1 |
+ |
2004-05-11 11:00 gezelter |
2 |
+ |
|
3 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
4 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
5 |
+ |
use the simplified cutoff stuff in the BASS library |
6 |
+ |
|
7 |
+ |
2004-05-10 23:21 gezelter |
8 |
+ |
|
9 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
10 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
11 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
12 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
13 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
14 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
15 |
+ |
Also restructured the plethora of cutoff radii into one |
16 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
17 |
+ |
useMolecularCutoffs keyword |
18 |
+ |
|
19 |
+ |
2004-05-10 15:28 tim |
20 |
+ |
|
21 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
22 |
+ |
DumpWriter |
23 |
+ |
|
24 |
+ |
2004-05-07 16:36 gezelter |
25 |
+ |
|
26 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
27 |
+ |
for fortran group-based switching function |
28 |
+ |
|
29 |
+ |
2004-05-07 16:35 gezelter |
30 |
+ |
|
31 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
32 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
33 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
34 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
35 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
36 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
37 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
38 |
+ |
work |
39 |
+ |
|
40 |
+ |
2004-05-01 13:52 tim |
41 |
+ |
|
42 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
43 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
44 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
45 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
46 |
+ |
libmdtools/fortranWrapDefines.hpp, |
47 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
48 |
+ |
|
49 |
+ |
2004-04-29 11:03 tim |
50 |
+ |
|
51 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
52 |
+ |
calc_charge_charge when using molecular cutoff |
53 |
+ |
|
54 |
+ |
2004-04-28 21:11 tim |
55 |
+ |
|
56 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
57 |
+ |
unmatched c/fortran interface |
58 |
+ |
|
59 |
+ |
2004-04-28 18:09 tim |
60 |
+ |
|
61 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
62 |
+ |
keep the previous position of cantilever in SMD |
63 |
+ |
|
64 |
+ |
2004-04-28 17:34 tim |
65 |
+ |
|
66 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
67 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
68 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
69 |
+ |
fix two bugs in ZconsVisitor |
70 |
+ |
|
71 |
+ |
2004-04-28 17:06 gezelter |
72 |
+ |
|
73 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
74 |
+ |
Adding molecular cutoffs |
75 |
+ |
|
76 |
+ |
2004-04-28 16:39 gezelter |
77 |
+ |
|
78 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
79 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
80 |
+ |
molecular cutoffs |
81 |
+ |
|
82 |
+ |
2004-04-28 16:39 gezelter |
83 |
+ |
|
84 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
85 |
+ |
Globals |
86 |
+ |
|
87 |
+ |
2004-04-27 11:26 tim |
88 |
+ |
|
89 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
90 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
91 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
92 |
+ |
molecule and massRation into atom class |
93 |
+ |
|
94 |
+ |
2004-04-26 16:16 mmeineke |
95 |
+ |
|
96 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
97 |
+ |
time and system init state. |
98 |
+ |
|
99 |
+ |
2004-04-26 09:29 gezelter |
100 |
+ |
|
101 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
102 |
+ |
calc_charge_charge.F90 |
103 |
+ |
|
104 |
+ |
2004-04-23 23:31 tim |
105 |
+ |
|
106 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
107 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
108 |
+ |
reaction field correction to charge-charge interaction |
109 |
+ |
|
110 |
+ |
2004-04-22 16:33 tim |
111 |
+ |
|
112 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
113 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
114 |
+ |
calculation of pressure tensor |
115 |
+ |
|
116 |
+ |
2004-04-22 09:55 tim |
117 |
+ |
|
118 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
119 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
120 |
+ |
|
121 |
+ |
2004-04-21 22:29 tim |
122 |
+ |
|
123 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
124 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
125 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
126 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
127 |
+ |
DumpWriter |
128 |
+ |
|
129 |
+ |
2004-04-21 00:32 tim |
130 |
+ |
|
131 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
132 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
133 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
134 |
+ |
useless files |
135 |
+ |
|
136 |
+ |
2004-04-20 11:56 tim |
137 |
+ |
|
138 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
139 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
140 |
+ |
velocitize at thermo |
141 |
+ |
|
142 |
+ |
2004-04-20 00:39 tim |
143 |
+ |
|
144 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
145 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
146 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
147 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
148 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
149 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
150 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
151 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
152 |
+ |
|
153 |
+ |
2004-04-19 17:13 gezelter |
154 |
+ |
|
155 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
156 |
+ |
Thermo.cpp: Fixed a charge bug |
157 |
+ |
|
158 |
+ |
2004-04-19 15:54 tim |
159 |
+ |
|
160 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
161 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
162 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
163 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
164 |
+ |
|
165 |
+ |
2004-04-19 12:44 tim |
166 |
+ |
|
167 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
168 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
169 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
170 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
171 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
172 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
173 |
+ |
counted |
174 |
+ |
|
175 |
+ |
2004-04-18 22:52 tim |
176 |
+ |
|
177 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
178 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
179 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
180 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
181 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
182 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
183 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
184 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
185 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
186 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
187 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
188 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
189 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
190 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
191 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
192 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
193 |
+ |
implement of quickLate using visitor and composite pattern |
194 |
+ |
|
195 |
+ |
2004-04-15 17:15 tim |
196 |
+ |
|
197 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
198 |
+ |
exclude list |
199 |
+ |
|
200 |
+ |
2004-04-15 11:18 tim |
201 |
+ |
|
202 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
203 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
204 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
205 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
206 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
207 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
208 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
209 |
+ |
whole bunch of bugs :-) |
210 |
+ |
|
211 |
+ |
2004-04-14 12:20 chrisfen |
212 |
+ |
|
213 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
214 |
+ |
|
215 |
+ |
2004-04-14 11:32 gezelter |
216 |
+ |
|
217 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
218 |
+ |
|
219 |
+ |
2004-04-14 10:37 tim |
220 |
+ |
|
221 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
222 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
223 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
224 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
225 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
226 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
227 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
228 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
229 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
230 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
231 |
+ |
Change DumpWriter and InitFromFile |
232 |
+ |
|
233 |
+ |
2004-04-13 11:26 gezelter |
234 |
+ |
|
235 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
236 |
+ |
molecules can keep track of their own IntegrableObjects (and |
237 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
238 |
+ |
RigidBodies (which was done incorrectly before). |
239 |
+ |
|
240 |
+ |
2004-04-13 11:25 gezelter |
241 |
+ |
|
242 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
243 |
+ |
(will back out momentarily) |
244 |
+ |
|
245 |
+ |
2004-04-13 10:10 gezelter |
246 |
+ |
|
247 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
248 |
+ |
Those were old. |
249 |
+ |
|
250 |
+ |
2004-04-13 10:09 gezelter |
251 |
+ |
|
252 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
253 |
+ |
to add IntegrableObjects |
254 |
+ |
|
255 |
+ |
2004-04-12 16:02 gezelter |
256 |
+ |
|
257 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
258 |
+ |
|
259 |
+ |
2004-04-12 15:32 gezelter |
260 |
+ |
|
261 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
262 |
+ |
test run |
263 |
+ |
|
264 |
+ |
2004-04-12 15:32 gezelter |
265 |
+ |
|
266 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
267 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
268 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
269 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
270 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
271 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
272 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
273 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
274 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
275 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
276 |
+ |
(Somewhat extensive) |
277 |
+ |
|
278 |
+ |
2004-04-12 15:31 gezelter |
279 |
+ |
|
280 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
281 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
282 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
283 |
+ |
Changes for RigidBody dynamics |
284 |
+ |
|
285 |
+ |
2004-03-17 09:22 tim |
286 |
+ |
|
287 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
288 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
289 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
290 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
291 |
+ |
does not sound a good choice, next commit will seperate SMD and |
292 |
+ |
ZConstraint |
293 |
+ |
|
294 |
+ |
2004-03-16 14:22 tim |
295 |
+ |
|
296 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
297 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
298 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
299 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
300 |
+ |
now can support sequential moving. Refactorying is needed to |
301 |
+ |
support SMD in ZConstraint |
302 |
+ |
|
303 |
+ |
2004-03-02 15:32 tim |
304 |
+ |
|
305 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
306 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
307 |
+ |
support large file |
308 |
+ |
|
309 |
+ |
2004-03-01 16:17 tim |
310 |
+ |
|
311 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
312 |
+ |
|
313 |
+ |
2004-03-01 15:01 tim |
314 |
+ |
|
315 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
316 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
317 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
318 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
319 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
320 |
+ |
program which can be used to replace atom type for zconstraint into |
321 |
+ |
OOPSE |
322 |
+ |
|
323 |
+ |
2004-02-24 11:36 tim |
324 |
+ |
|
325 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
326 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
327 |
+ |
message] |
328 |
+ |
|
329 |
+ |
2004-02-24 10:49 tim |
330 |
+ |
|
331 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
332 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
333 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
334 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
335 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
336 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
337 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
338 |
+ |
|
339 |
+ |
2004-02-24 10:44 tim |
340 |
+ |
|
341 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
342 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
343 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
344 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
345 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
346 |
+ |
compose to implement Minimizer both versions are working |
347 |
+ |
|
348 |
+ |
2004-02-17 14:23 tim |
349 |
+ |
|
350 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
351 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
352 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
353 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
354 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
355 |
+ |
to remove the constraint force along bond direction |
356 |
+ |
|
357 |
+ |
2004-02-10 16:33 tim |
358 |
+ |
|
359 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
360 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
361 |
+ |
single version of energy minimization is working. |
362 |
+ |
|
363 |
+ |
2004-02-09 15:38 mmeineke |
364 |
+ |
|
365 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
366 |
+ |
the massive memory overusage by OOPSE |
367 |
+ |
|
368 |
+ |
2004-02-09 09:48 chrisfen |
369 |
+ |
|
370 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
371 |
+ |
hardwired LJ_rcut |
372 |
+ |
|
373 |
+ |
2004-02-06 19:14 tim |
374 |
+ |
|
375 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
376 |
+ |
message] |
377 |
+ |
|
378 |
+ |
2004-02-06 16:37 tim |
379 |
+ |
|
380 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
381 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
382 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
383 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
384 |
+ |
energy minimization for argon is working, need to add constraint |
385 |
+ |
|
386 |
+ |
2004-02-06 14:05 tim |
387 |
+ |
|
388 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
389 |
+ |
one more file into Makefile.in |
390 |
+ |
|
391 |
+ |
2004-02-06 13:58 tim |
392 |
+ |
|
393 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
394 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
395 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
396 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
397 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
398 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
399 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
400 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
401 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
402 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
403 |
+ |
some lines into global.cpp to make it work with energy minimization |
404 |
+ |
|
405 |
+ |
2004-02-04 17:26 tim |
406 |
+ |
|
407 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
408 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
409 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
410 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
411 |
+ |
Single version of conjugate gradient with golden search linesearch |
412 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
413 |
+ |
|
414 |
+ |
2004-02-03 17:54 tim |
415 |
+ |
|
416 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
417 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
418 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
419 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
420 |
+ |
|
421 |
+ |
2004-02-03 15:47 tim |
422 |
+ |
|
423 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
424 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
425 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
426 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
427 |
+ |
SteepestDescent.hpp: [no log message] |
428 |
+ |
|
429 |
+ |
2004-02-03 15:43 tim |
430 |
+ |
|
431 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
432 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
433 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
434 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
435 |
+ |
constraint class |
436 |
+ |
|
437 |
+ |
2004-02-03 12:10 tim |
438 |
+ |
|
439 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
440 |
+ |
|
441 |
+ |
2004-02-03 10:21 tim |
442 |
+ |
|
443 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
444 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
445 |
+ |
|
446 |
+ |
2004-02-02 15:29 tim |
447 |
+ |
|
448 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
449 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
450 |
+ |
Adding GoldenSection and Brent LineSearch Method |
451 |
+ |
|
452 |
+ |
2004-01-30 16:47 tim |
453 |
+ |
|
454 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
455 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
456 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
457 |
+ |
MinimizerBase instead of a functor to do line seach |
458 |
+ |
|
459 |
+ |
2004-01-30 10:00 chrisfen |
460 |
+ |
|
461 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
462 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
463 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
464 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
465 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
466 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
467 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
468 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
469 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
470 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
471 |
+ |
This will be removed on the next commit... |
472 |
+ |
|
473 |
+ |
2004-01-29 18:00 gezelter |
474 |
+ |
|
475 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
476 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
477 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
478 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
479 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
480 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
481 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
482 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
483 |
+ |
member list fixes for rigid bodies |
484 |
+ |
|
485 |
+ |
2004-01-29 16:44 tim |
486 |
+ |
|
487 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
488 |
+ |
MinimizerParameterSet class. |
489 |
+ |
|
490 |
+ |
2004-01-28 17:44 tim |
491 |
+ |
|
492 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
493 |
+ |
NLModel0 and NLModel1 |
494 |
+ |
|
495 |
+ |
2004-01-28 15:40 tim |
496 |
+ |
|
497 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
498 |
+ |
of NLModel |
499 |
+ |
|
500 |
+ |
2004-01-27 15:34 gezelter |
501 |
+ |
|
502 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
503 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
504 |
+ |
|
505 |
+ |
2004-01-27 15:34 gezelter |
506 |
+ |
|
507 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
508 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
509 |
+ |
stuff |
510 |
+ |
|
511 |
+ |
2004-01-27 14:39 gezelter |
512 |
+ |
|
513 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
514 |
+ |
|
515 |
+ |
2004-01-27 14:39 gezelter |
516 |
+ |
|
517 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
518 |
+ |
|
519 |
+ |
2004-01-27 14:38 gezelter |
520 |
+ |
|
521 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
522 |
+ |
|
523 |
+ |
2004-01-27 14:38 gezelter |
524 |
+ |
|
525 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
526 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
527 |
+ |
morning |
528 |
+ |
|
529 |
+ |
2004-01-27 14:37 gezelter |
530 |
+ |
|
531 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
532 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
533 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
534 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
535 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
536 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
537 |
+ |
do new rigidBody scheme |
538 |
+ |
|
539 |
+ |
2004-01-27 14:15 tim |
540 |
+ |
|
541 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
542 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
543 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
544 |
+ |
constraint for Nonlinear Optimization Model |
545 |
+ |
|
546 |
+ |
2004-01-26 17:01 gezelter |
547 |
+ |
|
548 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
549 |
+ |
Euler angles for orientation instead of unit vectors required |
550 |
+ |
changes in MoLocator |
551 |
+ |
|
552 |
+ |
2004-01-26 16:53 gezelter |
553 |
+ |
|
554 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
555 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
556 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
557 |
+ |
euler angles |
558 |
+ |
|
559 |
+ |
2004-01-26 16:52 gezelter |
560 |
+ |
|
561 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
562 |
+ |
|
563 |
+ |
2004-01-26 16:45 gezelter |
564 |
+ |
|
565 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
566 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
567 |
+ |
the ability to set orientation using a unit vector |
568 |
+ |
|
569 |
+ |
2004-01-26 16:26 gezelter |
570 |
+ |
|
571 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
572 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
573 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
574 |
+ |
ability to set orientation using a unit vector |
575 |
+ |
|
576 |
+ |
2004-01-26 13:52 gezelter |
577 |
+ |
|
578 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
579 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
580 |
+ |
|
581 |
+ |
2004-01-22 12:34 chrisfen |
582 |
+ |
|
583 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
584 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
585 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
586 |
+ |
|
587 |
+ |
2004-01-21 17:16 tim |
588 |
+ |
|
589 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
590 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
591 |
+ |
|
592 |
+ |
2004-01-20 15:34 tim |
593 |
+ |
|
594 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
595 |
+ |
|
596 |
+ |
2004-01-20 15:32 tim |
597 |
+ |
|
598 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
599 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
600 |
+ |
|
601 |
+ |
2004-01-19 16:17 gezelter |
602 |
+ |
|
603 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
604 |
+ |
more user-friendly |
605 |
+ |
|
606 |
+ |
2004-01-19 13:51 chrisfen |
607 |
+ |
|
608 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
609 |
+ |
|
610 |
+ |
2004-01-19 13:36 tim |
611 |
+ |
|
612 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
613 |
+ |
time, status time, thermal time and reset time are not divisible by |
614 |
+ |
dt |
615 |
+ |
|
616 |
+ |
2004-01-19 11:10 gezelter |
617 |
+ |
|
618 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
619 |
+ |
won't complain |
620 |
+ |
|
621 |
+ |
2004-01-19 11:10 gezelter |
622 |
+ |
|
623 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
624 |
+ |
|
625 |
+ |
2004-01-19 11:09 gezelter |
626 |
+ |
|
627 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
628 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
629 |
+ |
in mpiSimulation.cpp |
630 |
+ |
|
631 |
+ |
2004-01-19 11:08 gezelter |
632 |
+ |
|
633 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
634 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
635 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
636 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
637 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
638 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
639 |
+ |
|
640 |
+ |
2004-01-16 16:55 tim |
641 |
+ |
|
642 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
643 |
+ |
eor file |
644 |
+ |
|
645 |
+ |
2004-01-16 16:51 mmeineke |
646 |
+ |
|
647 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
648 |
+ |
write eor files |
649 |
+ |
|
650 |
+ |
2004-01-16 10:01 mmeineke |
651 |
+ |
|
652 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
653 |
+ |
initialization of the AtomStruct |
654 |
+ |
|
655 |
+ |
2004-01-15 16:57 chuckv |
656 |
+ |
|
657 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
658 |
+ |
|
659 |
+ |
2004-01-15 10:51 gezelter |
660 |
+ |
|
661 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
662 |
+ |
|
663 |
+ |
2004-01-15 09:22 gezelter |
664 |
+ |
|
665 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
666 |
+ |
|
667 |
+ |
2004-01-14 23:33 gezelter |
668 |
+ |
|
669 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
670 |
+ |
|
671 |
+ |
2004-01-14 20:14 gezelter |
672 |
+ |
|
673 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
674 |
+ |
notifyCutoffs.F90: More work for adding charges |
675 |
+ |
|
676 |
+ |
2004-01-14 17:41 gezelter |
677 |
+ |
|
678 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
679 |
+ |
src/Makefile.in: autoconf fixes |
680 |
+ |
|
681 |
+ |
2004-01-14 11:28 mmeineke |
682 |
+ |
|
683 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
684 |
+ |
|
685 |
+ |
2004-01-14 10:48 gezelter |
686 |
+ |
|
687 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
688 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
689 |
+ |
changes for icc8 |
690 |
+ |
|
691 |
+ |
2004-01-13 18:01 gezelter |
692 |
+ |
|
693 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
694 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
695 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
696 |
+ |
Changes for adding direct charge-charge interactions (with |
697 |
+ |
switching function) |
698 |
+ |
|
699 |
+ |
2004-01-13 17:34 gezelter |
700 |
+ |
|
701 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
702 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
703 |
+ |
direct charge-charge interactions |
704 |
+ |
|
705 |
+ |
2004-01-13 17:11 tim |
706 |
+ |
|
707 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
708 |
+ |
|
709 |
+ |
2004-01-13 16:22 tim |
710 |
+ |
|
711 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
712 |
+ |
|
713 |
+ |
2004-01-13 15:35 tim |
714 |
+ |
|
715 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
716 |
+ |
eor file whenever it is used instead of rewinding it |
717 |
+ |
|
718 |
+ |
2004-01-13 15:04 tim |
719 |
+ |
|
720 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
721 |
+ |
of writeFrame |
722 |
+ |
|
723 |
+ |
2004-01-13 10:46 tim |
724 |
+ |
|
725 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
726 |
+ |
Merge the code of writeFinal and writeDump; |
727 |
+ |
Adding sortingIndex into DumpWriter; |
728 |
+ |
Fix a bug of writing last frame twice in integrator |
729 |
+ |
|
730 |
+ |
2004-01-12 17:54 tim |
731 |
+ |
|
732 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
733 |
+ |
a bug in copying string |
734 |
+ |
|
735 |
+ |
2004-01-12 15:37 tim |
736 |
+ |
|
737 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
738 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
739 |
+ |
master nodes |
740 |
+ |
|
741 |
+ |
2004-01-10 04:46 tim |
742 |
+ |
|
743 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
744 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
745 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
746 |
+ |
|
747 |
+ |
2004-01-09 21:15 tim |
748 |
+ |
|
749 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
750 |
+ |
|
751 |
+ |
2004-01-09 15:29 gezelter |
752 |
+ |
|
753 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
754 |
+ |
|
755 |
+ |
2004-01-08 17:25 chuckv |
756 |
+ |
|
757 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
758 |
+ |
|
759 |
+ |
2004-01-08 13:59 gezelter |
760 |
+ |
|
761 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
762 |
+ |
case |
763 |
+ |
|
764 |
+ |
2004-01-08 13:13 mmeineke |
765 |
+ |
|
766 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
767 |
+ |
state bug. |
768 |
+ |
|
769 |
+ |
2004-01-08 13:05 gezelter |
770 |
+ |
|
771 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
772 |
+ |
|
773 |
+ |
2004-01-08 12:57 mmeineke |
774 |
+ |
|
775 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
776 |
+ |
exstended state bug |
777 |
+ |
|
778 |
+ |
2004-01-08 12:40 gezelter |
779 |
+ |
|
780 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
781 |
+ |
|
782 |
+ |
2004-01-08 10:44 mmeineke |
783 |
+ |
|
784 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
785 |
+ |
XS state info flag |
786 |
+ |
|
787 |
+ |
2004-01-07 14:26 tim |
788 |
+ |
|
789 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
790 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
791 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
792 |
+ |
InitializeFromFile.cpp |
793 |
+ |
|
794 |
+ |
2004-01-06 14:49 chuckv |
795 |
+ |
|
796 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
797 |
+ |
performance fixes in the dipole dipole and reaction field code |
798 |
+ |
|
799 |
+ |
2004-01-06 13:54 chuckv |
800 |
+ |
|
801 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
802 |
+ |
little more sane |
803 |
+ |
|
804 |
+ |
2004-01-05 17:49 chuckv |
805 |
+ |
|
806 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
807 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
808 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
809 |
+ |
performance by reducing spurious function calls |
810 |
+ |
|
811 |
+ |
2004-01-05 17:18 chuckv |
812 |
+ |
|
813 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
814 |
+ |
|
815 |
+ |
2004-01-05 17:18 chuckv |
816 |
+ |
|
817 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
818 |
+ |
|
819 |
+ |
2004-01-05 17:12 chuckv |
820 |
+ |
|
821 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
822 |
+ |
|
823 |
+ |
2004-01-05 16:00 chuckv |
824 |
+ |
|
825 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
826 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
827 |
+ |
lookup |
828 |
+ |
|
829 |
+ |
2003-12-29 14:56 chuckv |
830 |
+ |
|
831 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
832 |
+ |
third-party directory for code not written by us. Also added |
833 |
+ |
Mersenne Twister random number generator code. This will eventually |
834 |
+ |
replace sprng as the random number generator used by OOPSE. |
835 |
+ |
|
836 |
+ |
2003-12-22 16:26 chuckv |
837 |
+ |
|
838 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
839 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
840 |
+ |
Fixes to profile code. |
841 |
+ |
|
842 |
+ |
2003-12-19 15:36 mmeineke |
843 |
+ |
|
844 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
845 |
+ |
timing.F90, timing.f90: More profiling fixes. |
846 |
+ |
|
847 |
+ |
2003-12-19 15:19 chuckv |
848 |
+ |
|
849 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
850 |
+ |
|
851 |
+ |
2003-12-19 15:17 chuckv |
852 |
+ |
|
853 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
854 |
+ |
|
855 |
+ |
2003-12-19 13:53 mmeineke |
856 |
+ |
|
857 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
858 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
859 |
+ |
the code |
860 |
+ |
|
861 |
+ |
2003-12-19 12:25 mmeineke |
862 |
+ |
|
863 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
864 |
+ |
some profiling routines |
865 |
+ |
|
866 |
+ |
2003-12-19 10:12 mmeineke |
867 |
+ |
|
868 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
869 |
+ |
and GofRomega |
870 |
+ |
|
871 |
+ |
additional work on randomBilayer |
872 |
+ |
|
873 |
+ |
2003-12-19 10:12 mmeineke |
874 |
+ |
|
875 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
876 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
877 |
+ |
GofRomega |
878 |
+ |
|
879 |
+ |
2003-12-18 16:47 mmeineke |
880 |
+ |
|
881 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
882 |
+ |
some profile functionality |
883 |
+ |
|
884 |
+ |
2003-12-18 15:46 chuckv |
885 |
+ |
|
886 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
887 |
+ |
Added functions for simple profiling in fortran. |
888 |
+ |
|
889 |
+ |
2003-12-17 15:13 chuckv |
890 |
+ |
|
891 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
892 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
893 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
894 |
+ |
zeros the array between scatters so half of the sum was being lost. |
895 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
896 |
+ |
nlocal. |
897 |
+ |
|
898 |
+ |
2003-12-16 15:49 mmeineke |
899 |
+ |
|
900 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
901 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
902 |
+ |
gofRomega. both need to be debugged and tested. |
903 |
+ |
|
904 |
+ |
2003-12-12 10:42 gezelter |
905 |
+ |
|
906 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
907 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
908 |
+ |
gradients (to do minimizations) |
909 |
+ |
|
910 |
+ |
2003-12-12 10:33 mmeineke |
911 |
+ |
|
912 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
913 |
+ |
header |
914 |
+ |
|
915 |
+ |
2003-12-10 11:52 mmeineke |
916 |
+ |
|
917 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
918 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
919 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
920 |
+ |
from bilayerSys to randomBilayer |
921 |
+ |
|
922 |
+ |
2003-11-25 10:44 mmeineke |
923 |
+ |
|
924 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
925 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
926 |
+ |
TB3 in DUFF.frc |
927 |
+ |
|
928 |
+ |
2003-11-21 15:09 mmeineke |
929 |
+ |
|
930 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
931 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
932 |
+ |
message in SimInfo. Added a more informative error message in |
933 |
+ |
InitializeFromFile |
934 |
+ |
|
935 |
+ |
2003-11-21 15:07 mmeineke |
936 |
+ |
|
937 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
938 |
+ |
ing in the GofR,CosTheta |
939 |
+ |
|
940 |
+ |
2003-11-21 14:31 chrisfen |
941 |
+ |
|
942 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
943 |
+ |
a bug in SimInfo ordering of radii |
944 |
+ |
|
945 |
+ |
2003-11-11 12:20 mmeineke |
946 |
+ |
|
947 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
948 |
+ |
a min function. |
949 |
+ |
|
950 |
+ |
2003-11-10 16:50 mmeineke |
951 |
+ |
|
952 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
953 |
+ |
reordered the rcut/ecr/boxSize initialization |
954 |
+ |
|
955 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
956 |
+ |
now exit when it runs into rcut or ecr. |
957 |
+ |
|
958 |
+ |
2003-11-07 16:46 chuckv |
959 |
+ |
|
960 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
961 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
962 |
+ |
use of mpich modules. We use mpif.h instead.: |
963 |
+ |
|
964 |
+ |
2003-11-07 12:09 mmeineke |
965 |
+ |
|
966 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
967 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
968 |
+ |
the atom loop in the NPT family of integrators. |
969 |
+ |
|
970 |
+ |
2003-11-06 17:01 mmeineke |
971 |
+ |
|
972 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
973 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
974 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
975 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
976 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
977 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
978 |
+ |
* useIntiTime => useInitialTime |
979 |
+ |
|
980 |
+ |
2003-11-06 14:24 mmeineke |
981 |
+ |
|
982 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
983 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
984 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
985 |
+ |
|
986 |
+ |
2003-11-06 14:11 mmeineke |
987 |
+ |
|
988 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
989 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
990 |
+ |
new-templateless branch to the main trunk. |
991 |
+ |
|
992 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
993 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
994 |
+ |
sudden deaths we saw. * some formating in the string when we |
995 |
+ |
write out the extended system state. * added NPT.cpp to the |
996 |
+ |
makefile.in |
997 |
+ |
|
998 |
+ |
2003-11-06 13:20 mmeineke |
999 |
+ |
|
1000 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
1001 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
1002 |
+ |
bug. The box was not switching between orthorhombic and |
1003 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
1004 |
+ |
the check.which should fix it. |
1005 |
+ |
|
1006 |
+ |
2003-11-05 14:16 mmeineke |
1007 |
+ |
|
1008 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
1009 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1010 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1011 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
1012 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1013 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
1014 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
1015 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
1016 |
+ |
some work on trying to find the compression bug |
1017 |
+ |
|
1018 |
+ |
2003-11-03 17:07 mmeineke |
1019 |
+ |
|
1020 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
1021 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
1022 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1023 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1024 |
+ |
most of standard template library from OOPSE. |
1025 |
+ |
|
1026 |
+ |
2003-10-31 16:06 mmeineke |
1027 |
+ |
|
1028 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1029 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1030 |
+ |
SimSetup.cpp: started work on template removal. |
1031 |
+ |
|
1032 |
+ |
2003-10-31 13:28 mmeineke |
1033 |
+ |
|
1034 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1035 |
+ |
added template stuff to the Maikefile template |
1036 |
+ |
|
1037 |
+ |
little changes to some printf format statements |
1038 |
+ |
|
1039 |
+ |
2003-10-31 13:28 mmeineke |
1040 |
+ |
|
1041 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
1042 |
+ |
template |
1043 |
+ |
|
1044 |
+ |
2003-10-30 13:59 gezelter |
1045 |
+ |
|
1046 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1047 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1048 |
+ |
rList problems |
1049 |
+ |
|
1050 |
+ |
2003-10-30 09:11 gezelter |
1051 |
+ |
|
1052 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1053 |
+ |
queried before q0 was allocated. |
1054 |
+ |
|
1055 |
+ |
2003-10-29 15:41 mmeineke |
1056 |
+ |
|
1057 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1058 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1059 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1060 |
+ |
in bass.l |
1061 |
+ |
|
1062 |
+ |
fixed a little bug in the first time step, regarding the setting of |
1063 |
+ |
ecr and est in fortran |
1064 |
+ |
|
1065 |
+ |
2003-10-29 15:40 mmeineke |
1066 |
+ |
|
1067 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1068 |
+ |
|
1069 |
+ |
2003-10-29 12:55 mmeineke |
1070 |
+ |
|
1071 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1072 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1073 |
+ |
rcut is setup, as well as additional debugging comments. |
1074 |
+ |
|
1075 |
+ |
2003-10-29 09:28 gezelter |
1076 |
+ |
|
1077 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1078 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1079 |
+ |
templates |
1080 |
+ |
|
1081 |
+ |
2003-10-28 22:16 gezelter |
1082 |
+ |
|
1083 |
+ |
* src/Makefile.in: Refixed broken makefile |
1084 |
+ |
|
1085 |
+ |
2003-10-28 22:06 gezelter |
1086 |
+ |
|
1087 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1088 |
+ |
fixes |
1089 |
+ |
|
1090 |
+ |
2003-10-28 19:19 tim |
1091 |
+ |
|
1092 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1093 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1094 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1095 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1096 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1097 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1098 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1099 |
+ |
file. |
1100 |
+ |
|
1101 |
+ |
2003-10-28 17:25 mmeineke |
1102 |
+ |
|
1103 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1104 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1105 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1106 |
+ |
how c calls fortran. All function pointers and fortran calls are |
1107 |
+ |
rigidly typecast now. |
1108 |
+ |
|
1109 |
+ |
2003-10-28 15:42 gezelter |
1110 |
+ |
|
1111 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1112 |
+ |
Portability fixes |
1113 |
+ |
|
1114 |
+ |
2003-10-28 15:09 gezelter |
1115 |
+ |
|
1116 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1117 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1118 |
+ |
src/Makefile.in: Compatibility fixes |
1119 |
+ |
|
1120 |
+ |
2003-10-28 12:08 mmeineke |
1121 |
+ |
|
1122 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1123 |
+ |
started work on template removal |
1124 |
+ |
|
1125 |
+ |
2003-10-28 12:04 gezelter |
1126 |
+ |
|
1127 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1128 |
+ |
trying to understand extern "C" stuff for pointers |
1129 |
+ |
|
1130 |
+ |
2003-10-28 11:20 gezelter |
1131 |
+ |
|
1132 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1133 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1134 |
+ |
|
1135 |
+ |
2003-10-28 11:03 gezelter |
1136 |
+ |
|
1137 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1138 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1139 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1140 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1141 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1142 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1143 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1144 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1145 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1146 |
+ |
more portable c header stuff Also, mod file fixes and portability |
1147 |
+ |
changes Some fortran changes will need to be reversed. |
1148 |
+ |
|
1149 |
+ |
2003-10-28 11:03 gezelter |
1150 |
+ |
|
1151 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1152 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1153 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1154 |
+ |
portable c header stuff Also, mod file fixes and portability |
1155 |
+ |
changes |
1156 |
+ |
|
1157 |
+ |
2003-10-28 11:02 gezelter |
1158 |
+ |
|
1159 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1160 |
+ |
stuff |
1161 |
+ |
|
1162 |
+ |
2003-10-27 18:00 gezelter |
1163 |
+ |
|
1164 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1165 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1166 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1167 |
+ |
|
1168 |
+ |
2003-10-27 17:08 mmeineke |
1169 |
+ |
|
1170 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1171 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1172 |
+ |
added routines for the sysbuilder to work with simSetup |
1173 |
+ |
|
1174 |
+ |
remved the QuickBass routines, and had all parsing go through |
1175 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
1176 |
+ |
|
1177 |
+ |
2003-10-27 17:07 mmeineke |
1178 |
+ |
|
1179 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1180 |
+ |
routines for the sysbuilder to work with simSetup |
1181 |
+ |
|
1182 |
+ |
2003-10-27 11:20 gezelter |
1183 |
+ |
|
1184 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1185 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1186 |
+ |
|
1187 |
+ |
2003-10-24 17:17 mmeineke |
1188 |
+ |
|
1189 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1190 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1191 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1192 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1193 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
1194 |
+ |
from the Makefile |
1195 |
+ |
|
1196 |
+ |
2003-10-24 12:36 gezelter |
1197 |
+ |
|
1198 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1199 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1200 |
+ |
builder |
1201 |
+ |
|
1202 |
+ |
2003-10-24 12:35 gezelter |
1203 |
+ |
|
1204 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1205 |
+ |
merge problem |
1206 |
+ |
|
1207 |
+ |
2003-10-23 14:57 mmeineke |
1208 |
+ |
|
1209 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
1210 |
+ |
init |
1211 |
+ |
|
1212 |
+ |
fixed an eam mpi parmeter setup bug |
1213 |
+ |
|
1214 |
+ |
added the init file to the makefile |
1215 |
+ |
|
1216 |
+ |
2003-10-23 14:57 mmeineke |
1217 |
+ |
|
1218 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1219 |
+ |
to the init |
1220 |
+ |
|
1221 |
+ |
fixed an eam mpi parmeter setup bug |
1222 |
+ |
|
1223 |
+ |
2003-10-23 14:57 mmeineke |
1224 |
+ |
|
1225 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
1226 |
+ |
|
1227 |
+ |
2003-10-22 16:17 mmeineke |
1228 |
+ |
|
1229 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1230 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1231 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1232 |
+ |
no box skew allowed. |
1233 |
+ |
|
1234 |
+ |
2003-10-21 14:33 mmeineke |
1235 |
+ |
|
1236 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1237 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1238 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1239 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
1240 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
1241 |
+ |
true; |
1242 |
+ |
|
1243 |
+ |
2003-10-17 16:19 mmeineke |
1244 |
+ |
|
1245 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1246 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1247 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1248 |
+ |
to the build list for both configure and configure.in |
1249 |
+ |
|
1250 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
1251 |
+ |
working. |
1252 |
+ |
|
1253 |
+ |
2003-10-17 16:18 mmeineke |
1254 |
+ |
|
1255 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
1256 |
+ |
build list for both configure and configure.in |
1257 |
+ |
|
1258 |
+ |
2003-10-17 16:17 mmeineke |
1259 |
+ |
|
1260 |
+ |
* configure: added the staticProps directory to the build list |
1261 |
+ |
|
1262 |
+ |
2003-10-16 14:16 mmeineke |
1263 |
+ |
|
1264 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1265 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1266 |
+ |
use linked lists instead of a vector. |
1267 |
+ |
|
1268 |
+ |
Fixed the makefile to build DumpReader.cpp |
1269 |
+ |
|
1270 |
+ |
Removed a comment output in Exclude.cpp |
1271 |
+ |
|
1272 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
1273 |
+ |
a frame is written. This lets the .eor file represent the last |
1274 |
+ |
written frame of a simulation. |
1275 |
+ |
|
1276 |
+ |
2003-10-10 12:10 mmeineke |
1277 |
+ |
|
1278 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1279 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1280 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1281 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
1282 |
+ |
over to staticProps |
1283 |
+ |
|
1284 |
+ |
2003-10-09 17:09 mmeineke |
1285 |
+ |
|
1286 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1287 |
+ |
a position where it will compile and run first runs. |
1288 |
+ |
|
1289 |
+ |
2003-10-04 13:46 chuckv |
1290 |
+ |
|
1291 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1292 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1293 |
+ |
|
1294 |
+ |
2003-10-04 13:08 chuckv |
1295 |
+ |
|
1296 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
1297 |
+ |
|
1298 |
+ |
2003-10-03 17:11 mmeineke |
1299 |
+ |
|
1300 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1301 |
+ |
entahlpy from the statwriter and thermo. |
1302 |
+ |
|
1303 |
+ |
2003-10-03 17:02 mmeineke |
1304 |
+ |
|
1305 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1306 |
+ |
statements in simError |
1307 |
+ |
|
1308 |
+ |
added a function to get the maxCutoff |
1309 |
+ |
|
1310 |
+ |
2003-10-03 17:01 mmeineke |
1311 |
+ |
|
1312 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
1313 |
+ |
statements in simError |
1314 |
+ |
|
1315 |
+ |
2003-09-30 11:00 mmeineke |
1316 |
+ |
|
1317 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1318 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
1319 |
+ |
|
1320 |
+ |
2003-09-29 17:06 mmeineke |
1321 |
+ |
|
1322 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1323 |
+ |
for conifig.in |
1324 |
+ |
|
1325 |
+ |
fixed wrappers to extern "C" |
1326 |
+ |
|
1327 |
+ |
2003-09-29 17:06 mmeineke |
1328 |
+ |
|
1329 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
1330 |
+ |
conifig.in |
1331 |
+ |
|
1332 |
+ |
2003-09-29 17:05 mmeineke |
1333 |
+ |
|
1334 |
+ |
* configure: added mpif90 mod check back |
1335 |
+ |
|
1336 |
+ |
2003-09-29 16:16 mmeineke |
1337 |
+ |
|
1338 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1339 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1340 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1341 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1342 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1343 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1344 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1345 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1346 |
+ |
found with SUN's SUNWspro.s1s7 |
1347 |
+ |
|
1348 |
+ |
2003-09-29 12:38 mmeineke |
1349 |
+ |
|
1350 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
1351 |
+ |
signifigant change. |
1352 |
+ |
|
1353 |
+ |
2003-09-25 16:17 mmeineke |
1354 |
+ |
|
1355 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1356 |
+ |
additional remarks from icc -w3 (extra verbose output) |
1357 |
+ |
|
1358 |
+ |
2003-09-25 14:27 mmeineke |
1359 |
+ |
|
1360 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1361 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1362 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1363 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1364 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1365 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1366 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1367 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1368 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1369 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1370 |
+ |
gcc -Wall and g++ -Wall |
1371 |
+ |
|
1372 |
+ |
2003-09-25 13:54 gezelter |
1373 |
+ |
|
1374 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
1375 |
+ |
|
1376 |
+ |
2003-09-25 11:42 gezelter |
1377 |
+ |
|
1378 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1379 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1380 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1381 |
+ |
fixes for configure |
1382 |
+ |
|
1383 |
+ |
2003-09-24 14:34 mmeineke |
1384 |
+ |
|
1385 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1386 |
+ |
that it is called before the first Statistics are written. |
1387 |
+ |
|
1388 |
+ |
2003-09-23 15:36 gezelter |
1389 |
+ |
|
1390 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1391 |
+ |
bunch of Make.dep files to CVS |
1392 |
+ |
|
1393 |
+ |
2003-09-23 15:34 mmeineke |
1394 |
+ |
|
1395 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1396 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1397 |
+ |
|
1398 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
1399 |
+ |
|
1400 |
+ |
2003-09-22 18:07 tim |
1401 |
+ |
|
1402 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1403 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
1404 |
+ |
|
1405 |
+ |
2003-09-22 16:23 mmeineke |
1406 |
+ |
|
1407 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1408 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1409 |
+ |
Converted NPTf to work with the NPT base class. |
1410 |
+ |
|
1411 |
+ |
Removed NPTfm and NPTim from cvs |
1412 |
+ |
|
1413 |
+ |
2003-09-19 15:00 mmeineke |
1414 |
+ |
|
1415 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1416 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1417 |
+ |
class. NPTi is up to date. NPTf is not. |
1418 |
+ |
|
1419 |
+ |
2003-09-19 11:03 mmeineke |
1420 |
+ |
|
1421 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1422 |
+ |
makefile |
1423 |
+ |
|
1424 |
+ |
2003-09-19 11:01 gezelter |
1425 |
+ |
|
1426 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1427 |
+ |
|
1428 |
+ |
2003-09-19 11:01 gezelter |
1429 |
+ |
|
1430 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1431 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
1432 |
+ |
|
1433 |
+ |
2003-09-19 10:20 mmeineke |
1434 |
+ |
|
1435 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
1436 |
+ |
|
1437 |
+ |
2003-09-19 09:55 gezelter |
1438 |
+ |
|
1439 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1440 |
+ |
samples/water/ssd.bass: [no log message] |
1441 |
+ |
|
1442 |
+ |
2003-09-19 09:22 tim |
1443 |
+ |
|
1444 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1445 |
+ |
|
1446 |
+ |
2003-09-17 09:22 mmeineke |
1447 |
+ |
|
1448 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1449 |
+ |
work with constraints. |
1450 |
+ |
|
1451 |
+ |
2003-09-16 15:02 tim |
1452 |
+ |
|
1453 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1454 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1455 |
+ |
|
1456 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
1457 |
+ |
|
1458 |
+ |
NPTi appears very stable. |
1459 |
+ |
|
1460 |
+ |
2003-09-15 11:52 tim |
1461 |
+ |
|
1462 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1463 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1464 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1465 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1466 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1467 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1468 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1469 |
+ |
statWriter fix bug of vector wrapping at NPTi |
1470 |
+ |
|
1471 |
+ |
2003-09-12 11:20 gezelter |
1472 |
+ |
|
1473 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1474 |
+ |
Makefile.in |
1475 |
+ |
|
1476 |
+ |
2003-09-12 11:20 gezelter |
1477 |
+ |
|
1478 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1479 |
+ |
|
1480 |
+ |
2003-09-09 15:35 mmeineke |
1481 |
+ |
|
1482 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1483 |
+ |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1484 |
+ |
|
1485 |
+ |
added two new NPT integrators, they still need work. |
1486 |
+ |
|
1487 |
+ |
2003-09-09 15:34 mmeineke |
1488 |
+ |
|
1489 |
+ |
* ChangeLog: updated the ChangeLog |
1490 |
+ |
|
1491 |
+ |
2003-09-05 17:45 gezelter |
1492 |
+ |
|
1493 |
+ |
* libmdtools/Make.dep: dependency on config.h |
1494 |
+ |
|
1495 |
+ |
2003-09-05 17:36 gezelter |
1496 |
+ |
|
1497 |
+ |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1498 |
+ |
|
1499 |
+ |
2003-09-05 16:29 gezelter |
1500 |
+ |
|
1501 |
+ |
* samples/metals/Makefile.in: New Makefile for metals sample |
1502 |
+ |
|
1503 |
+ |
2003-09-05 16:27 gezelter |
1504 |
+ |
|
1505 |
+ |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1506 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1507 |
+ |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1508 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1509 |
+ |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1510 |
+ |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1511 |
+ |
libmdtools/Makefile, libmdtools/Makefile.in, |
1512 |
+ |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1513 |
+ |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1514 |
+ |
libmdtools/fortranWrappers.cpp, |
1515 |
+ |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1516 |
+ |
libmdtools/simulation_module.F90, samples/Makefile, |
1517 |
+ |
samples/Makefile.in, samples/alkane/Makefile, |
1518 |
+ |
samples/alkane/Makefile.in, samples/argon/Makefile, |
1519 |
+ |
samples/argon/Makefile.in, samples/argon/argon.bass, |
1520 |
+ |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1521 |
+ |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1522 |
+ |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1523 |
+ |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1524 |
+ |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1525 |
+ |
autoconf / configure method of configuring OOPSE |
1526 |
+ |
|
1527 |
+ |
2003-09-04 16:48 mmeineke |
1528 |
+ |
|
1529 |
+ |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1530 |
+ |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
1531 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
1532 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
1533 |
+ |
added resetTime to the Global namespace. |
1534 |
+ |
|
1535 |
+ |
added ability to reset the integrators in the NVT and NPT family. |
1536 |
+ |
|
1537 |
+ |
2003-09-04 16:48 mmeineke |
1538 |
+ |
|
1539 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
1540 |
+ |
namespace. |
1541 |
+ |
|
1542 |
+ |
2003-09-02 09:30 tim |
1543 |
+ |
|
1544 |
+ |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
1545 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
1546 |
+ |
PolicyByMass |
1547 |
+ |
|
1548 |
+ |
2003-08-28 16:09 tim |
1549 |
+ |
|
1550 |
+ |
* ChangeLog, libmdtools/GenericData.cpp, |
1551 |
+ |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1552 |
+ |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1553 |
+ |
|
1554 |
+ |
2003-08-27 14:23 tim |
1555 |
+ |
|
1556 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1557 |
+ |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
1558 |
+ |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
1559 |
+ |
turn on the optimization flag, it causes a seg fault |
1560 |
+ |
|
1561 |
+ |
2003-08-27 11:25 gezelter |
1562 |
+ |
|
1563 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
1564 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
1565 |
+ |
stress tensor parallel bug. |
1566 |
+ |
|
1567 |
+ |
2003-08-27 11:16 tim |
1568 |
+ |
|
1569 |
+ |
* ChangeLog, libmdtools/DUFF.cpp, |
1570 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
1571 |
+ |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
1572 |
+ |
molMembershipList use global index instead of local index |
1573 |
+ |
|
1574 |
|
2003-08-26 15:37 tim |
1575 |
|
|
1576 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
1822 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1823 |
|
works..... |
1824 |
|
|
252 |
– |
2003-08-08 13:32 mmeineke |
253 |
– |
|
254 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
255 |
– |
moved frameCount's functionality into DumpReader. also split props |
256 |
– |
into staticProps and dynamicProps. (currently only have |
257 |
– |
staticProps) |
258 |
– |
|
1825 |
|
2003-08-08 12:48 mmeineke |
1826 |
|
|
1827 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1878 |
|
2003-07-29 11:32 mmeineke |
1879 |
|
|
1880 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1881 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1882 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
317 |
< |
src/Makefile: working on the props code |
1881 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1882 |
> |
working on the props code |
1883 |
|
|
1884 |
|
2003-07-29 11:32 mmeineke |
1885 |
|
|
3006 |
|
|
3007 |
|
2003-03-25 09:29 mmeineke |
3008 |
|
|
3009 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
3009 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3010 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3011 |
|
|
3012 |
|
2003-03-25 09:29 mmeineke |