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 |
1083 |
|
|
1084 |
|
2004-01-27 14:38 gezelter |
1085 |
|
|
1086 |
< |
* samples/argon/argon.bass: Longer run time to test argon |
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 |
|
|
1301 |
|
2004-01-12 15:37 tim |
1302 |
|
|
1303 |
|
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
1304 |
< |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
1305 |
< |
master nodes |
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 |
|
|
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 |
|
|
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 |
|
|
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 |
|
|
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, water/Makefile, |
3600 |
< |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
3601 |
< |
samples |
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 |
|
|
3733 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3734 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3735 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3736 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3737 |
< |
revision |
3736 |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3737 |
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Tree |
3738 |
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3739 |
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2003-03-21 12:42 mmeineke |
3740 |
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3791 |
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libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3792 |
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libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3793 |
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libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3794 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3795 |
< |
Tree |
3794 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3795 |
> |
revision |
3796 |
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