1 |
+ |
2004-06-11 14:46 gezelter |
2 |
+ |
|
3 |
+ |
* libmdtools/notifyCutoffs.F90: nicer error message formatting |
4 |
+ |
|
5 |
+ |
2004-06-11 14:24 gezelter |
6 |
+ |
|
7 |
+ |
* libmdtools/: Make.dep, Makefile.in: Fixed dependency bug (we |
8 |
+ |
hope) |
9 |
+ |
|
10 |
+ |
2004-06-11 12:16 tim |
11 |
+ |
|
12 |
+ |
* ChangeLog, libBASS/MoleculeStamp.cpp, |
13 |
+ |
libmdtools/ConstraintAlgorithm.cpp, |
14 |
+ |
libmdtools/ConstraintAlgorithm.hpp, |
15 |
+ |
libmdtools/ConstraintElement.cpp, libmdtools/DumpReader.cpp, |
16 |
+ |
libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
17 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
18 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
19 |
+ |
libmdtools/Mat3x3d.cpp, libmdtools/Mat3x3d.hpp, libmdtools/NPT.cpp, |
20 |
+ |
libmdtools/NVT.cpp, libmdtools/Rattle.hpp, libmdtools/Roll.cpp, |
21 |
+ |
libmdtools/Roll.hpp: roll in progress |
22 |
+ |
|
23 |
+ |
2004-06-11 11:46 gezelter |
24 |
+ |
|
25 |
+ |
* samples/metals/Au.bass: Sample now does variant |
26 |
+ |
|
27 |
+ |
2004-06-11 11:46 gezelter |
28 |
+ |
|
29 |
+ |
* libmdtools/EAM_FF.cpp: General fixes for formatting |
30 |
+ |
|
31 |
+ |
2004-06-11 11:45 gezelter |
32 |
+ |
|
33 |
+ |
* forceFields/: Ag.VC.funcfl, Al.VC.funcfl, Au.VC.funcfl, |
34 |
+ |
Cu.VC.funcfl, Ni.VC.funcfl, Pd.VC.funcfl, Pt.VC.funcfl: Converted |
35 |
+ |
D's to E's in the funcfl files so that C can read them. |
36 |
+ |
|
37 |
+ |
2004-06-11 11:35 gezelter |
38 |
+ |
|
39 |
+ |
* forceFields/: Ag.VC.funcfl, Ag.Voter.eam, Ag.u3.eam, |
40 |
+ |
Ag.u3.funcfl, Ag.u6.eam, Ag.u6.funcfl, Al.VC.funcfl, Al.Voter.eam, |
41 |
+ |
Au.VC.funcfl, Au.Voter.eam, Au.u3.eam, Au.u3.funcfl, Au.u6.eam, |
42 |
+ |
Au.u6.funcfl, Cu.VC.funcfl, Cu.Voter.eam, Cu.u3.eam, Cu.u3.funcfl, |
43 |
+ |
Cu.u6.eam, Cu.u6.funcfl, EAM.VC.frc, EAM.Voter.frc, EAM.frc, |
44 |
+ |
EAM.u3.frc, EAM.u6.frc, Ni.VC.funcfl, Ni.Voter.eam, Ni.u3.eam, |
45 |
+ |
Ni.u3.funcfl, Ni.u6.eam, Ni.u6.funcfl, Pd.VC.funcfl, Pd.Voter.eam, |
46 |
+ |
Pd.u3.eam, Pd.u3.funcfl, Pd.u6.eam, Pd.u6.funcfl, Pt.VC.funcfl, |
47 |
+ |
Pt.u3.eam, Pt.u3.funcfl, Pt.u6.eam, Pt.u6.funcfl: changing file |
48 |
+ |
extensions to be more in line with what's actually in the file |
49 |
+ |
|
50 |
+ |
2004-06-11 10:31 gezelter |
51 |
+ |
|
52 |
+ |
* forceFields/: Ag.Voter.eam, Ag.u3.eam, Ag.u6.eam, Al.Voter.eam, |
53 |
+ |
Au.Voter.eam, Au.u3.eam, Au.u6.eam, Cu.Voter.eam, Cu.u3.eam, |
54 |
+ |
Cu.u6.eam, EAM.frc, EAM.u6.frc, Ni.Voter.eam, Ni.u3.eam, Ni.u6.eam, |
55 |
+ |
Pd.Voter.eam, Pd.u3.eam, Pd.u6.eam, Pt.u3.eam, Pt.u6.eam, |
56 |
+ |
ag.u3.eam, au.u3.eam, cu.u3.eam, ni.u3.eam, pd.u3.eam, pt.u3.eam: |
57 |
+ |
Added a bunch of files for EAM variants |
58 |
+ |
|
59 |
+ |
2004-06-11 09:14 gezelter |
60 |
+ |
|
61 |
+ |
* samples/metals/Au.bass: Modified EAM to use forceFieldVariant, |
62 |
+ |
show sample in Au.bass |
63 |
+ |
|
64 |
+ |
2004-06-11 09:14 gezelter |
65 |
+ |
|
66 |
+ |
* libmdtools/: EAM_FF.cpp, ForceFields.hpp, SimSetup.cpp, |
67 |
+ |
SimSetup.hpp: Modified EAM to use forceFieldVariant |
68 |
+ |
|
69 |
+ |
2004-06-11 09:13 gezelter |
70 |
+ |
|
71 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added forceFieldVariant |
72 |
+ |
global |
73 |
+ |
|
74 |
+ |
2004-06-10 17:15 gezelter |
75 |
+ |
|
76 |
+ |
* forceFields/: EAM.Voter.frc, EAM.frc, EAM.u3.frc, EAM_FF.frc, |
77 |
+ |
ag.u3.eam, agu3.eam, au.u3.eam, auu3.eam, backup.DUFF.frc, |
78 |
+ |
cu.u3.eam, cuu3.eam, ni.u3.eam, niu3.eam, pd.u3.eam, pdu3.eam, |
79 |
+ |
pt.u3.eam, ptu3.eam: reorg of EAM force fields to have variants |
80 |
+ |
|
81 |
+ |
2004-06-10 12:09 chrisfen |
82 |
+ |
|
83 |
+ |
* libmdtools/ForceFields.cpp: Fixed a thermodynamic integration |
84 |
+ |
issue. Force and torque scaling loops over atoms, not stuntdoubles |
85 |
+ |
|
86 |
+ |
2004-06-10 10:00 gezelter |
87 |
+ |
|
88 |
+ |
* libBASS/: MakeStamps.cpp, MoleculeStamp.cpp: Removed debugging |
89 |
+ |
printf statements |
90 |
+ |
|
91 |
+ |
2004-06-10 09:59 gezelter |
92 |
+ |
|
93 |
+ |
* libBASS/: MakeStamps.cpp, MoleculeStamp.cpp, make_nodes.c: Fixed |
94 |
+ |
indexing bug in stamps |
95 |
+ |
|
96 |
+ |
2004-06-09 11:59 tim |
97 |
+ |
|
98 |
+ |
* ChangeLog, libmdtools/Roll.cpp: Roll in progress |
99 |
+ |
|
100 |
+ |
2004-06-09 11:16 tim |
101 |
+ |
|
102 |
+ |
* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
103 |
+ |
Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
104 |
+ |
Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
105 |
+ |
Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
106 |
+ |
Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
107 |
+ |
adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
108 |
+ |
Euler3) these classes use anonymous union and struct to support |
109 |
+ |
double[3], double[3][3] and double[4] 2. adding roll constraint |
110 |
+ |
algorithm |
111 |
+ |
|
112 |
+ |
2004-06-08 11:49 gezelter |
113 |
+ |
|
114 |
+ |
* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
115 |
+ |
Fixed a bug in NPTf (vScale was declared in the cpp file in |
116 |
+ |
addition to the declaration in Integrator.hpp file) |
117 |
+ |
|
118 |
+ |
2004-06-07 09:26 gezelter |
119 |
+ |
|
120 |
+ |
* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
121 |
+ |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
122 |
+ |
libmdtools/ConstraintIterator.hpp, |
123 |
+ |
libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
124 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
125 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
126 |
+ |
libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
127 |
+ |
libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
128 |
+ |
|
129 |
+ |
2004-06-07 09:09 chrisfen |
130 |
+ |
|
131 |
+ |
* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
132 |
+ |
bit... Got rid of some unnecessary lines of code in Thermo.cpp |
133 |
+ |
|
134 |
+ |
2004-06-04 16:00 gezelter |
135 |
+ |
|
136 |
+ |
* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
137 |
+ |
StuntDouble.cpp: small bugfixes |
138 |
+ |
|
139 |
+ |
2004-06-04 15:29 tim |
140 |
+ |
|
141 |
+ |
* libmdtools/Integrator.hpp: [no log message] |
142 |
+ |
|
143 |
+ |
2004-06-04 14:30 tim |
144 |
+ |
|
145 |
+ |
* ChangeLog, libmdtools/CallbackFunctor.cpp, |
146 |
+ |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
147 |
+ |
libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
148 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
149 |
+ |
libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
150 |
+ |
libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
151 |
+ |
working |
152 |
+ |
|
153 |
+ |
2004-06-04 11:23 gezelter |
154 |
+ |
|
155 |
+ |
* forceFields/charmm27.vdw: Moved to SHAPES |
156 |
+ |
|
157 |
+ |
2004-06-04 11:23 gezelter |
158 |
+ |
|
159 |
+ |
* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
160 |
+ |
message] |
161 |
+ |
|
162 |
+ |
2004-06-04 09:59 gezelter |
163 |
+ |
|
164 |
+ |
* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
165 |
+ |
More work on Fortran side of error handler |
166 |
+ |
|
167 |
+ |
2004-06-04 09:59 gezelter |
168 |
+ |
|
169 |
+ |
* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
170 |
+ |
|
171 |
+ |
2004-06-04 09:35 gezelter |
172 |
+ |
|
173 |
+ |
* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
174 |
+ |
the error handlers |
175 |
+ |
|
176 |
+ |
2004-06-04 09:17 gezelter |
177 |
+ |
|
178 |
+ |
* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
179 |
+ |
|
180 |
+ |
2004-06-04 09:11 gezelter |
181 |
+ |
|
182 |
+ |
* libBASS/: config.h.in, fError.c: forgot to add these |
183 |
+ |
|
184 |
+ |
2004-06-03 22:15 tim |
185 |
+ |
|
186 |
+ |
* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
187 |
+ |
libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
188 |
+ |
libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
189 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
190 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
191 |
+ |
libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
192 |
+ |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
193 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
194 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
195 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
196 |
+ |
libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
197 |
+ |
libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
198 |
+ |
is working |
199 |
+ |
|
200 |
+ |
2004-06-03 21:38 gezelter |
201 |
+ |
|
202 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
203 |
+ |
libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
204 |
+ |
libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
205 |
+ |
libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
206 |
+ |
fortran access to SimError |
207 |
+ |
|
208 |
+ |
2004-06-03 16:51 tim |
209 |
+ |
|
210 |
+ |
* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
211 |
+ |
ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
212 |
+ |
ConstraintElement.cpp, ConstraintElement.hpp, |
213 |
+ |
ConstraintIterator.hpp, ConstraintManager.cpp, |
214 |
+ |
ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
215 |
+ |
Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
216 |
+ |
implementation of constraint |
217 |
+ |
|
218 |
+ |
2004-06-03 16:06 tim |
219 |
+ |
|
220 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
221 |
+ |
first atom of a molecule |
222 |
+ |
|
223 |
+ |
2004-06-03 15:02 gezelter |
224 |
+ |
|
225 |
+ |
* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
226 |
+ |
|
227 |
+ |
2004-06-03 15:02 gezelter |
228 |
+ |
|
229 |
+ |
* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
230 |
+ |
autoconf |
231 |
+ |
|
232 |
+ |
2004-06-02 13:28 gezelter |
233 |
+ |
|
234 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
235 |
+ |
have been in CVS |
236 |
+ |
|
237 |
+ |
2004-06-02 13:28 gezelter |
238 |
+ |
|
239 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
240 |
+ |
in CVS? |
241 |
+ |
|
242 |
+ |
2004-06-02 13:27 gezelter |
243 |
+ |
|
244 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
245 |
+ |
Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
246 |
+ |
|
247 |
+ |
2004-06-02 13:27 gezelter |
248 |
+ |
|
249 |
+ |
* libBASS/simError.h: starting fortran-usable version of simError |
250 |
+ |
|
251 |
+ |
2004-06-02 09:56 chrisfen |
252 |
+ |
|
253 |
+ |
* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
254 |
+ |
shouldn't be in CVS |
255 |
+ |
|
256 |
+ |
2004-06-02 09:56 chrisfen |
257 |
+ |
|
258 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
259 |
+ |
Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
260 |
+ |
removed writeRaw |
261 |
+ |
|
262 |
+ |
2004-06-02 09:56 chrisfen |
263 |
+ |
|
264 |
+ |
* libBASS/simError.c: Formatting Changes |
265 |
+ |
|
266 |
+ |
2004-06-02 09:21 gezelter |
267 |
+ |
|
268 |
+ |
* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
269 |
+ |
severity levels in simError |
270 |
+ |
|
271 |
+ |
2004-06-01 16:45 gezelter |
272 |
+ |
|
273 |
+ |
* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
274 |
+ |
do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
275 |
+ |
simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
276 |
+ |
under MPI) |
277 |
+ |
|
278 |
+ |
2004-06-01 16:44 gezelter |
279 |
+ |
|
280 |
+ |
* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
281 |
+ |
|
282 |
+ |
2004-06-01 13:43 gezelter |
283 |
+ |
|
284 |
+ |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
285 |
+ |
|
286 |
+ |
2004-06-01 13:42 gezelter |
287 |
+ |
|
288 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
289 |
+ |
SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
290 |
+ |
mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
291 |
+ |
Cutoff Groups for MPI |
292 |
+ |
|
293 |
+ |
2004-06-01 13:07 chrisfen |
294 |
+ |
|
295 |
+ |
* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
296 |
+ |
useLiquidThermInt routine in ForceFields.cpp |
297 |
+ |
|
298 |
+ |
2004-06-01 12:15 chrisfen |
299 |
+ |
|
300 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
301 |
+ |
SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
302 |
+ |
solid and liquid thermodynamic integration routines |
303 |
+ |
|
304 |
+ |
2004-06-01 10:57 tim |
305 |
+ |
|
306 |
+ |
* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
307 |
+ |
progress |
308 |
+ |
|
309 |
+ |
2004-06-01 09:27 chrisfen |
310 |
+ |
|
311 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
312 |
+ |
keyword and changed useThermInt to useSolidThermInt |
313 |
+ |
|
314 |
+ |
2004-06-01 09:21 chrisfen |
315 |
+ |
|
316 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
317 |
+ |
solid and liquid thermodynamic integration routines |
318 |
+ |
|
319 |
+ |
2004-05-28 10:21 gezelter |
320 |
+ |
|
321 |
+ |
* libmdtools/do_Forces.F90: bugfix starting |
322 |
+ |
|
323 |
+ |
2004-05-27 15:06 chrisfen |
324 |
+ |
|
325 |
+ |
* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
326 |
+ |
Integrator.cpp where it called writeRaw() when useThermInt = |
327 |
+ |
false... |
328 |
+ |
|
329 |
+ |
2004-05-27 14:51 tim |
330 |
+ |
|
331 |
+ |
* ChangeLog, libmdtools/do_Forces.F90, |
332 |
+ |
libmdtools/simulation_module.F90: Bug fix for SkipList |
333 |
+ |
|
334 |
+ |
2004-05-27 14:26 gezelter |
335 |
+ |
|
336 |
+ |
* libmdtools/SimSetup.cpp: bugfix in simsetup? |
337 |
+ |
|
338 |
+ |
2004-05-27 13:59 gezelter |
339 |
+ |
|
340 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
341 |
+ |
InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
342 |
+ |
ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
343 |
+ |
mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
344 |
+ |
mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
345 |
+ |
Cutoff group changes under MPI |
346 |
+ |
|
347 |
+ |
2004-05-27 11:20 gezelter |
348 |
+ |
|
349 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
350 |
+ |
xlc++ |
351 |
+ |
|
352 |
+ |
2004-05-27 10:31 tim |
353 |
+ |
|
354 |
+ |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
355 |
+ |
atoms |
356 |
+ |
|
357 |
+ |
2004-05-27 10:21 gezelter |
358 |
+ |
|
359 |
+ |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
360 |
+ |
|
361 |
+ |
2004-05-27 10:21 gezelter |
362 |
+ |
|
363 |
+ |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
364 |
+ |
Fixed off-by-one error in groupStartRow and groupStartCol |
365 |
+ |
|
366 |
+ |
2004-05-26 19:48 tim |
367 |
+ |
|
368 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
369 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
370 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
371 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
372 |
+ |
libmdtools/calc_charge_charge.F90, |
373 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
374 |
+ |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
375 |
+ |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
376 |
+ |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
377 |
+ |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
378 |
+ |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
379 |
+ |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
380 |
+ |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
381 |
+ |
version of cutoff group |
382 |
+ |
|
383 |
+ |
2004-05-26 11:41 gezelter |
384 |
+ |
|
385 |
+ |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
386 |
+ |
force loop into one. |
387 |
+ |
|
388 |
+ |
2004-05-24 17:24 gezelter |
389 |
+ |
|
390 |
+ |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
391 |
+ |
|
392 |
+ |
2004-05-24 16:23 chrisfen |
393 |
+ |
|
394 |
+ |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
395 |
+ |
changed error messages in Restraints.cpp |
396 |
+ |
|
397 |
+ |
2004-05-24 16:03 gezelter |
398 |
+ |
|
399 |
+ |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
400 |
+ |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
401 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
402 |
+ |
for stress / pressure tensor by cutoff group |
403 |
+ |
|
404 |
+ |
2004-05-22 15:55 chrisfen |
405 |
+ |
|
406 |
+ |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
407 |
+ |
Too many arguements in a function call. |
408 |
+ |
|
409 |
+ |
2004-05-22 13:17 chrisfen |
410 |
+ |
|
411 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
412 |
+ |
useThermInt. |
413 |
+ |
|
414 |
+ |
2004-05-22 13:16 chrisfen |
415 |
+ |
|
416 |
+ |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
417 |
+ |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
418 |
+ |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
419 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
420 |
+ |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
421 |
+ |
code. |
422 |
+ |
|
423 |
+ |
2004-05-21 10:58 gezelter |
424 |
+ |
|
425 |
+ |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
426 |
+ |
to skipThisPair for efficiency |
427 |
+ |
|
428 |
+ |
2004-05-21 09:22 gezelter |
429 |
+ |
|
430 |
+ |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
431 |
+ |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
432 |
+ |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
433 |
+ |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
434 |
+ |
for SHAPES potential |
435 |
+ |
|
436 |
+ |
2004-05-20 15:27 chrisfen |
437 |
+ |
|
438 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
439 |
+ |
included the bass keywords |
440 |
+ |
|
441 |
+ |
2004-05-20 15:24 chrisfen |
442 |
+ |
|
443 |
+ |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
444 |
+ |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
445 |
+ |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
446 |
+ |
additions... Restraints.cpp and .hpp were included for restraining |
447 |
+ |
particles in thermodynamic integration. By including these, |
448 |
+ |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
449 |
+ |
StatWriter, and possibly some other files. Two bass keywords were |
450 |
+ |
also added for performing thermodynamic integration: a lambda value |
451 |
+ |
one and a k power one. |
452 |
+ |
|
453 |
+ |
2004-05-13 16:08 gezelter |
454 |
+ |
|
455 |
+ |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
456 |
+ |
|
457 |
+ |
2004-05-12 17:01 tim |
458 |
+ |
|
459 |
+ |
* samples/: argon/Makefile, argon/argonEM.bass, |
460 |
+ |
argon/init_argon.eor, minimizer/argon/Makefile, |
461 |
+ |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
462 |
+ |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
463 |
+ |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
464 |
+ |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
465 |
+ |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
466 |
+ |
minimizer sample |
467 |
+ |
|
468 |
+ |
2004-05-12 16:54 gezelter |
469 |
+ |
|
470 |
+ |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
471 |
+ |
compilation |
472 |
+ |
|
473 |
+ |
2004-05-12 15:54 gezelter |
474 |
+ |
|
475 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
476 |
+ |
for compilation under Mac OS X with IBM's xl compilers |
477 |
+ |
|
478 |
+ |
2004-05-12 15:14 gezelter |
479 |
+ |
|
480 |
+ |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
481 |
+ |
|
482 |
+ |
2004-05-12 15:14 gezelter |
483 |
+ |
|
484 |
+ |
* libmdtools/LJFF.cpp: Removed an extraneous write |
485 |
+ |
|
486 |
+ |
2004-05-12 15:13 gezelter |
487 |
+ |
|
488 |
+ |
* libBASS/simError.h: Starting to change the error model |
489 |
+ |
|
490 |
+ |
2004-05-12 14:45 gezelter |
491 |
+ |
|
492 |
+ |
* utils/Dump2XYZ.cpp: const char* fix |
493 |
+ |
|
494 |
+ |
2004-05-12 14:44 gezelter |
495 |
+ |
|
496 |
+ |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
497 |
+ |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
498 |
+ |
write statements |
499 |
+ |
|
500 |
+ |
2004-05-12 11:38 tim |
501 |
+ |
|
502 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
503 |
+ |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
504 |
+ |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
505 |
+ |
massratio from simState, creat cutoff group forevery atom which |
506 |
+ |
does not belong to cutoff group defined at mdl file |
507 |
+ |
|
508 |
+ |
2004-05-12 10:58 gezelter |
509 |
+ |
|
510 |
+ |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
511 |
+ |
CutoffGroup |
512 |
+ |
|
513 |
+ |
2004-05-12 10:35 gezelter |
514 |
+ |
|
515 |
+ |
* samples/water/water.mdl: Added the cutoff Groups to the default |
516 |
+ |
water.mdl file |
517 |
+ |
|
518 |
+ |
2004-05-12 10:02 tim |
519 |
+ |
|
520 |
+ |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
521 |
+ |
fixed a bug in CutoffGroup::getCOM() |
522 |
+ |
|
523 |
+ |
2004-05-12 09:29 gezelter |
524 |
+ |
|
525 |
+ |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
526 |
+ |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
527 |
+ |
samples/water/ssd.bass: bug fixes for cutoffGroups |
528 |
+ |
|
529 |
+ |
2004-05-11 17:28 tim |
530 |
+ |
|
531 |
+ |
* utils/Vector3.hpp: adding generic Vector3 class |
532 |
+ |
|
533 |
+ |
2004-05-11 16:44 tim |
534 |
+ |
|
535 |
+ |
* libmdtools/Integrator.hpp: adding instantiation of |
536 |
+ |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
537 |
+ |
|
538 |
+ |
2004-05-11 16:31 gezelter |
539 |
+ |
|
540 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
541 |
+ |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
542 |
+ |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
543 |
+ |
Fortran-side changes for group-based cutoffs |
544 |
+ |
|
545 |
+ |
2004-05-11 16:20 tim |
546 |
+ |
|
547 |
+ |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
548 |
+ |
|
549 |
+ |
2004-05-11 16:14 tim |
550 |
+ |
|
551 |
+ |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
552 |
+ |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
553 |
+ |
anoter one in CutoffGroup which causes seg fault |
554 |
+ |
|
555 |
+ |
2004-05-11 15:33 tim |
556 |
+ |
|
557 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
558 |
+ |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
559 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
560 |
+ |
into OOPSE |
561 |
+ |
|
562 |
+ |
2004-05-11 15:07 gezelter |
563 |
+ |
|
564 |
+ |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
565 |
+ |
|
566 |
+ |
2004-05-11 11:00 gezelter |
567 |
+ |
|
568 |
+ |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
569 |
+ |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
570 |
+ |
use the simplified cutoff stuff in the BASS library |
571 |
+ |
|
572 |
+ |
2004-05-10 23:21 gezelter |
573 |
+ |
|
574 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
575 |
+ |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
576 |
+ |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
577 |
+ |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
578 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
579 |
+ |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
580 |
+ |
Also restructured the plethora of cutoff radii into one |
581 |
+ |
cutoffRadius and one switchingRadius. Also removed the |
582 |
+ |
useMolecularCutoffs keyword |
583 |
+ |
|
584 |
+ |
2004-05-10 15:28 tim |
585 |
+ |
|
586 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
587 |
+ |
DumpWriter |
588 |
+ |
|
589 |
+ |
2004-05-07 16:36 gezelter |
590 |
+ |
|
591 |
+ |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
592 |
+ |
for fortran group-based switching function |
593 |
+ |
|
594 |
+ |
2004-05-07 16:35 gezelter |
595 |
+ |
|
596 |
+ |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
597 |
+ |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
598 |
+ |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
599 |
+ |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
600 |
+ |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
601 |
+ |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
602 |
+ |
simulation_module.F90: Many changes to get group-based cutoffs to |
603 |
+ |
work |
604 |
+ |
|
605 |
+ |
2004-05-01 13:52 tim |
606 |
+ |
|
607 |
+ |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
608 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
609 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
610 |
+ |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
611 |
+ |
libmdtools/fortranWrapDefines.hpp, |
612 |
+ |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
613 |
+ |
|
614 |
+ |
2004-04-29 11:03 tim |
615 |
+ |
|
616 |
+ |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
617 |
+ |
calc_charge_charge when using molecular cutoff |
618 |
+ |
|
619 |
+ |
2004-04-28 21:11 tim |
620 |
+ |
|
621 |
+ |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
622 |
+ |
unmatched c/fortran interface |
623 |
+ |
|
624 |
+ |
2004-04-28 18:09 tim |
625 |
+ |
|
626 |
+ |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
627 |
+ |
keep the previous position of cantilever in SMD |
628 |
+ |
|
629 |
+ |
2004-04-28 17:34 tim |
630 |
+ |
|
631 |
+ |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
632 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
633 |
+ |
in Molecule.cpp which initialize massRatio before creat the array. |
634 |
+ |
fix two bugs in ZconsVisitor |
635 |
+ |
|
636 |
+ |
2004-04-28 17:06 gezelter |
637 |
+ |
|
638 |
+ |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
639 |
+ |
Adding molecular cutoffs |
640 |
+ |
|
641 |
+ |
2004-04-28 16:39 gezelter |
642 |
+ |
|
643 |
+ |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
644 |
+ |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
645 |
+ |
molecular cutoffs |
646 |
+ |
|
647 |
+ |
2004-04-28 16:39 gezelter |
648 |
+ |
|
649 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
650 |
+ |
Globals |
651 |
+ |
|
652 |
+ |
2004-04-27 11:26 tim |
653 |
+ |
|
654 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
655 |
+ |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
656 |
+ |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
657 |
+ |
molecule and massRation into atom class |
658 |
+ |
|
659 |
+ |
2004-04-26 16:16 mmeineke |
660 |
+ |
|
661 |
+ |
* libBASS/Globals.cpp: modified the defaults for the system init |
662 |
+ |
time and system init state. |
663 |
+ |
|
664 |
+ |
2004-04-26 09:29 gezelter |
665 |
+ |
|
666 |
+ |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
667 |
+ |
calc_charge_charge.F90 |
668 |
+ |
|
669 |
+ |
2004-04-23 23:31 tim |
670 |
+ |
|
671 |
+ |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
672 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
673 |
+ |
reaction field correction to charge-charge interaction |
674 |
+ |
|
675 |
+ |
2004-04-22 16:33 tim |
676 |
+ |
|
677 |
+ |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
678 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
679 |
+ |
calculation of pressure tensor |
680 |
+ |
|
681 |
+ |
2004-04-22 09:55 tim |
682 |
+ |
|
683 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
684 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
685 |
+ |
|
686 |
+ |
2004-04-21 22:29 tim |
687 |
+ |
|
688 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
689 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
690 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
691 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
692 |
+ |
DumpWriter |
693 |
+ |
|
694 |
+ |
2004-04-21 00:32 tim |
695 |
+ |
|
696 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
697 |
+ |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
698 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
699 |
+ |
useless files |
700 |
+ |
|
701 |
+ |
2004-04-20 11:56 tim |
702 |
+ |
|
703 |
+ |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
704 |
+ |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
705 |
+ |
velocitize at thermo |
706 |
+ |
|
707 |
+ |
2004-04-20 00:39 tim |
708 |
+ |
|
709 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
710 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
711 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
712 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
713 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
714 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
715 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
716 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
717 |
+ |
|
718 |
+ |
2004-04-19 17:13 gezelter |
719 |
+ |
|
720 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
721 |
+ |
Thermo.cpp: Fixed a charge bug |
722 |
+ |
|
723 |
+ |
2004-04-19 15:54 tim |
724 |
+ |
|
725 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
726 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
727 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
728 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
729 |
+ |
|
730 |
+ |
2004-04-19 12:44 tim |
731 |
+ |
|
732 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
733 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
734 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
735 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
736 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
737 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
738 |
+ |
counted |
739 |
+ |
|
740 |
+ |
2004-04-18 22:52 tim |
741 |
+ |
|
742 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
743 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
744 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
745 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
746 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
747 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
748 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
749 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
750 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
751 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
752 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
753 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
754 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
755 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
756 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
757 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
758 |
+ |
implement of quickLate using visitor and composite pattern |
759 |
+ |
|
760 |
+ |
2004-04-15 17:15 tim |
761 |
+ |
|
762 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
763 |
+ |
exclude list |
764 |
+ |
|
765 |
+ |
2004-04-15 11:18 tim |
766 |
+ |
|
767 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
768 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
769 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
770 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
771 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
772 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
773 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
774 |
+ |
whole bunch of bugs :-) |
775 |
+ |
|
776 |
+ |
2004-04-14 12:20 chrisfen |
777 |
+ |
|
778 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
779 |
+ |
|
780 |
+ |
2004-04-14 11:32 gezelter |
781 |
+ |
|
782 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
783 |
+ |
|
784 |
+ |
2004-04-14 10:37 tim |
785 |
+ |
|
786 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
787 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
788 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
789 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
790 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
791 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
792 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
793 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
794 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
795 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
796 |
+ |
Change DumpWriter and InitFromFile |
797 |
+ |
|
798 |
+ |
2004-04-13 11:26 gezelter |
799 |
+ |
|
800 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
801 |
+ |
molecules can keep track of their own IntegrableObjects (and |
802 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
803 |
+ |
RigidBodies (which was done incorrectly before). |
804 |
+ |
|
805 |
+ |
2004-04-13 11:25 gezelter |
806 |
+ |
|
807 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
808 |
+ |
(will back out momentarily) |
809 |
+ |
|
810 |
+ |
2004-04-13 10:10 gezelter |
811 |
+ |
|
812 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
813 |
+ |
Those were old. |
814 |
+ |
|
815 |
+ |
2004-04-13 10:09 gezelter |
816 |
+ |
|
817 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
818 |
+ |
to add IntegrableObjects |
819 |
+ |
|
820 |
+ |
2004-04-12 16:02 gezelter |
821 |
+ |
|
822 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
823 |
+ |
|
824 |
+ |
2004-04-12 15:32 gezelter |
825 |
+ |
|
826 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
827 |
+ |
test run |
828 |
+ |
|
829 |
+ |
2004-04-12 15:32 gezelter |
830 |
+ |
|
831 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
832 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
833 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
834 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
835 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
836 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
837 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
838 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
839 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
840 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
841 |
+ |
(Somewhat extensive) |
842 |
+ |
|
843 |
+ |
2004-04-12 15:31 gezelter |
844 |
+ |
|
845 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
846 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
847 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
848 |
+ |
Changes for RigidBody dynamics |
849 |
+ |
|
850 |
+ |
2004-03-17 09:22 tim |
851 |
+ |
|
852 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
853 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
854 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
855 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
856 |
+ |
does not sound a good choice, next commit will seperate SMD and |
857 |
+ |
ZConstraint |
858 |
+ |
|
859 |
+ |
2004-03-16 14:22 tim |
860 |
+ |
|
861 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
862 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
863 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
864 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
865 |
+ |
now can support sequential moving. Refactorying is needed to |
866 |
+ |
support SMD in ZConstraint |
867 |
+ |
|
868 |
+ |
2004-03-02 15:32 tim |
869 |
+ |
|
870 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
871 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
872 |
+ |
support large file |
873 |
+ |
|
874 |
+ |
2004-03-01 16:17 tim |
875 |
+ |
|
876 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
877 |
+ |
|
878 |
+ |
2004-03-01 15:01 tim |
879 |
+ |
|
880 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
881 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
882 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
883 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
884 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
885 |
+ |
program which can be used to replace atom type for zconstraint into |
886 |
+ |
OOPSE |
887 |
+ |
|
888 |
+ |
2004-02-24 11:36 tim |
889 |
+ |
|
890 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
891 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
892 |
+ |
message] |
893 |
+ |
|
894 |
+ |
2004-02-24 10:49 tim |
895 |
+ |
|
896 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
897 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
898 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
899 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
900 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
901 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
902 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
903 |
+ |
|
904 |
+ |
2004-02-24 10:44 tim |
905 |
+ |
|
906 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
907 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
908 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
909 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
910 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
911 |
+ |
compose to implement Minimizer both versions are working |
912 |
+ |
|
913 |
+ |
2004-02-17 14:23 tim |
914 |
+ |
|
915 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
916 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
917 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
918 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
919 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
920 |
+ |
to remove the constraint force along bond direction |
921 |
+ |
|
922 |
+ |
2004-02-10 16:33 tim |
923 |
+ |
|
924 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
925 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
926 |
+ |
single version of energy minimization is working. |
927 |
+ |
|
928 |
+ |
2004-02-09 15:38 mmeineke |
929 |
+ |
|
930 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
931 |
+ |
the massive memory overusage by OOPSE |
932 |
+ |
|
933 |
+ |
2004-02-09 09:48 chrisfen |
934 |
+ |
|
935 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
936 |
+ |
hardwired LJ_rcut |
937 |
+ |
|
938 |
+ |
2004-02-06 19:14 tim |
939 |
+ |
|
940 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
941 |
+ |
message] |
942 |
+ |
|
943 |
+ |
2004-02-06 16:37 tim |
944 |
+ |
|
945 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
946 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
947 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
948 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
949 |
+ |
energy minimization for argon is working, need to add constraint |
950 |
+ |
|
951 |
+ |
2004-02-06 14:05 tim |
952 |
+ |
|
953 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
954 |
+ |
one more file into Makefile.in |
955 |
+ |
|
956 |
+ |
2004-02-06 13:58 tim |
957 |
+ |
|
958 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
959 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
960 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
961 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
962 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
963 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
964 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
965 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
966 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
967 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
968 |
+ |
some lines into global.cpp to make it work with energy minimization |
969 |
+ |
|
970 |
+ |
2004-02-04 17:26 tim |
971 |
+ |
|
972 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
973 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
974 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
975 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
976 |
+ |
Single version of conjugate gradient with golden search linesearch |
977 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
978 |
+ |
|
979 |
+ |
2004-02-03 17:54 tim |
980 |
+ |
|
981 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
982 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
983 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
984 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
985 |
+ |
|
986 |
+ |
2004-02-03 15:47 tim |
987 |
+ |
|
988 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
989 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
990 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
991 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
992 |
+ |
SteepestDescent.hpp: [no log message] |
993 |
+ |
|
994 |
+ |
2004-02-03 15:43 tim |
995 |
+ |
|
996 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
997 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
998 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
999 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
1000 |
+ |
constraint class |
1001 |
+ |
|
1002 |
+ |
2004-02-03 12:10 tim |
1003 |
+ |
|
1004 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
1005 |
+ |
|
1006 |
+ |
2004-02-03 10:21 tim |
1007 |
+ |
|
1008 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
1009 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
1010 |
+ |
|
1011 |
+ |
2004-02-02 15:29 tim |
1012 |
+ |
|
1013 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
1014 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
1015 |
+ |
Adding GoldenSection and Brent LineSearch Method |
1016 |
+ |
|
1017 |
+ |
2004-01-30 16:47 tim |
1018 |
+ |
|
1019 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
1020 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
1021 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
1022 |
+ |
MinimizerBase instead of a functor to do line seach |
1023 |
+ |
|
1024 |
+ |
2004-01-30 10:00 chrisfen |
1025 |
+ |
|
1026 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
1027 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
1028 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
1029 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
1030 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
1031 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
1032 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
1033 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
1034 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
1035 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
1036 |
+ |
This will be removed on the next commit... |
1037 |
+ |
|
1038 |
+ |
2004-01-29 18:00 gezelter |
1039 |
+ |
|
1040 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
1041 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1042 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
1043 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
1044 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
1045 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
1046 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
1047 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
1048 |
+ |
member list fixes for rigid bodies |
1049 |
+ |
|
1050 |
+ |
2004-01-29 16:44 tim |
1051 |
+ |
|
1052 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
1053 |
+ |
MinimizerParameterSet class. |
1054 |
+ |
|
1055 |
+ |
2004-01-28 17:44 tim |
1056 |
+ |
|
1057 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
1058 |
+ |
NLModel0 and NLModel1 |
1059 |
+ |
|
1060 |
+ |
2004-01-28 15:40 tim |
1061 |
+ |
|
1062 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
1063 |
+ |
of NLModel |
1064 |
+ |
|
1065 |
+ |
2004-01-27 15:34 gezelter |
1066 |
+ |
|
1067 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
1068 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
1069 |
+ |
|
1070 |
+ |
2004-01-27 15:34 gezelter |
1071 |
+ |
|
1072 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
1073 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
1074 |
+ |
stuff |
1075 |
+ |
|
1076 |
+ |
2004-01-27 14:39 gezelter |
1077 |
+ |
|
1078 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
1079 |
+ |
|
1080 |
+ |
2004-01-27 14:39 gezelter |
1081 |
+ |
|
1082 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
1083 |
+ |
|
1084 |
+ |
2004-01-27 14:38 gezelter |
1085 |
+ |
|
1086 |
+ |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
1087 |
+ |
run time to test argon |
1088 |
+ |
|
1089 |
+ |
2004-01-27 14:38 gezelter |
1090 |
+ |
|
1091 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
1092 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
1093 |
+ |
morning |
1094 |
+ |
|
1095 |
+ |
2004-01-27 14:37 gezelter |
1096 |
+ |
|
1097 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1098 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
1099 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
1100 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
1101 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
1102 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
1103 |
+ |
do new rigidBody scheme |
1104 |
+ |
|
1105 |
+ |
2004-01-27 14:15 tim |
1106 |
+ |
|
1107 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
1108 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
1109 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
1110 |
+ |
constraint for Nonlinear Optimization Model |
1111 |
+ |
|
1112 |
+ |
2004-01-26 17:01 gezelter |
1113 |
+ |
|
1114 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
1115 |
+ |
Euler angles for orientation instead of unit vectors required |
1116 |
+ |
changes in MoLocator |
1117 |
+ |
|
1118 |
+ |
2004-01-26 16:53 gezelter |
1119 |
+ |
|
1120 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
1121 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
1122 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
1123 |
+ |
euler angles |
1124 |
+ |
|
1125 |
+ |
2004-01-26 16:52 gezelter |
1126 |
+ |
|
1127 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
1128 |
+ |
|
1129 |
+ |
2004-01-26 16:45 gezelter |
1130 |
+ |
|
1131 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
1132 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
1133 |
+ |
the ability to set orientation using a unit vector |
1134 |
+ |
|
1135 |
+ |
2004-01-26 16:26 gezelter |
1136 |
+ |
|
1137 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
1138 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
1139 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
1140 |
+ |
ability to set orientation using a unit vector |
1141 |
+ |
|
1142 |
+ |
2004-01-26 13:52 gezelter |
1143 |
+ |
|
1144 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
1145 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
1146 |
+ |
|
1147 |
+ |
2004-01-22 12:34 chrisfen |
1148 |
+ |
|
1149 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
1150 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
1151 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
1152 |
+ |
|
1153 |
+ |
2004-01-21 17:16 tim |
1154 |
+ |
|
1155 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
1156 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
1157 |
+ |
|
1158 |
+ |
2004-01-20 15:34 tim |
1159 |
+ |
|
1160 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
1161 |
+ |
|
1162 |
+ |
2004-01-20 15:32 tim |
1163 |
+ |
|
1164 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
1165 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
1166 |
+ |
|
1167 |
+ |
2004-01-19 16:17 gezelter |
1168 |
+ |
|
1169 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
1170 |
+ |
more user-friendly |
1171 |
+ |
|
1172 |
+ |
2004-01-19 13:51 chrisfen |
1173 |
+ |
|
1174 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
1175 |
+ |
|
1176 |
+ |
2004-01-19 13:36 tim |
1177 |
+ |
|
1178 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
1179 |
+ |
time, status time, thermal time and reset time are not divisible by |
1180 |
+ |
dt |
1181 |
+ |
|
1182 |
+ |
2004-01-19 11:10 gezelter |
1183 |
+ |
|
1184 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
1185 |
+ |
won't complain |
1186 |
+ |
|
1187 |
+ |
2004-01-19 11:10 gezelter |
1188 |
+ |
|
1189 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
1190 |
+ |
|
1191 |
+ |
2004-01-19 11:09 gezelter |
1192 |
+ |
|
1193 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
1194 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
1195 |
+ |
in mpiSimulation.cpp |
1196 |
+ |
|
1197 |
+ |
2004-01-19 11:08 gezelter |
1198 |
+ |
|
1199 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
1200 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
1201 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
1202 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
1203 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
1204 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
1205 |
+ |
|
1206 |
+ |
2004-01-16 16:55 tim |
1207 |
+ |
|
1208 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
1209 |
+ |
eor file |
1210 |
+ |
|
1211 |
+ |
2004-01-16 16:51 mmeineke |
1212 |
+ |
|
1213 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
1214 |
+ |
write eor files |
1215 |
+ |
|
1216 |
+ |
2004-01-16 10:01 mmeineke |
1217 |
+ |
|
1218 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
1219 |
+ |
initialization of the AtomStruct |
1220 |
+ |
|
1221 |
+ |
2004-01-15 16:57 chuckv |
1222 |
+ |
|
1223 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
1224 |
+ |
|
1225 |
+ |
2004-01-15 10:51 gezelter |
1226 |
+ |
|
1227 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
1228 |
+ |
|
1229 |
+ |
2004-01-15 09:22 gezelter |
1230 |
+ |
|
1231 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
1232 |
+ |
|
1233 |
+ |
2004-01-14 23:33 gezelter |
1234 |
+ |
|
1235 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
1236 |
+ |
|
1237 |
+ |
2004-01-14 20:14 gezelter |
1238 |
+ |
|
1239 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
1240 |
+ |
notifyCutoffs.F90: More work for adding charges |
1241 |
+ |
|
1242 |
+ |
2004-01-14 17:41 gezelter |
1243 |
+ |
|
1244 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1245 |
+ |
src/Makefile.in: autoconf fixes |
1246 |
+ |
|
1247 |
+ |
2004-01-14 11:28 mmeineke |
1248 |
+ |
|
1249 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
1250 |
+ |
|
1251 |
+ |
2004-01-14 10:48 gezelter |
1252 |
+ |
|
1253 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1254 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
1255 |
+ |
changes for icc8 |
1256 |
+ |
|
1257 |
+ |
2004-01-13 18:01 gezelter |
1258 |
+ |
|
1259 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
1260 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
1261 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
1262 |
+ |
Changes for adding direct charge-charge interactions (with |
1263 |
+ |
switching function) |
1264 |
+ |
|
1265 |
+ |
2004-01-13 17:34 gezelter |
1266 |
+ |
|
1267 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
1268 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
1269 |
+ |
direct charge-charge interactions |
1270 |
+ |
|
1271 |
+ |
2004-01-13 17:11 tim |
1272 |
+ |
|
1273 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
1274 |
+ |
|
1275 |
+ |
2004-01-13 16:22 tim |
1276 |
+ |
|
1277 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
1278 |
+ |
|
1279 |
+ |
2004-01-13 15:35 tim |
1280 |
+ |
|
1281 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
1282 |
+ |
eor file whenever it is used instead of rewinding it |
1283 |
+ |
|
1284 |
+ |
2004-01-13 15:04 tim |
1285 |
+ |
|
1286 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
1287 |
+ |
of writeFrame |
1288 |
+ |
|
1289 |
+ |
2004-01-13 10:46 tim |
1290 |
+ |
|
1291 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
1292 |
+ |
Merge the code of writeFinal and writeDump; |
1293 |
+ |
Adding sortingIndex into DumpWriter; |
1294 |
+ |
Fix a bug of writing last frame twice in integrator |
1295 |
+ |
|
1296 |
+ |
2004-01-12 17:54 tim |
1297 |
+ |
|
1298 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
1299 |
+ |
a bug in copying string |
1300 |
+ |
|
1301 |
+ |
2004-01-12 15:37 tim |
1302 |
+ |
|
1303 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1304 |
+ |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
1305 |
+ |
Dumpwriter only write out the atoms on master nodes |
1306 |
+ |
|
1307 |
|
2004-01-10 04:46 tim |
1308 |
|
|
1309 |
|
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
1353 |
|
2004-01-07 14:26 tim |
1354 |
|
|
1355 |
|
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
1356 |
< |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
1357 |
< |
sending message from master node to itself in DumpWriter.cpp and |
1358 |
< |
InitializeFromFile.cpp |
1356 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
1357 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
1358 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
1359 |
|
|
1360 |
|
2004-01-06 14:49 chuckv |
1361 |
|
|
1661 |
|
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1662 |
|
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1663 |
|
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1664 |
< |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1665 |
< |
file. |
1664 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1665 |
> |
and eta to the comment line of dump file. |
1666 |
|
|
1667 |
|
2003-10-28 17:25 mmeineke |
1668 |
|
|
1841 |
|
|
1842 |
|
2003-10-10 12:10 mmeineke |
1843 |
|
|
1844 |
< |
* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
1845 |
< |
props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
1846 |
< |
props/PairCorrList.hpp, props/PairCorrType.cpp, |
1847 |
< |
props/PairCorrType.hpp, props/staticProps.cpp, |
1848 |
< |
staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
543 |
< |
staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
544 |
< |
staticProps/GofR.cpp, staticProps/Makefile.in, |
545 |
< |
staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
546 |
< |
staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
547 |
< |
staticProps/staticProps.cpp: removed the props directory, and moved |
548 |
< |
everything over to staticProps |
1844 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1845 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1846 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1847 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1848 |
> |
over to staticProps |
1849 |
|
|
1850 |
|
2003-10-09 17:09 mmeineke |
1851 |
|
|
1852 |
< |
* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
553 |
< |
props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
554 |
< |
props/PairCorrType.cpp, props/PairCorrType.hpp, |
555 |
< |
props/staticProps.cpp: Contiuned work on staticProps. should be in |
1852 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1853 |
|
a position where it will compile and run first runs. |
1854 |
|
|
1855 |
|
2003-10-04 13:46 chuckv |
1868 |
|
|
1869 |
|
2003-10-03 17:02 mmeineke |
1870 |
|
|
574 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
575 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
576 |
– |
staticProps.cpp: changed the formating ogf the error statements in |
577 |
– |
simError |
578 |
– |
|
579 |
– |
added a function to get the maxCutoff |
580 |
– |
|
581 |
– |
near completion of the staticProps code. still needs the pair loop, |
582 |
– |
and the loop to allocate and read each frame. |
583 |
– |
|
584 |
– |
2003-10-03 17:02 mmeineke |
585 |
– |
|
1871 |
|
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1872 |
|
statements in simError |
1873 |
|
|
1878 |
|
* libBASS/simError.c: changed the formating ogf the error |
1879 |
|
statements in simError |
1880 |
|
|
596 |
– |
2003-10-02 17:06 mmeineke |
597 |
– |
|
598 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
599 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
600 |
– |
staticProps.cpp: finishing up the constructs needed to get this |
601 |
– |
program up and running |
602 |
– |
|
1881 |
|
2003-09-30 11:00 mmeineke |
1882 |
|
|
1883 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
2034 |
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
2035 |
|
statWriter fix bug of vector wrapping at NPTi |
2036 |
|
|
759 |
– |
2003-09-12 15:51 mmeineke |
760 |
– |
|
761 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
762 |
– |
PairCorrType.hpp: added AllCorr. It eill still need some work |
763 |
– |
|
2037 |
|
2003-09-12 11:20 gezelter |
2038 |
|
|
2039 |
|
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
2043 |
|
|
2044 |
|
* ChangeLog: Entered changes for configure into ChangeLog |
2045 |
|
|
773 |
– |
2003-09-10 16:28 mmeineke |
774 |
– |
|
775 |
– |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
776 |
– |
work on getting gofR working. |
777 |
– |
|
778 |
– |
2003-09-09 16:50 mmeineke |
779 |
– |
|
780 |
– |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
781 |
– |
beginings of the GofR pair correlation. |
782 |
– |
|
783 |
– |
added identification of identI in matchI. |
784 |
– |
|
2046 |
|
2003-09-09 15:35 mmeineke |
2047 |
|
|
2048 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
2083 |
|
samples/Makefile.in, samples/alkane/Makefile, |
2084 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
2085 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
2086 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
2087 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
2088 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
2089 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
2090 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
2091 |
< |
autoconf / configure method of configuring OOPSE |
2086 |
> |
samples/minimizer/argon/Makefile, |
2087 |
> |
samples/minimizer/argon/Makefile.in, |
2088 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
2089 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
2090 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
2091 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
2092 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
2093 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
2094 |
> |
method of configuring OOPSE |
2095 |
|
|
2096 |
|
2003-09-04 16:48 mmeineke |
2097 |
|
|
2119 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
2120 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
2121 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
858 |
– |
|
859 |
– |
2003-08-28 11:59 mmeineke |
860 |
– |
|
861 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
862 |
– |
added the first functional parts of the PairCorrType Abstract |
863 |
– |
classes. |
2122 |
|
|
2123 |
|
2003-08-27 14:23 tim |
2124 |
|
|
2390 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
2391 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
2392 |
|
works..... |
1135 |
– |
|
1136 |
– |
2003-08-08 13:32 mmeineke |
2393 |
|
|
1138 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
1139 |
– |
moved frameCount's functionality into DumpReader. also split props |
1140 |
– |
into staticProps and dynamicProps. (currently only have |
1141 |
– |
staticProps) |
1142 |
– |
|
2394 |
|
2003-08-08 12:48 mmeineke |
2395 |
|
|
2396 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
2447 |
|
2003-07-29 11:32 mmeineke |
2448 |
|
|
2449 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
2450 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2451 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
1201 |
< |
src/Makefile: working on the props code |
2450 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
2451 |
> |
working on the props code |
2452 |
|
|
2453 |
|
2003-07-29 11:32 mmeineke |
2454 |
|
|
2680 |
|
2003-07-14 18:06 gezelter |
2681 |
|
|
2682 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2683 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2684 |
< |
for samples |
2683 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2684 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2685 |
> |
water/init_ssd.eor: Fixes for samples |
2686 |
|
|
2687 |
|
2003-07-14 18:06 gezelter |
2688 |
|
|
3355 |
|
|
3356 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
3357 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
3358 |
< |
samples/argon/argon.bass: more bug fixes.... |
3358 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
3359 |
> |
bug fixes.... |
3360 |
|
|
3361 |
|
2003-04-01 11:49 mmeineke |
3362 |
|
|
3563 |
|
2003-03-26 10:37 chuckv |
3564 |
|
|
3565 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3566 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
3566 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3567 |
> |
for Parallel thermalization |
3568 |
|
|
3569 |
|
2003-03-26 09:55 mmeineke |
3570 |
|
|
3578 |
|
|
3579 |
|
2003-03-25 09:29 mmeineke |
3580 |
|
|
3581 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
3581 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3582 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3583 |
|
|
3584 |
|
2003-03-25 09:29 mmeineke |
3588 |
|
|
3589 |
|
2003-03-24 20:07 gezelter |
3590 |
|
|
3591 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
3591 |
> |
* samples/Makefile: moving tests to samples |
3592 |
|
|
3593 |
|
2003-03-24 20:06 gezelter |
3594 |
|
|
3595 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
3596 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
3597 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
3598 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
3599 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
3600 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
3601 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
3602 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
2350 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
2351 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
2352 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
2353 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
2354 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
2355 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
2356 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
2357 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
2358 |
< |
tests/water/water.mdl: moved tests to samples |
3595 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
3596 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3597 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3598 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3599 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3600 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3601 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3602 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
3603 |
|
|
3604 |
|
2003-03-24 19:51 gezelter |
3605 |
|
|
3607 |
|
|
3608 |
|
2003-03-24 19:46 gezelter |
3609 |
|
|
3610 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
2367 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
2368 |
< |
Added makefiles in tests directories |
3610 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
3611 |
|
|
3612 |
|
2003-03-24 16:55 gezelter |
3613 |
|
|
3624 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
3625 |
|
do_Forces.F90: little bug fixes here and there |
3626 |
|
|
2385 |
– |
2003-03-24 11:04 mmeineke |
2386 |
– |
|
2387 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
2388 |
– |
test simulation |
2389 |
– |
|
2390 |
– |
2003-03-24 11:02 mmeineke |
2391 |
– |
|
2392 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
2393 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
2394 |
– |
water/water.mdl: [no log message] |
2395 |
– |
|
2396 |
– |
2003-03-24 11:02 mmeineke |
2397 |
– |
|
2398 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
2399 |
– |
some test bass files for experimenting with |
2400 |
– |
|
3627 |
|
2003-03-24 10:26 mmeineke |
3628 |
|
|
3629 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |