1 |
+ |
2004-03-02 15:32 tim |
2 |
+ |
|
3 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
4 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
5 |
+ |
support large file |
6 |
+ |
|
7 |
+ |
2004-03-01 16:17 tim |
8 |
+ |
|
9 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
10 |
+ |
|
11 |
+ |
2004-03-01 15:01 tim |
12 |
+ |
|
13 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
14 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
15 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
16 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
17 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
18 |
+ |
program which can be used to replace atom type for zconstraint into |
19 |
+ |
OOPSE |
20 |
+ |
|
21 |
+ |
2004-02-24 11:36 tim |
22 |
+ |
|
23 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
24 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
25 |
+ |
message] |
26 |
+ |
|
27 |
+ |
2004-02-24 10:49 tim |
28 |
+ |
|
29 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
30 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
31 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
32 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
33 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
34 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
35 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
36 |
+ |
|
37 |
+ |
2004-02-24 10:44 tim |
38 |
+ |
|
39 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
40 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
41 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
42 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
43 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
44 |
+ |
compose to implement Minimizer both versions are working |
45 |
+ |
|
46 |
+ |
2004-02-17 14:23 tim |
47 |
+ |
|
48 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
49 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
50 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
51 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
52 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
53 |
+ |
to remove the constraint force along bond direction |
54 |
+ |
|
55 |
+ |
2004-02-10 16:33 tim |
56 |
+ |
|
57 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
58 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
59 |
+ |
single version of energy minimization is working. |
60 |
+ |
|
61 |
+ |
2004-02-09 15:38 mmeineke |
62 |
+ |
|
63 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
64 |
+ |
the massive memory overusage by OOPSE |
65 |
+ |
|
66 |
+ |
2004-02-09 09:48 chrisfen |
67 |
+ |
|
68 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
69 |
+ |
hardwired LJ_rcut |
70 |
+ |
|
71 |
+ |
2004-02-06 19:14 tim |
72 |
+ |
|
73 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
74 |
+ |
message] |
75 |
+ |
|
76 |
+ |
2004-02-06 16:37 tim |
77 |
+ |
|
78 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
79 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
80 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
81 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
82 |
+ |
energy minimization for argon is working, need to add constraint |
83 |
+ |
|
84 |
+ |
2004-02-06 14:05 tim |
85 |
+ |
|
86 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
87 |
+ |
one more file into Makefile.in |
88 |
+ |
|
89 |
+ |
2004-02-06 13:58 tim |
90 |
+ |
|
91 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
92 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
93 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
94 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
95 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
96 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
97 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
98 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
99 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
100 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
101 |
+ |
some lines into global.cpp to make it work with energy minimization |
102 |
+ |
|
103 |
+ |
2004-02-04 17:26 tim |
104 |
+ |
|
105 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
106 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
107 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
108 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
109 |
+ |
Single version of conjugate gradient with golden search linesearch |
110 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
111 |
+ |
|
112 |
+ |
2004-02-03 17:54 tim |
113 |
+ |
|
114 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
115 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
116 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
117 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
118 |
+ |
|
119 |
+ |
2004-02-03 15:47 tim |
120 |
+ |
|
121 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
122 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
123 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
124 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
125 |
+ |
SteepestDescent.hpp: [no log message] |
126 |
+ |
|
127 |
+ |
2004-02-03 15:43 tim |
128 |
+ |
|
129 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
130 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
131 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
132 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
133 |
+ |
constraint class |
134 |
+ |
|
135 |
+ |
2004-02-03 12:10 tim |
136 |
+ |
|
137 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
138 |
+ |
|
139 |
+ |
2004-02-03 10:21 tim |
140 |
+ |
|
141 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
142 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
143 |
+ |
|
144 |
+ |
2004-02-02 15:29 tim |
145 |
+ |
|
146 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
147 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
148 |
+ |
Adding GoldenSection and Brent LineSearch Method |
149 |
+ |
|
150 |
+ |
2004-01-30 16:47 tim |
151 |
+ |
|
152 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
153 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
154 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
155 |
+ |
MinimizerBase instead of a functor to do line seach |
156 |
+ |
|
157 |
+ |
2004-01-30 10:00 chrisfen |
158 |
+ |
|
159 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
160 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
161 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
162 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
163 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
164 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
165 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
166 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
167 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
168 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
169 |
+ |
This will be removed on the next commit... |
170 |
+ |
|
171 |
+ |
2004-01-29 18:00 gezelter |
172 |
+ |
|
173 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
174 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
175 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
176 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
177 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
178 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
179 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
180 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
181 |
+ |
member list fixes for rigid bodies |
182 |
+ |
|
183 |
+ |
2004-01-29 16:44 tim |
184 |
+ |
|
185 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
186 |
+ |
MinimizerParameterSet class. |
187 |
+ |
|
188 |
+ |
2004-01-28 17:44 tim |
189 |
+ |
|
190 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
191 |
+ |
NLModel0 and NLModel1 |
192 |
+ |
|
193 |
+ |
2004-01-28 15:40 tim |
194 |
+ |
|
195 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
196 |
+ |
of NLModel |
197 |
+ |
|
198 |
+ |
2004-01-27 15:34 gezelter |
199 |
+ |
|
200 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
201 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
202 |
+ |
|
203 |
+ |
2004-01-27 15:34 gezelter |
204 |
+ |
|
205 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
206 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
207 |
+ |
stuff |
208 |
+ |
|
209 |
+ |
2004-01-27 14:39 gezelter |
210 |
+ |
|
211 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
212 |
+ |
|
213 |
+ |
2004-01-27 14:39 gezelter |
214 |
+ |
|
215 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
216 |
+ |
|
217 |
+ |
2004-01-27 14:38 gezelter |
218 |
+ |
|
219 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
220 |
+ |
|
221 |
+ |
2004-01-27 14:38 gezelter |
222 |
+ |
|
223 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
224 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
225 |
+ |
morning |
226 |
+ |
|
227 |
+ |
2004-01-27 14:37 gezelter |
228 |
+ |
|
229 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
230 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
231 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
232 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
233 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
234 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
235 |
+ |
do new rigidBody scheme |
236 |
+ |
|
237 |
+ |
2004-01-27 14:15 tim |
238 |
+ |
|
239 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
240 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
241 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
242 |
+ |
constraint for Nonlinear Optimization Model |
243 |
+ |
|
244 |
+ |
2004-01-26 17:01 gezelter |
245 |
+ |
|
246 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
247 |
+ |
Euler angles for orientation instead of unit vectors required |
248 |
+ |
changes in MoLocator |
249 |
+ |
|
250 |
+ |
2004-01-26 16:53 gezelter |
251 |
+ |
|
252 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
253 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
254 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
255 |
+ |
euler angles |
256 |
+ |
|
257 |
+ |
2004-01-26 16:52 gezelter |
258 |
+ |
|
259 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
260 |
+ |
|
261 |
+ |
2004-01-26 16:45 gezelter |
262 |
+ |
|
263 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
264 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
265 |
+ |
the ability to set orientation using a unit vector |
266 |
+ |
|
267 |
+ |
2004-01-26 16:26 gezelter |
268 |
+ |
|
269 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
270 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
271 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
272 |
+ |
ability to set orientation using a unit vector |
273 |
+ |
|
274 |
+ |
2004-01-26 13:52 gezelter |
275 |
+ |
|
276 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
277 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
278 |
+ |
|
279 |
+ |
2004-01-22 12:34 chrisfen |
280 |
+ |
|
281 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
282 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
283 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
284 |
+ |
|
285 |
+ |
2004-01-21 17:16 tim |
286 |
+ |
|
287 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
288 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
289 |
+ |
|
290 |
+ |
2004-01-20 15:34 tim |
291 |
+ |
|
292 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
293 |
+ |
|
294 |
+ |
2004-01-20 15:32 tim |
295 |
+ |
|
296 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
297 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
298 |
+ |
|
299 |
+ |
2004-01-19 16:17 gezelter |
300 |
+ |
|
301 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
302 |
+ |
more user-friendly |
303 |
+ |
|
304 |
+ |
2004-01-19 13:51 chrisfen |
305 |
+ |
|
306 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
307 |
+ |
|
308 |
+ |
2004-01-19 13:36 tim |
309 |
+ |
|
310 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
311 |
+ |
time, status time, thermal time and reset time are not divisible by |
312 |
+ |
dt |
313 |
+ |
|
314 |
+ |
2004-01-19 11:10 gezelter |
315 |
+ |
|
316 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
317 |
+ |
won't complain |
318 |
+ |
|
319 |
+ |
2004-01-19 11:10 gezelter |
320 |
+ |
|
321 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
322 |
+ |
|
323 |
+ |
2004-01-19 11:09 gezelter |
324 |
+ |
|
325 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
326 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
327 |
+ |
in mpiSimulation.cpp |
328 |
+ |
|
329 |
+ |
2004-01-19 11:08 gezelter |
330 |
+ |
|
331 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
332 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
333 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
334 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
335 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
336 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
337 |
+ |
|
338 |
+ |
2004-01-16 16:55 tim |
339 |
+ |
|
340 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
341 |
+ |
eor file |
342 |
+ |
|
343 |
+ |
2004-01-16 16:51 mmeineke |
344 |
+ |
|
345 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
346 |
+ |
write eor files |
347 |
+ |
|
348 |
+ |
2004-01-16 10:01 mmeineke |
349 |
+ |
|
350 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
351 |
+ |
initialization of the AtomStruct |
352 |
+ |
|
353 |
+ |
2004-01-15 16:57 chuckv |
354 |
+ |
|
355 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
356 |
+ |
|
357 |
+ |
2004-01-15 10:51 gezelter |
358 |
+ |
|
359 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
360 |
+ |
|
361 |
+ |
2004-01-15 09:22 gezelter |
362 |
+ |
|
363 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
364 |
+ |
|
365 |
+ |
2004-01-14 23:33 gezelter |
366 |
+ |
|
367 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
368 |
+ |
|
369 |
+ |
2004-01-14 20:14 gezelter |
370 |
+ |
|
371 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
372 |
+ |
notifyCutoffs.F90: More work for adding charges |
373 |
+ |
|
374 |
+ |
2004-01-14 17:41 gezelter |
375 |
+ |
|
376 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
377 |
+ |
src/Makefile.in: autoconf fixes |
378 |
+ |
|
379 |
+ |
2004-01-14 11:28 mmeineke |
380 |
+ |
|
381 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
382 |
+ |
|
383 |
+ |
2004-01-14 10:48 gezelter |
384 |
+ |
|
385 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
386 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
387 |
+ |
changes for icc8 |
388 |
+ |
|
389 |
+ |
2004-01-13 18:01 gezelter |
390 |
+ |
|
391 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
392 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
393 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
394 |
+ |
Changes for adding direct charge-charge interactions (with |
395 |
+ |
switching function) |
396 |
+ |
|
397 |
+ |
2004-01-13 17:34 gezelter |
398 |
+ |
|
399 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
400 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
401 |
+ |
direct charge-charge interactions |
402 |
+ |
|
403 |
+ |
2004-01-13 17:11 tim |
404 |
+ |
|
405 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
406 |
+ |
|
407 |
+ |
2004-01-13 16:22 tim |
408 |
+ |
|
409 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
410 |
+ |
|
411 |
+ |
2004-01-13 15:35 tim |
412 |
+ |
|
413 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
414 |
+ |
eor file whenever it is used instead of rewinding it |
415 |
+ |
|
416 |
+ |
2004-01-13 15:04 tim |
417 |
+ |
|
418 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
419 |
+ |
of writeFrame |
420 |
+ |
|
421 |
+ |
2004-01-13 10:46 tim |
422 |
+ |
|
423 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
424 |
+ |
Merge the code of writeFinal and writeDump; |
425 |
+ |
Adding sortingIndex into DumpWriter; |
426 |
+ |
Fix a bug of writing last frame twice in integrator |
427 |
+ |
|
428 |
+ |
2004-01-12 17:54 tim |
429 |
+ |
|
430 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
431 |
+ |
a bug in copying string |
432 |
+ |
|
433 |
+ |
2004-01-12 15:37 tim |
434 |
+ |
|
435 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
436 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
437 |
+ |
master nodes |
438 |
+ |
|
439 |
+ |
2004-01-10 04:46 tim |
440 |
+ |
|
441 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
442 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
443 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
444 |
+ |
|
445 |
+ |
2004-01-09 21:15 tim |
446 |
+ |
|
447 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
448 |
+ |
|
449 |
+ |
2004-01-09 15:29 gezelter |
450 |
+ |
|
451 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
452 |
+ |
|
453 |
+ |
2004-01-08 17:25 chuckv |
454 |
+ |
|
455 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
456 |
+ |
|
457 |
+ |
2004-01-08 13:59 gezelter |
458 |
+ |
|
459 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
460 |
+ |
case |
461 |
+ |
|
462 |
+ |
2004-01-08 13:13 mmeineke |
463 |
+ |
|
464 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
465 |
+ |
state bug. |
466 |
+ |
|
467 |
+ |
2004-01-08 13:05 gezelter |
468 |
+ |
|
469 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
470 |
+ |
|
471 |
+ |
2004-01-08 12:57 mmeineke |
472 |
+ |
|
473 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
474 |
+ |
exstended state bug |
475 |
+ |
|
476 |
+ |
2004-01-08 12:40 gezelter |
477 |
+ |
|
478 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
479 |
+ |
|
480 |
+ |
2004-01-08 10:44 mmeineke |
481 |
+ |
|
482 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
483 |
+ |
XS state info flag |
484 |
+ |
|
485 |
+ |
2004-01-07 14:26 tim |
486 |
+ |
|
487 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
488 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
489 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
490 |
+ |
InitializeFromFile.cpp |
491 |
+ |
|
492 |
+ |
2004-01-06 14:49 chuckv |
493 |
+ |
|
494 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
495 |
+ |
performance fixes in the dipole dipole and reaction field code |
496 |
+ |
|
497 |
+ |
2004-01-06 13:54 chuckv |
498 |
+ |
|
499 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
500 |
+ |
little more sane |
501 |
+ |
|
502 |
+ |
2004-01-05 17:49 chuckv |
503 |
+ |
|
504 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
505 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
506 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
507 |
+ |
performance by reducing spurious function calls |
508 |
+ |
|
509 |
+ |
2004-01-05 17:18 chuckv |
510 |
+ |
|
511 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
512 |
+ |
|
513 |
+ |
2004-01-05 17:18 chuckv |
514 |
+ |
|
515 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
516 |
+ |
|
517 |
+ |
2004-01-05 17:12 chuckv |
518 |
+ |
|
519 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
520 |
+ |
|
521 |
+ |
2004-01-05 16:00 chuckv |
522 |
+ |
|
523 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
524 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
525 |
+ |
lookup |
526 |
+ |
|
527 |
|
2003-12-29 14:56 chuckv |
528 |
|
|
529 |
|
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
2704 |
|
|
2705 |
|
2003-03-25 09:29 mmeineke |
2706 |
|
|
2707 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2707 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2708 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2709 |
|
|
2710 |
|
2003-03-25 09:29 mmeineke |
2858 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2859 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2860 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2861 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
2862 |
< |
Tree |
2861 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
2862 |
> |
revision |
2863 |
|
|
2864 |
|
2003-03-21 12:42 mmeineke |
2865 |
|
|
2916 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2917 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2918 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2919 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
2920 |
< |
revision |
2919 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
2920 |
> |
Tree |
2921 |
|
|