> |
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
2385 |
> |
beadLipid/water.mdl: Added bead lipid model to the sample directory |
2386 |
> |
|
2387 |
> |
2003-05-13 15:34 mmeineke |
2388 |
> |
|
2389 |
> |
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
2390 |
> |
the Trappe extended force field |
2391 |
> |
|
2392 |
> |
2003-05-13 12:01 mmeineke |
2393 |
> |
|
2394 |
> |
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
2395 |
> |
TraPPe_Ex forceField |
2396 |
> |
|
2397 |
> |
2003-05-09 14:51 mmeineke |
2398 |
> |
|
2399 |
> |
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
2400 |
> |
there were some duplicate entries |
2401 |
> |
|
2402 |
> |
added a two chain lipid to the lipid.mdl in sample |
2403 |
> |
|
2404 |
> |
2003-05-09 14:51 mmeineke |
2405 |
> |
|
2406 |
> |
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
2407 |
> |
there were some duplicate entries |
2408 |
> |
|
2409 |
> |
2003-05-09 11:56 mmeineke |
2410 |
> |
|
2411 |
> |
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
2412 |
> |
configure script |
2413 |
> |
|
2414 |
> |
added the CH branching group to the TraPPE_Ex fource field |
2415 |
> |
|
2416 |
> |
2003-05-09 11:55 mmeineke |
2417 |
> |
|
2418 |
> |
* ac-tools/configure.in: added the utils subdirectory to the |
2419 |
> |
configure script |
2420 |
> |
|
2421 |
> |
2003-04-25 11:02 mmeineke |
2422 |
> |
|
2423 |
> |
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
2424 |
> |
bilayer builder |
2425 |
> |
|
2426 |
> |
2003-04-24 21:00 mmeineke |
2427 |
> |
|
2428 |
> |
* libmdtools/f_verlet_constrained.F90: added a new test for |
2429 |
> |
constraint failure |
2430 |
> |
|
2431 |
> |
2003-04-17 16:54 mmeineke |
2432 |
> |
|
2433 |
> |
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
2434 |
> |
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
2435 |
> |
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
2436 |
> |
build our systems |
2437 |
> |
|
2438 |
> |
2003-04-16 16:11 mmeineke |
2439 |
> |
|
2440 |
> |
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
2441 |
> |
|
2442 |
> |
2003-04-15 16:47 mmeineke |
2443 |
> |
|
2444 |
> |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
2445 |
> |
and sysBuild both will build now. woot! |
2446 |
> |
|
2447 |
> |
2003-04-15 16:20 mmeineke |
2448 |
> |
|
2449 |
> |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
2450 |
> |
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
2451 |
> |
|
2452 |
> |
sysBuild still need to write the bass file. |
2453 |
> |
|
2454 |
> |
MoLocator.cpp is currently empty |
2455 |
> |
|
2456 |
> |
2003-04-15 15:40 chuckv |
2457 |
> |
|
2458 |
> |
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
2459 |
> |
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
2460 |
> |
forceFields/pdu3.eam, forceFields/ptu3.eam, |
2461 |
> |
libmdtools/ForceFields.hpp: Added eam force files... |
2462 |
> |
|
2463 |
> |
2003-04-15 11:37 chuckv |
2464 |
> |
|
2465 |
> |
* libmdtools/EAM_FF.cpp: More eam work. |
2466 |
> |
|
2467 |
> |
2003-04-14 16:22 mmeineke |
2468 |
> |
|
2469 |
> |
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
2470 |
> |
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
2471 |
> |
working on the system builder |
2472 |
> |
|
2473 |
> |
2003-04-14 16:16 chuckv |
2474 |
> |
|
2475 |
> |
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
2476 |
> |
ordering on NVT calculation in integrators. |
2477 |
> |
|
2478 |
> |
2003-04-14 14:51 mmeineke |
2479 |
> |
|
2480 |
> |
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
2481 |
> |
obj/placeHolder: working on a system builder |
2482 |
> |
|
2483 |
> |
2003-04-14 14:04 mmeineke |
2484 |
> |
|
2485 |
> |
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
2486 |
> |
|
2487 |
> |
added sysBuild to the utils Makefile |
2488 |
> |
|
2489 |
> |
2003-04-14 14:03 mmeineke |
2490 |
> |
|
2491 |
> |
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
2492 |
> |
Ghost bends to the TraPPE_Ex forceField |
2493 |
> |
|
2494 |
> |
2003-04-14 13:19 chuckv |
2495 |
> |
|
2496 |
> |
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
2497 |
> |
|
2498 |
> |
2003-04-11 13:46 mmeineke |
2499 |
> |
|
2500 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
2501 |
> |
simulation_module.F90: fixed a memory bug in Fortran, where |
2502 |
> |
molMembershipArray was declared nLocal instead of nGlobal. |
2503 |
> |
|
2504 |
> |
2003-04-11 10:16 gezelter |
2505 |
> |
|
2506 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
2507 |
> |
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
2508 |
> |
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
2509 |
> |
for NPT |
2510 |
> |
|
2511 |
> |
2003-04-10 15:08 mmeineke |
2512 |
> |
|
2513 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
2514 |
> |
globalIndex counter to Molecule |
2515 |
> |
|
2516 |
> |
2003-04-10 11:35 gezelter |
2517 |
> |
|
2518 |
> |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
2519 |
> |
ConstantStress |
2520 |
> |
|
2521 |
> |
2003-04-10 11:27 mmeineke |
2522 |
> |
|
2523 |
> |
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
2524 |
> |
caused a miscalculation of nLocal. |
2525 |
> |
|
2526 |
> |
2003-04-10 11:21 mmeineke |
2527 |
> |
|
2528 |
> |
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
2529 |
> |
do_Forces.F90: fixed a bug in symplectic, where presure was only |
2530 |
> |
being calculated the first time through. |
2531 |
> |
|
2532 |
> |
2003-04-09 11:20 chuckv |
2533 |
> |
|
2534 |
> |
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
2535 |
> |
file |
2536 |
> |
|
2537 |
> |
2003-04-09 08:59 gezelter |
2538 |
> |
|
2539 |
> |
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
2540 |
> |
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
2541 |
> |
|
2542 |
> |
2003-04-08 23:06 gezelter |
2543 |
> |
|
2544 |
> |
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
2545 |
> |
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
2546 |
> |
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
2547 |
> |
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
2548 |
> |
calc_reaction_field.F90, calc_sticky_pair.F90, |
2549 |
> |
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
2550 |
> |
NVT |
2551 |
> |
|
2552 |
> |
2003-04-08 17:38 chuckv |
2553 |
> |
|
2554 |
> |
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
2555 |
> |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
2556 |
> |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2557 |
> |
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
2558 |
> |
(kinda)... |
2559 |
> |
|
2560 |
> |
2003-04-08 16:35 gezelter |
2561 |
> |
|
2562 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2563 |
> |
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
2564 |
> |
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
2565 |
> |
|
2566 |
> |
2003-04-08 12:16 chuckv |
2567 |
> |
|
2568 |
> |
* libmdtools/: do_Forces.F90, neighborLists.F90, |
2569 |
> |
simulation_module.F90: Moved expand neighborlist to init_FF. |
2570 |
> |
|
2571 |
> |
2003-04-08 10:20 chuckv |
2572 |
> |
|
2573 |
> |
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
2574 |
> |
NVT |
2575 |
> |
|
2576 |
> |
2003-04-08 09:39 gezelter |
2577 |
> |
|
2578 |
> |
* libmdtools/Verlet.cpp: fixes for nvt / npt |
2579 |
> |
|
2580 |
> |
2003-04-08 09:34 gezelter |
2581 |
> |
|
2582 |
> |
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
2583 |
> |
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
2584 |
> |
|
2585 |
> |
2003-04-08 07:50 gezelter |
2586 |
> |
|
2587 |
> |
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
2588 |
> |
|
2589 |
> |
2003-04-08 07:44 gezelter |
2590 |
> |
|
2591 |
> |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
2592 |
> |
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
2593 |
> |
NVT and NPT ensembles |
2594 |
> |
|
2595 |
> |
2003-04-07 16:42 gezelter |
2596 |
> |
|
2597 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
2598 |
> |
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
2599 |
> |
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
2600 |
> |
|
2601 |
> |
2003-04-07 16:20 mmeineke |
2602 |
> |
|
2603 |
> |
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
2604 |
> |
portion of SSD. |
2605 |
> |
|
2606 |
> |
2003-04-07 16:16 mmeineke |
2607 |
> |
|
2608 |
> |
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
2609 |
> |
doing some testing in sticky through Symplectic. |
2610 |
> |
|
2611 |
> |
2003-04-07 15:51 gezelter |
2612 |
> |
|
2613 |
> |
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
2614 |
> |
|
2615 |
> |
2003-04-07 15:50 chuckv |
2616 |
> |
|
2617 |
> |
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
2618 |
> |
tau and virial. |
2619 |
> |
|
2620 |
> |
2003-04-07 15:06 mmeineke |
2621 |
> |
|
2622 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
2623 |
> |
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
2624 |
> |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
2625 |
> |
src/Makefile: bug fixes |
2626 |
> |
|
2627 |
> |
2003-04-07 11:56 gezelter |
2628 |
> |
|
2629 |
> |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
2630 |
> |
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
2631 |
> |
Many fixes to add extended system |
2632 |
> |
|
2633 |
> |
2003-04-07 09:30 gezelter |
2634 |
> |
|
2635 |
> |
* src/Makefile: Fixed a bug caused by my experimentation |
2636 |
> |
|
2637 |
> |
2003-04-07 09:30 gezelter |
2638 |
> |
|
2639 |
> |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
2640 |
> |
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
2641 |
> |
Added ExtendedSystem infrastructure for NPT and NVT calculations |
2642 |
> |
|
2643 |
> |
2003-04-07 09:30 gezelter |
2644 |
> |
|
2645 |
> |
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
2646 |
> |
|
2647 |
> |
2003-04-04 23:07 gezelter |
2648 |
> |
|
2649 |
> |
* src/Makefile: final mods to try a fortran compiler |
2650 |
> |
|
2651 |
> |
2003-04-04 22:39 gezelter |
2652 |
> |
|
2653 |
> |
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
2654 |
> |
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
2655 |
> |
|
2656 |
> |
2003-04-04 21:56 gezelter |
2657 |
> |
|
2658 |
> |
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
2659 |
> |
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
2660 |
> |
|
2661 |
> |
2003-04-04 21:45 gezelter |
2662 |
> |
|
2663 |
> |
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
2664 |
> |
fixes to fortran wrappers |
2665 |
> |
|
2666 |
> |
2003-04-04 17:22 chuckv |
2667 |
> |
|
2668 |
> |
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
2669 |
> |
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
2670 |
> |
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
2671 |
> |
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
2672 |
> |
smarter, fortran gets dumber... |
2673 |
> |
|
2674 |
> |
2003-04-04 14:57 mmeineke |
2675 |
> |
|
2676 |
> |
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
2677 |
> |
neighborLists.F90: fixed a memory read bug in neighborlist |
2678 |
> |
|
2679 |
> |
2003-04-04 14:47 gezelter |
2680 |
> |
|
2681 |
> |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
2682 |
> |
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
2683 |
> |
|
2684 |
> |
2003-04-04 14:16 gezelter |
2685 |
> |
|
2686 |
> |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
2687 |
> |
SimInfo.hpp: Fixes for ExtendedSystem |
2688 |
> |
|
2689 |
> |
2003-04-03 20:57 gezelter |
2690 |
> |
|
2691 |
> |
* libmdtools/ExtendedSystem.hpp: Added extended system header |
2692 |
> |
|
2693 |
> |
2003-04-03 20:57 gezelter |
2694 |
> |
|
2695 |
> |
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
2696 |
> |
for extended system code |
2697 |
> |
|
2698 |
> |
2003-04-03 18:49 gezelter |
2699 |
> |
|
2700 |
> |
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
2701 |
> |
extendedsystem |
2702 |
> |
|
2703 |
> |
2003-04-03 17:19 mmeineke |
2704 |
> |
|
2705 |
> |
* libmdtools/Molecule.hpp: added some little fixes here and there. |
2706 |
> |
|
2707 |
> |
2003-04-03 17:01 mmeineke |
2708 |
> |
|
2709 |
> |
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
2710 |
> |
initialize bug. |
2711 |
> |
|
2712 |
> |
2003-04-03 16:12 mmeineke |
2713 |
> |
|
2714 |
> |
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
2715 |
> |
little things like deleteing unused variables and such. |
2716 |
> |
|
2717 |
> |
2003-04-03 15:57 mmeineke |
2718 |
> |
|
2719 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
2720 |
> |
simError.h also some fixes to Molecule.hpp |
2721 |
> |
|
2722 |
> |
2003-04-03 15:57 mmeineke |
2723 |
> |
|
2724 |
> |
* libBASS/simError.h: a few fixes to simError.h |
2725 |
> |
|
2726 |
> |
2003-04-03 15:21 mmeineke |
2727 |
> |
|
2728 |
> |
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
2729 |
> |
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
2730 |
> |
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
2731 |
> |
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
2732 |
> |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
2733 |
> |
src/Makefile, src/oopse.cpp: fixed some small things with |
2734 |
> |
simError.h |
2735 |
> |
|
2736 |
> |
2003-04-03 15:19 gezelter |
2737 |
> |
|
2738 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
2739 |
> |
|
2740 |
> |
2003-04-03 14:58 gezelter |
2741 |
> |
|
2742 |
> |
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
2743 |
> |
now) |
2744 |
> |
|
2745 |
> |
2003-04-03 08:42 gezelter |
2746 |
> |
|
2747 |
> |
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
2748 |
> |
Changed Readme, added some files |
2749 |
> |
|
2750 |
> |
2003-04-02 17:19 mmeineke |
2751 |
> |
|
2752 |
> |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
2753 |
> |
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
2754 |
> |
dipoles mostly work, but there is a memory leak somewhere. |
2755 |
> |
|
2756 |
> |
2003-04-02 10:01 mmeineke |
2757 |
> |
|
2758 |
> |
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
2759 |
> |
the proper atomIdents. |
2760 |
> |
|
2761 |
> |
2003-04-01 11:50 chuckv |
2762 |
> |
|
2763 |
> |
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
2764 |
> |
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
2765 |
> |
samples/argon/argon.bass: more bug fixes.... |
2766 |
> |
|
2767 |
> |
2003-04-01 11:49 mmeineke |
2768 |
> |
|
2769 |
> |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
2770 |
> |
DumpWriter to be more robust to errors. also added a little |
2771 |
> |
namespace to InitFromFile to wrap it's helper functions in MPI |
2772 |
> |
|
2773 |
> |
2003-03-31 17:09 chuckv |
2774 |
> |
|
2775 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
2776 |
> |
not zeroed. |
2777 |
> |
|
2778 |
> |
2003-03-31 16:50 chuckv |
2779 |
> |
|
2780 |
> |
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
2781 |
> |
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
2782 |
> |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
2783 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
2784 |
> |
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
2785 |
> |
samples/alkane/butane.bass: Fixes in MPI force calc and in |
2786 |
> |
Trappe_Ex parsing. |
2787 |
> |
|
2788 |
> |
2003-03-28 17:34 chuckv |
2789 |
> |
|
2790 |
> |
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
2791 |
> |
|
2792 |
> |
2003-03-28 16:45 chuckv |
2793 |
> |
|
2794 |
> |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2795 |
> |
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
2796 |
> |
routines. |
2797 |
> |
|
2798 |
> |
2003-03-28 14:33 mmeineke |
2799 |
> |
|
2800 |
> |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
2801 |
> |
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
2802 |
> |
bug where the Excludes were not being created properly |
2803 |
> |
|
2804 |
> |
2003-03-28 14:30 chuckv |
2805 |
> |
|
2806 |
> |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
2807 |
> |
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
2808 |
> |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
2809 |
> |
and debugging mpi read write from file. |
2810 |
> |
|
2811 |
> |
2003-03-28 10:28 mmeineke |
2812 |
> |
|
2813 |
> |
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
2814 |
> |
interactions in Trappe |
2815 |
> |
|
2816 |
> |
2003-03-27 18:33 chuckv |
2817 |
> |
|
2818 |
> |
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
2819 |
> |
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
2820 |
> |
|
2821 |
> |
2003-03-27 17:16 mmeineke |
2822 |
> |
|
2823 |
> |
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
2824 |
> |
excludes were not being initialized |
2825 |
> |
|
2826 |
> |
2003-03-27 16:52 mmeineke |
2827 |
> |
|
2828 |
> |
* src/Makefile: [no log message] |
2829 |
> |
|
2830 |
> |
2003-03-27 16:52 mmeineke |
2831 |
> |
|
2832 |
> |
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
2833 |
> |
|
2834 |
> |
2003-03-27 16:07 mmeineke |
2835 |
> |
|
2836 |
> |
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
2837 |
> |
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
2838 |
> |
Verlet.cpp: fixed the compile time bugs, Source builds and links |
2839 |
> |
|
2840 |
> |
2003-03-27 15:48 mmeineke |
2841 |
> |
|
2842 |
> |
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
2843 |
> |
more bugs. |
2844 |
> |
|
2845 |
> |
2003-03-27 15:40 mmeineke |
2846 |
> |
|
2847 |
> |
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
2848 |
> |
|
2849 |
> |
2003-03-27 15:39 mmeineke |
2850 |
> |
|
2851 |
> |
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
2852 |
> |
|
2853 |
> |
2003-03-27 15:36 mmeineke |
2854 |
> |
|
2855 |
> |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
2856 |
> |
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
2857 |
> |
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
2858 |
> |
|
2859 |
> |
2003-03-27 15:12 mmeineke |
2860 |
> |
|
2861 |
> |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
2862 |
> |
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
2863 |
> |
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
2864 |
> |
to. will now attempt to compile. |
2865 |
> |
|
2866 |
> |
2003-03-27 14:21 mmeineke |
2867 |
> |
|
2868 |
> |
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
2869 |
> |
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
2870 |
> |
updating SimSetup to initialize and use the new MPI division of |
2871 |
> |
labour, and Molecule class |
2872 |
> |
|
2873 |
> |
2003-03-27 12:55 mmeineke |
2874 |
> |
|
2875 |
> |
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
2876 |
> |
use Molecule |
2877 |
> |
|
2878 |
> |
2003-03-27 12:32 mmeineke |
2879 |
> |
|
2880 |
> |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
2881 |
> |
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
2882 |
> |
converted to the new Molecule model. TraPPE_Ex is currently being |
2883 |
> |
updated. SimSetups routines are writtten, but not yet called. |
2884 |
> |
|
2885 |
> |
2003-03-27 10:07 gezelter |
2886 |
> |
|
2887 |
> |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
2888 |
> |
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
2889 |
> |
numbering in MPI |
2890 |
> |
|
2891 |
> |
2003-03-27 09:30 mmeineke |
2892 |
> |
|
2893 |
> |
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
2894 |
> |
|
2895 |
> |
2003-03-26 20:49 gezelter |
2896 |
> |
|
2897 |
> |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
2898 |
> |
fileio for MPI |
2899 |
> |
|
2900 |
> |
2003-03-26 18:14 gezelter |
2901 |
> |
|
2902 |
> |
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
2903 |
> |
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
2904 |
> |
fixes many bug fixes |
2905 |
> |
|
2906 |
> |
2003-03-26 17:24 gezelter |
2907 |
> |
|
2908 |
> |
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
2909 |
> |
sequence of atoms on the other processors. Node 0 now fires |
2910 |
> |
potatoes at other processors to get them to send french fries back. |
2911 |
> |
|
2912 |
> |
2003-03-26 17:02 mmeineke |
2913 |
> |
|
2914 |
> |
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
2915 |
> |
making the molecules is in place. ForceField needs to be updated |
2916 |
> |
next. |
2917 |
> |
|
2918 |
> |
2003-03-26 16:54 mmeineke |
2919 |
> |
|
2920 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
2921 |
> |
the "static" bugs in Atom and Exclude |
2922 |
> |
|
2923 |
> |
2003-03-26 16:50 mmeineke |
2924 |
> |
|
2925 |
> |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
2926 |
> |
SimSetup.cpp: still working on the SimSetup routine. also fixed |
2927 |
> |
some things in Exclude.hpp |
2928 |
> |
|
2929 |
> |
2003-03-26 16:24 gezelter |
2930 |
> |
|
2931 |
> |
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
2932 |
> |
|
2933 |
> |
2003-03-26 16:23 gezelter |
2934 |
> |
|
2935 |
> |
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
2936 |
> |
and Exclude list |
2937 |
> |
|
2938 |
> |
2003-03-26 16:04 gezelter |
2939 |
> |
|
2940 |
> |
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
2941 |
> |
delete ranges of atoms |
2942 |
> |
|
2943 |
> |
2003-03-26 15:45 mmeineke |
2944 |
> |
|
2945 |
> |
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
2946 |
> |
with static arrays similar to the Atom class |
2947 |
> |
|
2948 |
> |
2003-03-26 15:22 mmeineke |
2949 |
> |
|
2950 |
> |
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
2951 |
> |
overhauling the molecule class to contain it's own bonds, bends, |
2952 |
> |
and torsions. |
2953 |
> |
|
2954 |
> |
may god have mercy on my soul. |
2955 |
> |
|
2956 |
> |
2003-03-26 14:34 chuckv |
2957 |
> |
|
2958 |
> |
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
2959 |
> |
|
2960 |
> |
2003-03-26 13:02 gezelter |
2961 |
> |
|
2962 |
> |
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
2963 |
> |
mpiSimulation.hpp: MPI stuff for passing out molecules |
2964 |
> |
|
2965 |
> |
2003-03-26 11:12 chuckv |
2966 |
> |
|
2967 |
> |
* libmdtools/mpiSimulation.cpp: working on load balancing |
2968 |
> |
|
2969 |
> |
2003-03-26 10:37 chuckv |
2970 |
> |
|
2971 |
> |
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
2972 |
> |
samples/argon/argon.bass: Fixes for Parallel thermalization |
2973 |
> |
|
2974 |
> |
2003-03-26 09:55 mmeineke |
2975 |
> |
|
2976 |
> |
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
2977 |
> |
THermo.cpp |
2978 |
> |
|
2979 |
> |
2003-03-25 17:54 chuckv |
2980 |
> |
|
2981 |
> |
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
2982 |
> |
of potential energy and temperature. |
2983 |
> |
|
2984 |
> |
2003-03-25 09:29 mmeineke |
2985 |
> |
|
2986 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2987 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2988 |
|
|
2989 |
|
2003-03-25 09:29 mmeineke |