1 |
+ |
2004-04-14 12:20 chrisfen |
2 |
+ |
|
3 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
4 |
+ |
|
5 |
+ |
2004-04-14 11:32 gezelter |
6 |
+ |
|
7 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
8 |
+ |
|
9 |
+ |
2004-04-14 10:37 tim |
10 |
+ |
|
11 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
12 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
13 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
14 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
15 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
16 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
17 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
18 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
19 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
20 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
21 |
+ |
Change DumpWriter and InitFromFile |
22 |
+ |
|
23 |
+ |
2004-04-13 11:26 gezelter |
24 |
+ |
|
25 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
26 |
+ |
molecules can keep track of their own IntegrableObjects (and |
27 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
28 |
+ |
RigidBodies (which was done incorrectly before). |
29 |
+ |
|
30 |
+ |
2004-04-13 11:25 gezelter |
31 |
+ |
|
32 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
33 |
+ |
(will back out momentarily) |
34 |
+ |
|
35 |
+ |
2004-04-13 10:10 gezelter |
36 |
+ |
|
37 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
38 |
+ |
Those were old. |
39 |
+ |
|
40 |
+ |
2004-04-13 10:09 gezelter |
41 |
+ |
|
42 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
43 |
+ |
to add IntegrableObjects |
44 |
+ |
|
45 |
+ |
2004-04-12 16:02 gezelter |
46 |
+ |
|
47 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
48 |
+ |
|
49 |
+ |
2004-04-12 15:32 gezelter |
50 |
+ |
|
51 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
52 |
+ |
test run |
53 |
+ |
|
54 |
+ |
2004-04-12 15:32 gezelter |
55 |
+ |
|
56 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
57 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
58 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
59 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
60 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
61 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
62 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
63 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
64 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
65 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
66 |
+ |
(Somewhat extensive) |
67 |
+ |
|
68 |
+ |
2004-04-12 15:31 gezelter |
69 |
+ |
|
70 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
71 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
72 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
73 |
+ |
Changes for RigidBody dynamics |
74 |
+ |
|
75 |
+ |
2004-03-17 09:22 tim |
76 |
+ |
|
77 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
78 |
+ |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
79 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
80 |
+ |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
81 |
+ |
does not sound a good choice, next commit will seperate SMD and |
82 |
+ |
ZConstraint |
83 |
+ |
|
84 |
+ |
2004-03-16 14:22 tim |
85 |
+ |
|
86 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
87 |
+ |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
88 |
+ |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
89 |
+ |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
90 |
+ |
now can support sequential moving. Refactorying is needed to |
91 |
+ |
support SMD in ZConstraint |
92 |
+ |
|
93 |
+ |
2004-03-02 15:32 tim |
94 |
+ |
|
95 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
96 |
+ |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
97 |
+ |
support large file |
98 |
+ |
|
99 |
+ |
2004-03-01 16:17 tim |
100 |
+ |
|
101 |
+ |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
102 |
+ |
|
103 |
+ |
2004-03-01 15:01 tim |
104 |
+ |
|
105 |
+ |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
106 |
+ |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
107 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
108 |
+ |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
109 |
+ |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
110 |
+ |
program which can be used to replace atom type for zconstraint into |
111 |
+ |
OOPSE |
112 |
+ |
|
113 |
+ |
2004-02-24 11:36 tim |
114 |
+ |
|
115 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
116 |
+ |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
117 |
+ |
message] |
118 |
+ |
|
119 |
+ |
2004-02-24 10:49 tim |
120 |
+ |
|
121 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
122 |
+ |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
123 |
+ |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
124 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
125 |
+ |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
126 |
+ |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
127 |
+ |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
128 |
+ |
|
129 |
+ |
2004-02-24 10:44 tim |
130 |
+ |
|
131 |
+ |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
132 |
+ |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
133 |
+ |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
134 |
+ |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
135 |
+ |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
136 |
+ |
compose to implement Minimizer both versions are working |
137 |
+ |
|
138 |
+ |
2004-02-17 14:23 tim |
139 |
+ |
|
140 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
141 |
+ |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
142 |
+ |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
143 |
+ |
libmdtools/MinimizerParameterSet.hpp, |
144 |
+ |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
145 |
+ |
to remove the constraint force along bond direction |
146 |
+ |
|
147 |
+ |
2004-02-10 16:33 tim |
148 |
+ |
|
149 |
+ |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
150 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
151 |
+ |
single version of energy minimization is working. |
152 |
+ |
|
153 |
+ |
2004-02-09 15:38 mmeineke |
154 |
+ |
|
155 |
+ |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
156 |
+ |
the massive memory overusage by OOPSE |
157 |
+ |
|
158 |
+ |
2004-02-09 09:48 chrisfen |
159 |
+ |
|
160 |
+ |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
161 |
+ |
hardwired LJ_rcut |
162 |
+ |
|
163 |
+ |
2004-02-06 19:14 tim |
164 |
+ |
|
165 |
+ |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
166 |
+ |
message] |
167 |
+ |
|
168 |
+ |
2004-02-06 16:37 tim |
169 |
+ |
|
170 |
+ |
* ChangeLog, libBASS/Globals.cpp, |
171 |
+ |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
172 |
+ |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
173 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
174 |
+ |
energy minimization for argon is working, need to add constraint |
175 |
+ |
|
176 |
+ |
2004-02-06 14:05 tim |
177 |
+ |
|
178 |
+ |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
179 |
+ |
one more file into Makefile.in |
180 |
+ |
|
181 |
+ |
2004-02-06 13:58 tim |
182 |
+ |
|
183 |
+ |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
184 |
+ |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
185 |
+ |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
186 |
+ |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
187 |
+ |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
188 |
+ |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
189 |
+ |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
190 |
+ |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
191 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
192 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
193 |
+ |
some lines into global.cpp to make it work with energy minimization |
194 |
+ |
|
195 |
+ |
2004-02-04 17:26 tim |
196 |
+ |
|
197 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
198 |
+ |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
199 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
200 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
201 |
+ |
Single version of conjugate gradient with golden search linesearch |
202 |
+ |
pass a couple of functions test. Brent's algorithm is still broken |
203 |
+ |
|
204 |
+ |
2004-02-03 17:54 tim |
205 |
+ |
|
206 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
207 |
+ |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
208 |
+ |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
209 |
+ |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
210 |
+ |
|
211 |
+ |
2004-02-03 15:47 tim |
212 |
+ |
|
213 |
+ |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
214 |
+ |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
215 |
+ |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
216 |
+ |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
217 |
+ |
SteepestDescent.hpp: [no log message] |
218 |
+ |
|
219 |
+ |
2004-02-03 15:43 tim |
220 |
+ |
|
221 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
222 |
+ |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
223 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
224 |
+ |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
225 |
+ |
constraint class |
226 |
+ |
|
227 |
+ |
2004-02-03 12:10 tim |
228 |
+ |
|
229 |
+ |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
230 |
+ |
|
231 |
+ |
2004-02-03 10:21 tim |
232 |
+ |
|
233 |
+ |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
234 |
+ |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
235 |
+ |
|
236 |
+ |
2004-02-02 15:29 tim |
237 |
+ |
|
238 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
239 |
+ |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
240 |
+ |
Adding GoldenSection and Brent LineSearch Method |
241 |
+ |
|
242 |
+ |
2004-01-30 16:47 tim |
243 |
+ |
|
244 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
245 |
+ |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
246 |
+ |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
247 |
+ |
MinimizerBase instead of a functor to do line seach |
248 |
+ |
|
249 |
+ |
2004-01-30 10:00 chrisfen |
250 |
+ |
|
251 |
+ |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
252 |
+ |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
253 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
254 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
255 |
+ |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
256 |
+ |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
257 |
+ |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
258 |
+ |
has a working WATER.cpp forcefield and parser. This involved |
259 |
+ |
changes to WATER.cpp and ForceFields amoung other files. One |
260 |
+ |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
261 |
+ |
This will be removed on the next commit... |
262 |
+ |
|
263 |
+ |
2004-01-29 18:00 gezelter |
264 |
+ |
|
265 |
+ |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
266 |
+ |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
267 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
268 |
+ |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
269 |
+ |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
270 |
+ |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
271 |
+ |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
272 |
+ |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
273 |
+ |
member list fixes for rigid bodies |
274 |
+ |
|
275 |
+ |
2004-01-29 16:44 tim |
276 |
+ |
|
277 |
+ |
* libmdtools/MinimizerParameterSet.hpp: Adding |
278 |
+ |
MinimizerParameterSet class. |
279 |
+ |
|
280 |
+ |
2004-01-28 17:44 tim |
281 |
+ |
|
282 |
+ |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
283 |
+ |
NLModel0 and NLModel1 |
284 |
+ |
|
285 |
+ |
2004-01-28 15:40 tim |
286 |
+ |
|
287 |
+ |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
288 |
+ |
of NLModel |
289 |
+ |
|
290 |
+ |
2004-01-27 15:34 gezelter |
291 |
+ |
|
292 |
+ |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
293 |
+ |
water.mdl file, updated ssd.bass to use new SSD name |
294 |
+ |
|
295 |
+ |
2004-01-27 15:34 gezelter |
296 |
+ |
|
297 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
298 |
+ |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
299 |
+ |
stuff |
300 |
+ |
|
301 |
+ |
2004-01-27 14:39 gezelter |
302 |
+ |
|
303 |
+ |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
304 |
+ |
|
305 |
+ |
2004-01-27 14:39 gezelter |
306 |
+ |
|
307 |
+ |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
308 |
+ |
|
309 |
+ |
2004-01-27 14:38 gezelter |
310 |
+ |
|
311 |
+ |
* samples/argon/argon.bass: Longer run time to test argon |
312 |
+ |
|
313 |
+ |
2004-01-27 14:38 gezelter |
314 |
+ |
|
315 |
+ |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
316 |
+ |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
317 |
+ |
morning |
318 |
+ |
|
319 |
+ |
2004-01-27 14:37 gezelter |
320 |
+ |
|
321 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
322 |
+ |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
323 |
+ |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
324 |
+ |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
325 |
+ |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
326 |
+ |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
327 |
+ |
do new rigidBody scheme |
328 |
+ |
|
329 |
+ |
2004-01-27 14:15 tim |
330 |
+ |
|
331 |
+ |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
332 |
+ |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
333 |
+ |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
334 |
+ |
constraint for Nonlinear Optimization Model |
335 |
+ |
|
336 |
+ |
2004-01-26 17:01 gezelter |
337 |
+ |
|
338 |
+ |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
339 |
+ |
Euler angles for orientation instead of unit vectors required |
340 |
+ |
changes in MoLocator |
341 |
+ |
|
342 |
+ |
2004-01-26 16:53 gezelter |
343 |
+ |
|
344 |
+ |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
345 |
+ |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
346 |
+ |
water/water.mdl: Changed orientation lines from unit vectors to |
347 |
+ |
euler angles |
348 |
+ |
|
349 |
+ |
2004-01-26 16:52 gezelter |
350 |
+ |
|
351 |
+ |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
352 |
+ |
|
353 |
+ |
2004-01-26 16:45 gezelter |
354 |
+ |
|
355 |
+ |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
356 |
+ |
use Euler angles in the following order: phi, theta, psi Removed |
357 |
+ |
the ability to set orientation using a unit vector |
358 |
+ |
|
359 |
+ |
2004-01-26 16:26 gezelter |
360 |
+ |
|
361 |
+ |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
362 |
+ |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
363 |
+ |
Euler angles in the following order: phi, theta, psi Removed the |
364 |
+ |
ability to set orientation using a unit vector |
365 |
+ |
|
366 |
+ |
2004-01-26 13:52 gezelter |
367 |
+ |
|
368 |
+ |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
369 |
+ |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
370 |
+ |
|
371 |
+ |
2004-01-22 12:34 chrisfen |
372 |
+ |
|
373 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
374 |
+ |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
375 |
+ |
Corrected spelling in several directories, and stated WATER.cpp |
376 |
+ |
|
377 |
+ |
2004-01-21 17:16 tim |
378 |
+ |
|
379 |
+ |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
380 |
+ |
NLOPModel.hpp: constraint class in energy minimization |
381 |
+ |
|
382 |
+ |
2004-01-20 15:34 tim |
383 |
+ |
|
384 |
+ |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
385 |
+ |
|
386 |
+ |
2004-01-20 15:32 tim |
387 |
+ |
|
388 |
+ |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
389 |
+ |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
390 |
+ |
|
391 |
+ |
2004-01-19 16:17 gezelter |
392 |
+ |
|
393 |
+ |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
394 |
+ |
more user-friendly |
395 |
+ |
|
396 |
+ |
2004-01-19 13:51 chrisfen |
397 |
+ |
|
398 |
+ |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
399 |
+ |
|
400 |
+ |
2004-01-19 13:36 tim |
401 |
+ |
|
402 |
+ |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
403 |
+ |
time, status time, thermal time and reset time are not divisible by |
404 |
+ |
dt |
405 |
+ |
|
406 |
+ |
2004-01-19 11:10 gezelter |
407 |
+ |
|
408 |
+ |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
409 |
+ |
won't complain |
410 |
+ |
|
411 |
+ |
2004-01-19 11:10 gezelter |
412 |
+ |
|
413 |
+ |
* samples/lipid/5x5.bass: Fixed old bass file |
414 |
+ |
|
415 |
+ |
2004-01-19 11:09 gezelter |
416 |
+ |
|
417 |
+ |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
418 |
+ |
required a change in how the MoleculeStamps are used by divideLabor |
419 |
+ |
in mpiSimulation.cpp |
420 |
+ |
|
421 |
+ |
2004-01-19 11:08 gezelter |
422 |
+ |
|
423 |
+ |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
424 |
+ |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
425 |
+ |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
426 |
+ |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
427 |
+ |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
428 |
+ |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
429 |
+ |
|
430 |
+ |
2004-01-16 16:55 tim |
431 |
+ |
|
432 |
+ |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
433 |
+ |
eor file |
434 |
+ |
|
435 |
+ |
2004-01-16 16:51 mmeineke |
436 |
+ |
|
437 |
+ |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
438 |
+ |
write eor files |
439 |
+ |
|
440 |
+ |
2004-01-16 10:01 mmeineke |
441 |
+ |
|
442 |
+ |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
443 |
+ |
initialization of the AtomStruct |
444 |
+ |
|
445 |
+ |
2004-01-15 16:57 chuckv |
446 |
+ |
|
447 |
+ |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
448 |
+ |
|
449 |
+ |
2004-01-15 10:51 gezelter |
450 |
+ |
|
451 |
+ |
* ac-tools/aclocal.m4: Changes for altivec |
452 |
+ |
|
453 |
+ |
2004-01-15 09:22 gezelter |
454 |
+ |
|
455 |
+ |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
456 |
+ |
|
457 |
+ |
2004-01-14 23:33 gezelter |
458 |
+ |
|
459 |
+ |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
460 |
+ |
|
461 |
+ |
2004-01-14 20:14 gezelter |
462 |
+ |
|
463 |
+ |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
464 |
+ |
notifyCutoffs.F90: More work for adding charges |
465 |
+ |
|
466 |
+ |
2004-01-14 17:41 gezelter |
467 |
+ |
|
468 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
469 |
+ |
src/Makefile.in: autoconf fixes |
470 |
+ |
|
471 |
+ |
2004-01-14 11:28 mmeineke |
472 |
+ |
|
473 |
+ |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
474 |
+ |
|
475 |
+ |
2004-01-14 10:48 gezelter |
476 |
+ |
|
477 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
478 |
+ |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
479 |
+ |
changes for icc8 |
480 |
+ |
|
481 |
+ |
2004-01-13 18:01 gezelter |
482 |
+ |
|
483 |
+ |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
484 |
+ |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
485 |
+ |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
486 |
+ |
Changes for adding direct charge-charge interactions (with |
487 |
+ |
switching function) |
488 |
+ |
|
489 |
+ |
2004-01-13 17:34 gezelter |
490 |
+ |
|
491 |
+ |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
492 |
+ |
oopseMPI_module.F90: Some changes for new MPI organization and |
493 |
+ |
direct charge-charge interactions |
494 |
+ |
|
495 |
+ |
2004-01-13 17:11 tim |
496 |
+ |
|
497 |
+ |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
498 |
+ |
|
499 |
+ |
2004-01-13 16:22 tim |
500 |
+ |
|
501 |
+ |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
502 |
+ |
|
503 |
+ |
2004-01-13 15:35 tim |
504 |
+ |
|
505 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
506 |
+ |
eor file whenever it is used instead of rewinding it |
507 |
+ |
|
508 |
+ |
2004-01-13 15:04 tim |
509 |
+ |
|
510 |
+ |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
511 |
+ |
of writeFrame |
512 |
+ |
|
513 |
+ |
2004-01-13 10:46 tim |
514 |
+ |
|
515 |
+ |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
516 |
+ |
Merge the code of writeFinal and writeDump; |
517 |
+ |
Adding sortingIndex into DumpWriter; |
518 |
+ |
Fix a bug of writing last frame twice in integrator |
519 |
+ |
|
520 |
+ |
2004-01-12 17:54 tim |
521 |
+ |
|
522 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
523 |
+ |
a bug in copying string |
524 |
+ |
|
525 |
+ |
2004-01-12 15:37 tim |
526 |
+ |
|
527 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
528 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
529 |
+ |
master nodes |
530 |
+ |
|
531 |
+ |
2004-01-10 04:46 tim |
532 |
+ |
|
533 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
534 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
535 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
536 |
+ |
|
537 |
+ |
2004-01-09 21:15 tim |
538 |
+ |
|
539 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
540 |
+ |
|
541 |
+ |
2004-01-09 15:29 gezelter |
542 |
+ |
|
543 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
544 |
+ |
|
545 |
+ |
2004-01-08 17:25 chuckv |
546 |
+ |
|
547 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
548 |
+ |
|
549 |
+ |
2004-01-08 13:59 gezelter |
550 |
+ |
|
551 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
552 |
+ |
case |
553 |
+ |
|
554 |
+ |
2004-01-08 13:13 mmeineke |
555 |
+ |
|
556 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
557 |
+ |
state bug. |
558 |
+ |
|
559 |
+ |
2004-01-08 13:05 gezelter |
560 |
+ |
|
561 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
562 |
+ |
|
563 |
+ |
2004-01-08 12:57 mmeineke |
564 |
+ |
|
565 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
566 |
+ |
exstended state bug |
567 |
+ |
|
568 |
+ |
2004-01-08 12:40 gezelter |
569 |
+ |
|
570 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
571 |
+ |
|
572 |
+ |
2004-01-08 10:44 mmeineke |
573 |
+ |
|
574 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
575 |
+ |
XS state info flag |
576 |
+ |
|
577 |
+ |
2004-01-07 14:26 tim |
578 |
+ |
|
579 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
580 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
581 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
582 |
+ |
InitializeFromFile.cpp |
583 |
+ |
|
584 |
+ |
2004-01-06 14:49 chuckv |
585 |
+ |
|
586 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
587 |
+ |
performance fixes in the dipole dipole and reaction field code |
588 |
+ |
|
589 |
+ |
2004-01-06 13:54 chuckv |
590 |
+ |
|
591 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
592 |
+ |
little more sane |
593 |
+ |
|
594 |
+ |
2004-01-05 17:49 chuckv |
595 |
+ |
|
596 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
597 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
598 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
599 |
+ |
performance by reducing spurious function calls |
600 |
+ |
|
601 |
+ |
2004-01-05 17:18 chuckv |
602 |
+ |
|
603 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
604 |
+ |
|
605 |
+ |
2004-01-05 17:18 chuckv |
606 |
+ |
|
607 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
608 |
+ |
|
609 |
+ |
2004-01-05 17:12 chuckv |
610 |
+ |
|
611 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
612 |
+ |
|
613 |
+ |
2004-01-05 16:00 chuckv |
614 |
+ |
|
615 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
616 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
617 |
+ |
lookup |
618 |
+ |
|
619 |
+ |
2003-12-29 14:56 chuckv |
620 |
+ |
|
621 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
622 |
+ |
third-party directory for code not written by us. Also added |
623 |
+ |
Mersenne Twister random number generator code. This will eventually |
624 |
+ |
replace sprng as the random number generator used by OOPSE. |
625 |
+ |
|
626 |
+ |
2003-12-22 16:26 chuckv |
627 |
+ |
|
628 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
629 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
630 |
+ |
Fixes to profile code. |
631 |
+ |
|
632 |
+ |
2003-12-19 15:36 mmeineke |
633 |
+ |
|
634 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
635 |
+ |
timing.F90, timing.f90: More profiling fixes. |
636 |
+ |
|
637 |
+ |
2003-12-19 15:19 chuckv |
638 |
+ |
|
639 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
640 |
+ |
|
641 |
+ |
2003-12-19 15:17 chuckv |
642 |
+ |
|
643 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
644 |
+ |
|
645 |
+ |
2003-12-19 13:53 mmeineke |
646 |
+ |
|
647 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
648 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
649 |
+ |
the code |
650 |
+ |
|
651 |
+ |
2003-12-19 12:25 mmeineke |
652 |
+ |
|
653 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
654 |
+ |
some profiling routines |
655 |
+ |
|
656 |
+ |
2003-12-19 10:12 mmeineke |
657 |
+ |
|
658 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
659 |
+ |
and GofRomega |
660 |
+ |
|
661 |
+ |
additional work on randomBilayer |
662 |
+ |
|
663 |
+ |
2003-12-19 10:12 mmeineke |
664 |
+ |
|
665 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
666 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
667 |
+ |
GofRomega |
668 |
+ |
|
669 |
+ |
2003-12-18 16:47 mmeineke |
670 |
+ |
|
671 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
672 |
+ |
some profile functionality |
673 |
+ |
|
674 |
+ |
2003-12-18 15:46 chuckv |
675 |
+ |
|
676 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
677 |
+ |
Added functions for simple profiling in fortran. |
678 |
+ |
|
679 |
+ |
2003-12-17 15:13 chuckv |
680 |
+ |
|
681 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
682 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
683 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
684 |
+ |
zeros the array between scatters so half of the sum was being lost. |
685 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
686 |
+ |
nlocal. |
687 |
+ |
|
688 |
+ |
2003-12-16 15:49 mmeineke |
689 |
+ |
|
690 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
691 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
692 |
+ |
gofRomega. both need to be debugged and tested. |
693 |
+ |
|
694 |
+ |
2003-12-12 10:42 gezelter |
695 |
+ |
|
696 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
697 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
698 |
+ |
gradients (to do minimizations) |
699 |
+ |
|
700 |
+ |
2003-12-12 10:33 mmeineke |
701 |
+ |
|
702 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
703 |
+ |
header |
704 |
+ |
|
705 |
+ |
2003-12-10 11:52 mmeineke |
706 |
+ |
|
707 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
708 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
709 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
710 |
+ |
from bilayerSys to randomBilayer |
711 |
+ |
|
712 |
+ |
2003-11-25 10:44 mmeineke |
713 |
+ |
|
714 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
715 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
716 |
+ |
TB3 in DUFF.frc |
717 |
+ |
|
718 |
+ |
2003-11-21 15:09 mmeineke |
719 |
+ |
|
720 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
721 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
722 |
+ |
message in SimInfo. Added a more informative error message in |
723 |
+ |
InitializeFromFile |
724 |
+ |
|
725 |
+ |
2003-11-21 15:07 mmeineke |
726 |
+ |
|
727 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
728 |
+ |
ing in the GofR,CosTheta |
729 |
+ |
|
730 |
+ |
2003-11-21 14:31 chrisfen |
731 |
+ |
|
732 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
733 |
+ |
a bug in SimInfo ordering of radii |
734 |
+ |
|
735 |
+ |
2003-11-11 12:20 mmeineke |
736 |
+ |
|
737 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
738 |
+ |
a min function. |
739 |
+ |
|
740 |
+ |
2003-11-10 16:50 mmeineke |
741 |
+ |
|
742 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
743 |
+ |
reordered the rcut/ecr/boxSize initialization |
744 |
+ |
|
745 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
746 |
+ |
now exit when it runs into rcut or ecr. |
747 |
+ |
|
748 |
+ |
2003-11-07 16:46 chuckv |
749 |
+ |
|
750 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
751 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
752 |
+ |
use of mpich modules. We use mpif.h instead.: |
753 |
+ |
|
754 |
+ |
2003-11-07 12:09 mmeineke |
755 |
+ |
|
756 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
757 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
758 |
+ |
the atom loop in the NPT family of integrators. |
759 |
+ |
|
760 |
+ |
2003-11-06 17:01 mmeineke |
761 |
+ |
|
762 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
763 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
764 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
765 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
766 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
767 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
768 |
+ |
* useIntiTime => useInitialTime |
769 |
+ |
|
770 |
+ |
2003-11-06 14:24 mmeineke |
771 |
+ |
|
772 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
773 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
774 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
775 |
+ |
|
776 |
+ |
2003-11-06 14:11 mmeineke |
777 |
+ |
|
778 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
779 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
780 |
+ |
new-templateless branch to the main trunk. |
781 |
+ |
|
782 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
783 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
784 |
+ |
sudden deaths we saw. * some formating in the string when we |
785 |
+ |
write out the extended system state. * added NPT.cpp to the |
786 |
+ |
makefile.in |
787 |
+ |
|
788 |
+ |
2003-11-06 13:20 mmeineke |
789 |
+ |
|
790 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
791 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
792 |
+ |
bug. The box was not switching between orthorhombic and |
793 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
794 |
+ |
the check.which should fix it. |
795 |
+ |
|
796 |
+ |
2003-11-05 14:16 mmeineke |
797 |
+ |
|
798 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
799 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
800 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
801 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
802 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
803 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
804 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
805 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
806 |
+ |
some work on trying to find the compression bug |
807 |
+ |
|
808 |
+ |
2003-11-03 17:07 mmeineke |
809 |
+ |
|
810 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
811 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
812 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
813 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
814 |
+ |
most of standard template library from OOPSE. |
815 |
+ |
|
816 |
+ |
2003-10-31 16:06 mmeineke |
817 |
+ |
|
818 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
819 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
820 |
+ |
SimSetup.cpp: started work on template removal. |
821 |
+ |
|
822 |
+ |
2003-10-31 13:28 mmeineke |
823 |
+ |
|
824 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
825 |
+ |
added template stuff to the Maikefile template |
826 |
+ |
|
827 |
+ |
little changes to some printf format statements |
828 |
+ |
|
829 |
+ |
2003-10-31 13:28 mmeineke |
830 |
+ |
|
831 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
832 |
+ |
template |
833 |
+ |
|
834 |
+ |
2003-10-30 13:59 gezelter |
835 |
+ |
|
836 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
837 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
838 |
+ |
rList problems |
839 |
+ |
|
840 |
+ |
2003-10-30 09:11 gezelter |
841 |
+ |
|
842 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
843 |
+ |
queried before q0 was allocated. |
844 |
+ |
|
845 |
+ |
2003-10-29 15:41 mmeineke |
846 |
+ |
|
847 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
848 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
849 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
850 |
+ |
in bass.l |
851 |
+ |
|
852 |
+ |
fixed a little bug in the first time step, regarding the setting of |
853 |
+ |
ecr and est in fortran |
854 |
+ |
|
855 |
+ |
2003-10-29 15:40 mmeineke |
856 |
+ |
|
857 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
858 |
+ |
|
859 |
+ |
2003-10-29 12:55 mmeineke |
860 |
+ |
|
861 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
862 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
863 |
+ |
rcut is setup, as well as additional debugging comments. |
864 |
+ |
|
865 |
+ |
2003-10-29 09:28 gezelter |
866 |
+ |
|
867 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
868 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
869 |
+ |
templates |
870 |
+ |
|
871 |
+ |
2003-10-28 22:16 gezelter |
872 |
+ |
|
873 |
+ |
* src/Makefile.in: Refixed broken makefile |
874 |
+ |
|
875 |
+ |
2003-10-28 22:06 gezelter |
876 |
+ |
|
877 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
878 |
+ |
fixes |
879 |
+ |
|
880 |
+ |
2003-10-28 19:19 tim |
881 |
+ |
|
882 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
883 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
884 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
885 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
886 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
887 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
888 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
889 |
+ |
file. |
890 |
+ |
|
891 |
+ |
2003-10-28 17:25 mmeineke |
892 |
+ |
|
893 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
894 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
895 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
896 |
+ |
how c calls fortran. All function pointers and fortran calls are |
897 |
+ |
rigidly typecast now. |
898 |
+ |
|
899 |
+ |
2003-10-28 15:42 gezelter |
900 |
+ |
|
901 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
902 |
+ |
Portability fixes |
903 |
+ |
|
904 |
+ |
2003-10-28 15:09 gezelter |
905 |
+ |
|
906 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
907 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
908 |
+ |
src/Makefile.in: Compatibility fixes |
909 |
+ |
|
910 |
+ |
2003-10-28 12:08 mmeineke |
911 |
+ |
|
912 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
913 |
+ |
started work on template removal |
914 |
+ |
|
915 |
+ |
2003-10-28 12:04 gezelter |
916 |
+ |
|
917 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
918 |
+ |
trying to understand extern "C" stuff for pointers |
919 |
+ |
|
920 |
+ |
2003-10-28 11:20 gezelter |
921 |
+ |
|
922 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
923 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
924 |
+ |
|
925 |
+ |
2003-10-28 11:03 gezelter |
926 |
+ |
|
927 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
928 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
929 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
930 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
931 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
932 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
933 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
934 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
935 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
936 |
+ |
more portable c header stuff Also, mod file fixes and portability |
937 |
+ |
changes Some fortran changes will need to be reversed. |
938 |
+ |
|
939 |
+ |
2003-10-28 11:03 gezelter |
940 |
+ |
|
941 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
942 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
943 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
944 |
+ |
portable c header stuff Also, mod file fixes and portability |
945 |
+ |
changes |
946 |
+ |
|
947 |
+ |
2003-10-28 11:02 gezelter |
948 |
+ |
|
949 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
950 |
+ |
stuff |
951 |
+ |
|
952 |
+ |
2003-10-27 18:00 gezelter |
953 |
+ |
|
954 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
955 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
956 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
957 |
+ |
|
958 |
+ |
2003-10-27 17:08 mmeineke |
959 |
+ |
|
960 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
961 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
962 |
+ |
added routines for the sysbuilder to work with simSetup |
963 |
+ |
|
964 |
+ |
remved the QuickBass routines, and had all parsing go through |
965 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
966 |
+ |
|
967 |
+ |
2003-10-27 17:07 mmeineke |
968 |
+ |
|
969 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
970 |
+ |
routines for the sysbuilder to work with simSetup |
971 |
+ |
|
972 |
+ |
2003-10-27 11:20 gezelter |
973 |
+ |
|
974 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
975 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
976 |
+ |
|
977 |
+ |
2003-10-24 17:17 mmeineke |
978 |
+ |
|
979 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
980 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
981 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
982 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
983 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
984 |
+ |
from the Makefile |
985 |
+ |
|
986 |
+ |
2003-10-24 12:36 gezelter |
987 |
+ |
|
988 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
989 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
990 |
+ |
builder |
991 |
+ |
|
992 |
+ |
2003-10-24 12:35 gezelter |
993 |
+ |
|
994 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
995 |
+ |
merge problem |
996 |
+ |
|
997 |
+ |
2003-10-23 14:57 mmeineke |
998 |
+ |
|
999 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
1000 |
+ |
init |
1001 |
+ |
|
1002 |
+ |
fixed an eam mpi parmeter setup bug |
1003 |
+ |
|
1004 |
+ |
added the init file to the makefile |
1005 |
+ |
|
1006 |
+ |
2003-10-23 14:57 mmeineke |
1007 |
+ |
|
1008 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1009 |
+ |
to the init |
1010 |
+ |
|
1011 |
+ |
fixed an eam mpi parmeter setup bug |
1012 |
+ |
|
1013 |
+ |
2003-10-23 14:57 mmeineke |
1014 |
+ |
|
1015 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
1016 |
+ |
|
1017 |
+ |
2003-10-22 16:17 mmeineke |
1018 |
+ |
|
1019 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1020 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1021 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1022 |
+ |
no box skew allowed. |
1023 |
+ |
|
1024 |
+ |
2003-10-21 14:33 mmeineke |
1025 |
+ |
|
1026 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1027 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1028 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1029 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
1030 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
1031 |
+ |
true; |
1032 |
+ |
|
1033 |
+ |
2003-10-17 16:19 mmeineke |
1034 |
+ |
|
1035 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1036 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1037 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1038 |
+ |
to the build list for both configure and configure.in |
1039 |
+ |
|
1040 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
1041 |
+ |
working. |
1042 |
+ |
|
1043 |
+ |
2003-10-17 16:18 mmeineke |
1044 |
+ |
|
1045 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
1046 |
+ |
build list for both configure and configure.in |
1047 |
+ |
|
1048 |
+ |
2003-10-17 16:17 mmeineke |
1049 |
+ |
|
1050 |
+ |
* configure: added the staticProps directory to the build list |
1051 |
+ |
|
1052 |
+ |
2003-10-16 14:16 mmeineke |
1053 |
+ |
|
1054 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1055 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1056 |
+ |
use linked lists instead of a vector. |
1057 |
+ |
|
1058 |
+ |
Fixed the makefile to build DumpReader.cpp |
1059 |
+ |
|
1060 |
+ |
Removed a comment output in Exclude.cpp |
1061 |
+ |
|
1062 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
1063 |
+ |
a frame is written. This lets the .eor file represent the last |
1064 |
+ |
written frame of a simulation. |
1065 |
+ |
|
1066 |
+ |
2003-10-10 12:10 mmeineke |
1067 |
+ |
|
1068 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1069 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1070 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1071 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
1072 |
+ |
over to staticProps |
1073 |
+ |
|
1074 |
+ |
2003-10-09 17:09 mmeineke |
1075 |
+ |
|
1076 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1077 |
+ |
a position where it will compile and run first runs. |
1078 |
+ |
|
1079 |
+ |
2003-10-04 13:46 chuckv |
1080 |
+ |
|
1081 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1082 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1083 |
+ |
|
1084 |
+ |
2003-10-04 13:08 chuckv |
1085 |
+ |
|
1086 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
1087 |
+ |
|
1088 |
+ |
2003-10-03 17:11 mmeineke |
1089 |
+ |
|
1090 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1091 |
+ |
entahlpy from the statwriter and thermo. |
1092 |
+ |
|
1093 |
+ |
2003-10-03 17:02 mmeineke |
1094 |
+ |
|
1095 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1096 |
+ |
statements in simError |
1097 |
+ |
|
1098 |
+ |
added a function to get the maxCutoff |
1099 |
+ |
|
1100 |
+ |
2003-10-03 17:01 mmeineke |
1101 |
+ |
|
1102 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
1103 |
+ |
statements in simError |
1104 |
+ |
|
1105 |
+ |
2003-09-30 11:00 mmeineke |
1106 |
+ |
|
1107 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1108 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
1109 |
+ |
|
1110 |
+ |
2003-09-29 17:06 mmeineke |
1111 |
+ |
|
1112 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1113 |
+ |
for conifig.in |
1114 |
+ |
|
1115 |
+ |
fixed wrappers to extern "C" |
1116 |
+ |
|
1117 |
+ |
2003-09-29 17:06 mmeineke |
1118 |
+ |
|
1119 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
1120 |
+ |
conifig.in |
1121 |
+ |
|
1122 |
+ |
2003-09-29 17:05 mmeineke |
1123 |
+ |
|
1124 |
+ |
* configure: added mpif90 mod check back |
1125 |
+ |
|
1126 |
+ |
2003-09-29 16:16 mmeineke |
1127 |
+ |
|
1128 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1129 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1130 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1131 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1132 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1133 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1134 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1135 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1136 |
+ |
found with SUN's SUNWspro.s1s7 |
1137 |
+ |
|
1138 |
+ |
2003-09-29 12:38 mmeineke |
1139 |
+ |
|
1140 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
1141 |
+ |
signifigant change. |
1142 |
+ |
|
1143 |
+ |
2003-09-25 16:17 mmeineke |
1144 |
+ |
|
1145 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1146 |
+ |
additional remarks from icc -w3 (extra verbose output) |
1147 |
+ |
|
1148 |
+ |
2003-09-25 14:27 mmeineke |
1149 |
+ |
|
1150 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1151 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1152 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1153 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1154 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1155 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1156 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1157 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1158 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1159 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1160 |
+ |
gcc -Wall and g++ -Wall |
1161 |
+ |
|
1162 |
+ |
2003-09-25 13:54 gezelter |
1163 |
+ |
|
1164 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
1165 |
+ |
|
1166 |
+ |
2003-09-25 11:42 gezelter |
1167 |
+ |
|
1168 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1169 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1170 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1171 |
+ |
fixes for configure |
1172 |
+ |
|
1173 |
+ |
2003-09-24 14:34 mmeineke |
1174 |
+ |
|
1175 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1176 |
+ |
that it is called before the first Statistics are written. |
1177 |
+ |
|
1178 |
+ |
2003-09-23 15:36 gezelter |
1179 |
+ |
|
1180 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1181 |
+ |
bunch of Make.dep files to CVS |
1182 |
+ |
|
1183 |
+ |
2003-09-23 15:34 mmeineke |
1184 |
+ |
|
1185 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1186 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1187 |
+ |
|
1188 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
1189 |
+ |
|
1190 |
+ |
2003-09-22 18:07 tim |
1191 |
+ |
|
1192 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1193 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
1194 |
+ |
|
1195 |
+ |
2003-09-22 16:23 mmeineke |
1196 |
+ |
|
1197 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1198 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1199 |
+ |
Converted NPTf to work with the NPT base class. |
1200 |
+ |
|
1201 |
+ |
Removed NPTfm and NPTim from cvs |
1202 |
+ |
|
1203 |
+ |
2003-09-19 15:00 mmeineke |
1204 |
+ |
|
1205 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1206 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1207 |
+ |
class. NPTi is up to date. NPTf is not. |
1208 |
+ |
|
1209 |
+ |
2003-09-19 11:03 mmeineke |
1210 |
+ |
|
1211 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1212 |
+ |
makefile |
1213 |
+ |
|
1214 |
+ |
2003-09-19 11:01 gezelter |
1215 |
+ |
|
1216 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1217 |
+ |
|
1218 |
+ |
2003-09-19 11:01 gezelter |
1219 |
+ |
|
1220 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1221 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
1222 |
+ |
|
1223 |
+ |
2003-09-19 10:20 mmeineke |
1224 |
+ |
|
1225 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
1226 |
+ |
|
1227 |
+ |
2003-09-19 09:55 gezelter |
1228 |
+ |
|
1229 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1230 |
+ |
samples/water/ssd.bass: [no log message] |
1231 |
+ |
|
1232 |
+ |
2003-09-19 09:22 tim |
1233 |
+ |
|
1234 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1235 |
+ |
|
1236 |
+ |
2003-09-17 09:22 mmeineke |
1237 |
+ |
|
1238 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1239 |
+ |
work with constraints. |
1240 |
+ |
|
1241 |
+ |
2003-09-16 15:02 tim |
1242 |
+ |
|
1243 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1244 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1245 |
+ |
|
1246 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
1247 |
+ |
|
1248 |
+ |
NPTi appears very stable. |
1249 |
+ |
|
1250 |
+ |
2003-09-15 11:52 tim |
1251 |
+ |
|
1252 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1253 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1254 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1255 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1256 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1257 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1258 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1259 |
+ |
statWriter fix bug of vector wrapping at NPTi |
1260 |
+ |
|
1261 |
+ |
2003-09-12 11:20 gezelter |
1262 |
+ |
|
1263 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1264 |
+ |
Makefile.in |
1265 |
+ |
|
1266 |
+ |
2003-09-12 11:20 gezelter |
1267 |
+ |
|
1268 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1269 |
+ |
|
1270 |
+ |
2003-09-09 15:35 mmeineke |
1271 |
+ |
|
1272 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1273 |
+ |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
1274 |
+ |
|
1275 |
+ |
added two new NPT integrators, they still need work. |
1276 |
+ |
|
1277 |
+ |
2003-09-09 15:34 mmeineke |
1278 |
+ |
|
1279 |
+ |
* ChangeLog: updated the ChangeLog |
1280 |
+ |
|
1281 |
+ |
2003-09-05 17:45 gezelter |
1282 |
+ |
|
1283 |
+ |
* libmdtools/Make.dep: dependency on config.h |
1284 |
+ |
|
1285 |
+ |
2003-09-05 17:36 gezelter |
1286 |
+ |
|
1287 |
+ |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
1288 |
+ |
|
1289 |
+ |
2003-09-05 16:29 gezelter |
1290 |
+ |
|
1291 |
+ |
* samples/metals/Makefile.in: New Makefile for metals sample |
1292 |
+ |
|
1293 |
+ |
2003-09-05 16:27 gezelter |
1294 |
+ |
|
1295 |
+ |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
1296 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
1297 |
+ |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
1298 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
1299 |
+ |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
1300 |
+ |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
1301 |
+ |
libmdtools/Makefile, libmdtools/Makefile.in, |
1302 |
+ |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
1303 |
+ |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
1304 |
+ |
libmdtools/fortranWrappers.cpp, |
1305 |
+ |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
1306 |
+ |
libmdtools/simulation_module.F90, samples/Makefile, |
1307 |
+ |
samples/Makefile.in, samples/alkane/Makefile, |
1308 |
+ |
samples/alkane/Makefile.in, samples/argon/Makefile, |
1309 |
+ |
samples/argon/Makefile.in, samples/argon/argon.bass, |
1310 |
+ |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1311 |
+ |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1312 |
+ |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1313 |
+ |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1314 |
+ |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1315 |
+ |
autoconf / configure method of configuring OOPSE |
1316 |
+ |
|
1317 |
+ |
2003-09-04 16:48 mmeineke |
1318 |
+ |
|
1319 |
+ |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1320 |
+ |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
1321 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
1322 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
1323 |
+ |
added resetTime to the Global namespace. |
1324 |
+ |
|
1325 |
+ |
added ability to reset the integrators in the NVT and NPT family. |
1326 |
+ |
|
1327 |
+ |
2003-09-04 16:48 mmeineke |
1328 |
+ |
|
1329 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
1330 |
+ |
namespace. |
1331 |
+ |
|
1332 |
+ |
2003-09-02 09:30 tim |
1333 |
+ |
|
1334 |
+ |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
1335 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
1336 |
+ |
PolicyByMass |
1337 |
+ |
|
1338 |
+ |
2003-08-28 16:09 tim |
1339 |
+ |
|
1340 |
+ |
* ChangeLog, libmdtools/GenericData.cpp, |
1341 |
+ |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1342 |
+ |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1343 |
+ |
|
1344 |
+ |
2003-08-27 14:23 tim |
1345 |
+ |
|
1346 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1347 |
+ |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
1348 |
+ |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
1349 |
+ |
turn on the optimization flag, it causes a seg fault |
1350 |
+ |
|
1351 |
+ |
2003-08-27 11:25 gezelter |
1352 |
+ |
|
1353 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
1354 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
1355 |
+ |
stress tensor parallel bug. |
1356 |
+ |
|
1357 |
+ |
2003-08-27 11:16 tim |
1358 |
+ |
|
1359 |
+ |
* ChangeLog, libmdtools/DUFF.cpp, |
1360 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
1361 |
+ |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
1362 |
+ |
molMembershipList use global index instead of local index |
1363 |
+ |
|
1364 |
|
2003-08-26 15:37 tim |
1365 |
|
|
1366 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
1611 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1612 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1613 |
|
works..... |
251 |
– |
|
252 |
– |
2003-08-08 13:32 mmeineke |
1614 |
|
|
254 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
255 |
– |
moved frameCount's functionality into DumpReader. also split props |
256 |
– |
into staticProps and dynamicProps. (currently only have |
257 |
– |
staticProps) |
258 |
– |
|
1615 |
|
2003-08-08 12:48 mmeineke |
1616 |
|
|
1617 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1668 |
|
2003-07-29 11:32 mmeineke |
1669 |
|
|
1670 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1671 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1672 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
317 |
< |
src/Makefile: working on the props code |
1671 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1672 |
> |
working on the props code |
1673 |
|
|
1674 |
|
2003-07-29 11:32 mmeineke |
1675 |
|
|
2796 |
|
|
2797 |
|
2003-03-25 09:29 mmeineke |
2798 |
|
|
2799 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2799 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2800 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2801 |
|
|
2802 |
|
2003-03-25 09:29 mmeineke |
2950 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2951 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2952 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2953 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
2954 |
< |
Tree |
2953 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
2954 |
> |
revision |
2955 |
|
|
2956 |
|
2003-03-21 12:42 mmeineke |
2957 |
|
|
3008 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3009 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3010 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3011 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3012 |
< |
revision |
3011 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3012 |
> |
Tree |
3013 |
|
|