1 |
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2003-09-10 16:28 mmeineke |
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2004-04-22 16:33 tim |
2 |
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3 |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
4 |
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work on getting gofR working. |
3 |
> |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
4 |
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Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
5 |
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calculation of pressure tensor |
6 |
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|
7 |
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2003-09-09 16:50 mmeineke |
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2004-04-22 09:55 tim |
8 |
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|
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
10 |
< |
beginings of the GofR pair correlation. |
9 |
> |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
10 |
> |
another bug in InitFromFile. MPI verion of OOPSE is working again |
11 |
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|
12 |
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2004-04-21 22:29 tim |
13 |
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|
14 |
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* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
15 |
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InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
16 |
> |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
17 |
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bugs in MPI version of InitfromFile and one unmatch MPI command in |
18 |
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DumpWriter |
19 |
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|
20 |
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2004-04-21 00:32 tim |
21 |
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|
22 |
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* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
23 |
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libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
24 |
> |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
25 |
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useless files |
26 |
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|
27 |
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2004-04-20 11:56 tim |
28 |
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|
29 |
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* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
30 |
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SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
31 |
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velocitize at thermo |
32 |
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|
33 |
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2004-04-20 00:39 tim |
34 |
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|
35 |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
36 |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
37 |
> |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
38 |
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libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
39 |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
40 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
41 |
> |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
42 |
> |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
43 |
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|
44 |
> |
2004-04-19 17:13 gezelter |
45 |
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|
46 |
> |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
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Thermo.cpp: Fixed a charge bug |
48 |
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|
49 |
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2004-04-19 15:54 tim |
50 |
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|
51 |
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* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
52 |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
53 |
> |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
54 |
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a bug in CompositeVisitor which cause the double counting problem |
55 |
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|
56 |
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2004-04-19 12:44 tim |
57 |
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|
58 |
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* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
59 |
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libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
60 |
> |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
61 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
62 |
> |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
63 |
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Dump2XYZ is almost working except atoms in rigidbody are double |
64 |
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counted |
65 |
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|
66 |
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2004-04-18 22:52 tim |
67 |
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|
68 |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
69 |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
70 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
71 |
> |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
72 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
73 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
74 |
> |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
75 |
> |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
76 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
77 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
78 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
79 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
80 |
> |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
81 |
> |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
82 |
> |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
83 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
84 |
> |
implement of quickLate using visitor and composite pattern |
85 |
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|
86 |
> |
2004-04-15 17:15 tim |
87 |
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|
88 |
> |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
89 |
> |
exclude list |
90 |
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|
91 |
> |
2004-04-15 11:18 tim |
92 |
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|
93 |
> |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
94 |
> |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
95 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
96 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
97 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
98 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
99 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
100 |
> |
whole bunch of bugs :-) |
101 |
> |
|
102 |
> |
2004-04-14 12:20 chrisfen |
103 |
> |
|
104 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
105 |
> |
|
106 |
> |
2004-04-14 11:32 gezelter |
107 |
> |
|
108 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
109 |
> |
|
110 |
> |
2004-04-14 10:37 tim |
111 |
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|
112 |
> |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
113 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
114 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
115 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
116 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
117 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
118 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
119 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
120 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
121 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
122 |
> |
Change DumpWriter and InitFromFile |
123 |
> |
|
124 |
> |
2004-04-13 11:26 gezelter |
125 |
> |
|
126 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
127 |
> |
molecules can keep track of their own IntegrableObjects (and |
128 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
129 |
> |
RigidBodies (which was done incorrectly before). |
130 |
> |
|
131 |
> |
2004-04-13 11:25 gezelter |
132 |
> |
|
133 |
> |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
134 |
> |
(will back out momentarily) |
135 |
> |
|
136 |
> |
2004-04-13 10:10 gezelter |
137 |
> |
|
138 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
139 |
> |
Those were old. |
140 |
> |
|
141 |
> |
2004-04-13 10:09 gezelter |
142 |
> |
|
143 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
144 |
> |
to add IntegrableObjects |
145 |
> |
|
146 |
> |
2004-04-12 16:02 gezelter |
147 |
> |
|
148 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
149 |
> |
|
150 |
> |
2004-04-12 15:32 gezelter |
151 |
> |
|
152 |
> |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
153 |
> |
test run |
154 |
> |
|
155 |
> |
2004-04-12 15:32 gezelter |
156 |
> |
|
157 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
158 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
159 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
160 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
161 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
162 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
163 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
164 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
165 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
166 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
167 |
> |
(Somewhat extensive) |
168 |
> |
|
169 |
> |
2004-04-12 15:31 gezelter |
170 |
> |
|
171 |
> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
172 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
173 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
174 |
> |
Changes for RigidBody dynamics |
175 |
> |
|
176 |
> |
2004-03-17 09:22 tim |
177 |
> |
|
178 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
179 |
> |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
180 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
181 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
182 |
> |
does not sound a good choice, next commit will seperate SMD and |
183 |
> |
ZConstraint |
184 |
> |
|
185 |
> |
2004-03-16 14:22 tim |
186 |
> |
|
187 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
188 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
189 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
190 |
> |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
191 |
> |
now can support sequential moving. Refactorying is needed to |
192 |
> |
support SMD in ZConstraint |
193 |
> |
|
194 |
> |
2004-03-02 15:32 tim |
195 |
> |
|
196 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
197 |
> |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
198 |
> |
support large file |
199 |
> |
|
200 |
> |
2004-03-01 16:17 tim |
201 |
> |
|
202 |
> |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
203 |
> |
|
204 |
> |
2004-03-01 15:01 tim |
205 |
> |
|
206 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
207 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
208 |
> |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
209 |
> |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
210 |
> |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
211 |
> |
program which can be used to replace atom type for zconstraint into |
212 |
> |
OOPSE |
213 |
> |
|
214 |
> |
2004-02-24 11:36 tim |
215 |
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|
216 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
217 |
> |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
218 |
> |
message] |
219 |
> |
|
220 |
> |
2004-02-24 10:49 tim |
221 |
> |
|
222 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
223 |
> |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
224 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
225 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
226 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
227 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
228 |
> |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
229 |
> |
|
230 |
> |
2004-02-24 10:44 tim |
231 |
> |
|
232 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
233 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
234 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
235 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
236 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
237 |
> |
compose to implement Minimizer both versions are working |
238 |
> |
|
239 |
> |
2004-02-17 14:23 tim |
240 |
> |
|
241 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
242 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
243 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
244 |
> |
libmdtools/MinimizerParameterSet.hpp, |
245 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
246 |
> |
to remove the constraint force along bond direction |
247 |
> |
|
248 |
> |
2004-02-10 16:33 tim |
249 |
> |
|
250 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
251 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
252 |
> |
single version of energy minimization is working. |
253 |
> |
|
254 |
> |
2004-02-09 15:38 mmeineke |
255 |
> |
|
256 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
257 |
> |
the massive memory overusage by OOPSE |
258 |
> |
|
259 |
> |
2004-02-09 09:48 chrisfen |
260 |
> |
|
261 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
262 |
> |
hardwired LJ_rcut |
263 |
> |
|
264 |
> |
2004-02-06 19:14 tim |
265 |
> |
|
266 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
267 |
> |
message] |
268 |
> |
|
269 |
> |
2004-02-06 16:37 tim |
270 |
> |
|
271 |
> |
* ChangeLog, libBASS/Globals.cpp, |
272 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
273 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
274 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
275 |
> |
energy minimization for argon is working, need to add constraint |
276 |
> |
|
277 |
> |
2004-02-06 14:05 tim |
278 |
> |
|
279 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
280 |
> |
one more file into Makefile.in |
281 |
> |
|
282 |
> |
2004-02-06 13:58 tim |
283 |
> |
|
284 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
285 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
286 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
287 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
288 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
289 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
290 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
291 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
292 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
293 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
294 |
> |
some lines into global.cpp to make it work with energy minimization |
295 |
> |
|
296 |
> |
2004-02-04 17:26 tim |
297 |
> |
|
298 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
299 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
300 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
301 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
302 |
> |
Single version of conjugate gradient with golden search linesearch |
303 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
304 |
> |
|
305 |
> |
2004-02-03 17:54 tim |
306 |
> |
|
307 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
308 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
309 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
310 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
311 |
> |
|
312 |
> |
2004-02-03 15:47 tim |
313 |
> |
|
314 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
315 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
316 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
317 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
318 |
> |
SteepestDescent.hpp: [no log message] |
319 |
> |
|
320 |
> |
2004-02-03 15:43 tim |
321 |
> |
|
322 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
323 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
324 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
325 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
326 |
> |
constraint class |
327 |
> |
|
328 |
> |
2004-02-03 12:10 tim |
329 |
> |
|
330 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
331 |
> |
|
332 |
> |
2004-02-03 10:21 tim |
333 |
> |
|
334 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
335 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
336 |
> |
|
337 |
> |
2004-02-02 15:29 tim |
338 |
> |
|
339 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
340 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
341 |
> |
Adding GoldenSection and Brent LineSearch Method |
342 |
> |
|
343 |
> |
2004-01-30 16:47 tim |
344 |
> |
|
345 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
346 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
347 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
348 |
> |
MinimizerBase instead of a functor to do line seach |
349 |
> |
|
350 |
> |
2004-01-30 10:00 chrisfen |
351 |
> |
|
352 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
353 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
354 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
355 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
356 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
357 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
358 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
359 |
> |
has a working WATER.cpp forcefield and parser. This involved |
360 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
361 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
362 |
> |
This will be removed on the next commit... |
363 |
> |
|
364 |
> |
2004-01-29 18:00 gezelter |
365 |
> |
|
366 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
367 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
368 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
369 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
370 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
371 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
372 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
373 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
374 |
> |
member list fixes for rigid bodies |
375 |
> |
|
376 |
> |
2004-01-29 16:44 tim |
377 |
> |
|
378 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
379 |
> |
MinimizerParameterSet class. |
380 |
> |
|
381 |
> |
2004-01-28 17:44 tim |
382 |
> |
|
383 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
384 |
> |
NLModel0 and NLModel1 |
385 |
> |
|
386 |
> |
2004-01-28 15:40 tim |
387 |
> |
|
388 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
389 |
> |
of NLModel |
390 |
> |
|
391 |
> |
2004-01-27 15:34 gezelter |
392 |
> |
|
393 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
394 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
395 |
> |
|
396 |
> |
2004-01-27 15:34 gezelter |
397 |
> |
|
398 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
399 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
400 |
> |
stuff |
401 |
> |
|
402 |
> |
2004-01-27 14:39 gezelter |
403 |
> |
|
404 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
405 |
> |
|
406 |
> |
2004-01-27 14:39 gezelter |
407 |
> |
|
408 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
409 |
> |
|
410 |
> |
2004-01-27 14:38 gezelter |
411 |
> |
|
412 |
> |
* samples/argon/argon.bass: Longer run time to test argon |
413 |
> |
|
414 |
> |
2004-01-27 14:38 gezelter |
415 |
> |
|
416 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
417 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
418 |
> |
morning |
419 |
> |
|
420 |
> |
2004-01-27 14:37 gezelter |
421 |
> |
|
422 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
423 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
424 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
425 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
426 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
427 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
428 |
> |
do new rigidBody scheme |
429 |
> |
|
430 |
> |
2004-01-27 14:15 tim |
431 |
> |
|
432 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
433 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
434 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
435 |
> |
constraint for Nonlinear Optimization Model |
436 |
> |
|
437 |
> |
2004-01-26 17:01 gezelter |
438 |
> |
|
439 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
440 |
> |
Euler angles for orientation instead of unit vectors required |
441 |
> |
changes in MoLocator |
442 |
> |
|
443 |
> |
2004-01-26 16:53 gezelter |
444 |
> |
|
445 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
446 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
447 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
448 |
> |
euler angles |
449 |
> |
|
450 |
> |
2004-01-26 16:52 gezelter |
451 |
> |
|
452 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
453 |
> |
|
454 |
> |
2004-01-26 16:45 gezelter |
455 |
> |
|
456 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
457 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
458 |
> |
the ability to set orientation using a unit vector |
459 |
> |
|
460 |
> |
2004-01-26 16:26 gezelter |
461 |
> |
|
462 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
463 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
464 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
465 |
> |
ability to set orientation using a unit vector |
466 |
> |
|
467 |
> |
2004-01-26 13:52 gezelter |
468 |
> |
|
469 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
470 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
471 |
> |
|
472 |
> |
2004-01-22 12:34 chrisfen |
473 |
> |
|
474 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
475 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
476 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
477 |
> |
|
478 |
> |
2004-01-21 17:16 tim |
479 |
> |
|
480 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
481 |
> |
NLOPModel.hpp: constraint class in energy minimization |
482 |
> |
|
483 |
> |
2004-01-20 15:34 tim |
484 |
> |
|
485 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
486 |
> |
|
487 |
> |
2004-01-20 15:32 tim |
488 |
> |
|
489 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
490 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
491 |
> |
|
492 |
> |
2004-01-19 16:17 gezelter |
493 |
> |
|
494 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
495 |
> |
more user-friendly |
496 |
> |
|
497 |
> |
2004-01-19 13:51 chrisfen |
498 |
> |
|
499 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
500 |
> |
|
501 |
> |
2004-01-19 13:36 tim |
502 |
> |
|
503 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
504 |
> |
time, status time, thermal time and reset time are not divisible by |
505 |
> |
dt |
506 |
> |
|
507 |
> |
2004-01-19 11:10 gezelter |
508 |
> |
|
509 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
510 |
> |
won't complain |
511 |
> |
|
512 |
> |
2004-01-19 11:10 gezelter |
513 |
> |
|
514 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
515 |
> |
|
516 |
> |
2004-01-19 11:09 gezelter |
517 |
> |
|
518 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
519 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
520 |
> |
in mpiSimulation.cpp |
521 |
> |
|
522 |
> |
2004-01-19 11:08 gezelter |
523 |
> |
|
524 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
525 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
526 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
527 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
528 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
529 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
530 |
> |
|
531 |
> |
2004-01-16 16:55 tim |
532 |
> |
|
533 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
534 |
> |
eor file |
535 |
> |
|
536 |
> |
2004-01-16 16:51 mmeineke |
537 |
> |
|
538 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
539 |
> |
write eor files |
540 |
> |
|
541 |
> |
2004-01-16 10:01 mmeineke |
542 |
> |
|
543 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
544 |
> |
initialization of the AtomStruct |
545 |
> |
|
546 |
> |
2004-01-15 16:57 chuckv |
547 |
> |
|
548 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
549 |
> |
|
550 |
> |
2004-01-15 10:51 gezelter |
551 |
> |
|
552 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
553 |
> |
|
554 |
> |
2004-01-15 09:22 gezelter |
555 |
> |
|
556 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
557 |
> |
|
558 |
> |
2004-01-14 23:33 gezelter |
559 |
> |
|
560 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
561 |
> |
|
562 |
> |
2004-01-14 20:14 gezelter |
563 |
> |
|
564 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
565 |
> |
notifyCutoffs.F90: More work for adding charges |
566 |
> |
|
567 |
> |
2004-01-14 17:41 gezelter |
568 |
> |
|
569 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
570 |
> |
src/Makefile.in: autoconf fixes |
571 |
> |
|
572 |
> |
2004-01-14 11:28 mmeineke |
573 |
> |
|
574 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
575 |
> |
|
576 |
> |
2004-01-14 10:48 gezelter |
577 |
> |
|
578 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
579 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
580 |
> |
changes for icc8 |
581 |
> |
|
582 |
> |
2004-01-13 18:01 gezelter |
583 |
> |
|
584 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
585 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
586 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
587 |
> |
Changes for adding direct charge-charge interactions (with |
588 |
> |
switching function) |
589 |
> |
|
590 |
> |
2004-01-13 17:34 gezelter |
591 |
> |
|
592 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
593 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
594 |
> |
direct charge-charge interactions |
595 |
> |
|
596 |
> |
2004-01-13 17:11 tim |
597 |
> |
|
598 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
599 |
> |
|
600 |
> |
2004-01-13 16:22 tim |
601 |
> |
|
602 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
603 |
> |
|
604 |
> |
2004-01-13 15:35 tim |
605 |
> |
|
606 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
607 |
> |
eor file whenever it is used instead of rewinding it |
608 |
> |
|
609 |
> |
2004-01-13 15:04 tim |
610 |
> |
|
611 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
612 |
> |
of writeFrame |
613 |
> |
|
614 |
> |
2004-01-13 10:46 tim |
615 |
> |
|
616 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
617 |
> |
Merge the code of writeFinal and writeDump; |
618 |
> |
Adding sortingIndex into DumpWriter; |
619 |
> |
Fix a bug of writing last frame twice in integrator |
620 |
> |
|
621 |
> |
2004-01-12 17:54 tim |
622 |
> |
|
623 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
624 |
> |
a bug in copying string |
625 |
> |
|
626 |
> |
2004-01-12 15:37 tim |
627 |
> |
|
628 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
629 |
> |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
630 |
> |
master nodes |
631 |
> |
|
632 |
> |
2004-01-10 04:46 tim |
633 |
> |
|
634 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
635 |
> |
roll it back fix a bug of copying string to a pointer Still have |
636 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
637 |
> |
|
638 |
> |
2004-01-09 21:15 tim |
639 |
> |
|
640 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
641 |
> |
|
642 |
> |
2004-01-09 15:29 gezelter |
643 |
> |
|
644 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
645 |
> |
|
646 |
> |
2004-01-08 17:25 chuckv |
647 |
> |
|
648 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
649 |
> |
|
650 |
> |
2004-01-08 13:59 gezelter |
651 |
> |
|
652 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
653 |
> |
case |
654 |
> |
|
655 |
> |
2004-01-08 13:13 mmeineke |
656 |
> |
|
657 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
658 |
> |
state bug. |
659 |
> |
|
660 |
> |
2004-01-08 13:05 gezelter |
661 |
> |
|
662 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
663 |
> |
|
664 |
> |
2004-01-08 12:57 mmeineke |
665 |
> |
|
666 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
667 |
> |
exstended state bug |
668 |
> |
|
669 |
> |
2004-01-08 12:40 gezelter |
670 |
> |
|
671 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
672 |
> |
|
673 |
> |
2004-01-08 10:44 mmeineke |
674 |
> |
|
675 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
676 |
> |
XS state info flag |
677 |
> |
|
678 |
> |
2004-01-07 14:26 tim |
679 |
> |
|
680 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
681 |
> |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
682 |
> |
sending message from master node to itself in DumpWriter.cpp and |
683 |
> |
InitializeFromFile.cpp |
684 |
> |
|
685 |
> |
2004-01-06 14:49 chuckv |
686 |
> |
|
687 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
688 |
> |
performance fixes in the dipole dipole and reaction field code |
689 |
> |
|
690 |
> |
2004-01-06 13:54 chuckv |
691 |
> |
|
692 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
693 |
> |
little more sane |
694 |
> |
|
695 |
> |
2004-01-05 17:49 chuckv |
696 |
> |
|
697 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
698 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
699 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
700 |
> |
performance by reducing spurious function calls |
701 |
> |
|
702 |
> |
2004-01-05 17:18 chuckv |
703 |
> |
|
704 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
705 |
> |
|
706 |
> |
2004-01-05 17:18 chuckv |
707 |
> |
|
708 |
> |
* configure, ac-tools/configure.in: mpich mucking |
709 |
> |
|
710 |
> |
2004-01-05 17:12 chuckv |
711 |
> |
|
712 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
713 |
> |
|
714 |
> |
2004-01-05 16:00 chuckv |
715 |
> |
|
716 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
717 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
718 |
> |
lookup |
719 |
> |
|
720 |
> |
2003-12-29 14:56 chuckv |
721 |
> |
|
722 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
723 |
> |
third-party directory for code not written by us. Also added |
724 |
> |
Mersenne Twister random number generator code. This will eventually |
725 |
> |
replace sprng as the random number generator used by OOPSE. |
726 |
> |
|
727 |
> |
2003-12-22 16:26 chuckv |
728 |
> |
|
729 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
730 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
731 |
> |
Fixes to profile code. |
732 |
> |
|
733 |
> |
2003-12-19 15:36 mmeineke |
734 |
> |
|
735 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
736 |
> |
timing.F90, timing.f90: More profiling fixes. |
737 |
> |
|
738 |
> |
2003-12-19 15:19 chuckv |
739 |
> |
|
740 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
741 |
> |
|
742 |
> |
2003-12-19 15:17 chuckv |
743 |
> |
|
744 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
745 |
> |
|
746 |
> |
2003-12-19 13:53 mmeineke |
747 |
> |
|
748 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
749 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
750 |
> |
the code |
751 |
> |
|
752 |
> |
2003-12-19 12:25 mmeineke |
753 |
> |
|
754 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
755 |
> |
some profiling routines |
756 |
> |
|
757 |
> |
2003-12-19 10:12 mmeineke |
758 |
> |
|
759 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
760 |
> |
and GofRomega |
761 |
|
|
762 |
< |
added identification of identI in matchI. |
762 |
> |
additional work on randomBilayer |
763 |
> |
|
764 |
> |
2003-12-19 10:12 mmeineke |
765 |
> |
|
766 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
767 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
768 |
> |
GofRomega |
769 |
> |
|
770 |
> |
2003-12-18 16:47 mmeineke |
771 |
> |
|
772 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
773 |
> |
some profile functionality |
774 |
> |
|
775 |
> |
2003-12-18 15:46 chuckv |
776 |
> |
|
777 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
778 |
> |
Added functions for simple profiling in fortran. |
779 |
> |
|
780 |
> |
2003-12-17 15:13 chuckv |
781 |
> |
|
782 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
783 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
784 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
785 |
> |
zeros the array between scatters so half of the sum was being lost. |
786 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
787 |
> |
nlocal. |
788 |
> |
|
789 |
> |
2003-12-16 15:49 mmeineke |
790 |
> |
|
791 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
792 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
793 |
> |
gofRomega. both need to be debugged and tested. |
794 |
> |
|
795 |
> |
2003-12-12 10:42 gezelter |
796 |
> |
|
797 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
798 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
799 |
> |
gradients (to do minimizations) |
800 |
> |
|
801 |
> |
2003-12-12 10:33 mmeineke |
802 |
> |
|
803 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
804 |
> |
header |
805 |
> |
|
806 |
> |
2003-12-10 11:52 mmeineke |
807 |
> |
|
808 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
809 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
810 |
> |
randomBilayer to the build. Also move the random bilayer builder |
811 |
> |
from bilayerSys to randomBilayer |
812 |
> |
|
813 |
> |
2003-11-25 10:44 mmeineke |
814 |
> |
|
815 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
816 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
817 |
> |
TB3 in DUFF.frc |
818 |
> |
|
819 |
> |
2003-11-21 15:09 mmeineke |
820 |
> |
|
821 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
822 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
823 |
> |
message in SimInfo. Added a more informative error message in |
824 |
> |
InitializeFromFile |
825 |
> |
|
826 |
> |
2003-11-21 15:07 mmeineke |
827 |
> |
|
828 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
829 |
> |
ing in the GofR,CosTheta |
830 |
> |
|
831 |
> |
2003-11-21 14:31 chrisfen |
832 |
> |
|
833 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
834 |
> |
a bug in SimInfo ordering of radii |
835 |
> |
|
836 |
> |
2003-11-11 12:20 mmeineke |
837 |
> |
|
838 |
> |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
839 |
> |
a min function. |
840 |
> |
|
841 |
> |
2003-11-10 16:50 mmeineke |
842 |
> |
|
843 |
> |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
844 |
> |
reordered the rcut/ecr/boxSize initialization |
845 |
> |
|
846 |
> |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
847 |
> |
now exit when it runs into rcut or ecr. |
848 |
> |
|
849 |
> |
2003-11-07 16:46 chuckv |
850 |
> |
|
851 |
> |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
852 |
> |
oopseMPI_module.F90: Added support for compiling fortran without |
853 |
> |
use of mpich modules. We use mpif.h instead.: |
854 |
> |
|
855 |
> |
2003-11-07 12:09 mmeineke |
856 |
> |
|
857 |
> |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
858 |
> |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
859 |
> |
the atom loop in the NPT family of integrators. |
860 |
> |
|
861 |
> |
2003-11-06 17:01 mmeineke |
862 |
> |
|
863 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
864 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
865 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
866 |
> |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
867 |
> |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
868 |
> |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
869 |
> |
* useIntiTime => useInitialTime |
870 |
> |
|
871 |
> |
2003-11-06 14:24 mmeineke |
872 |
> |
|
873 |
> |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
874 |
> |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
875 |
> |
parse_tree.h: fixed the includes in the Make.dep |
876 |
> |
|
877 |
> |
2003-11-06 14:11 mmeineke |
878 |
> |
|
879 |
> |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
880 |
> |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
881 |
> |
new-templateless branch to the main trunk. |
882 |
> |
|
883 |
> |
bug Fixes include: * fixed the switching function from ortho to |
884 |
> |
non-ortho box. !!!!! THis was responsible for all of the |
885 |
> |
sudden deaths we saw. * some formating in the string when we |
886 |
> |
write out the extended system state. * added NPT.cpp to the |
887 |
> |
makefile.in |
888 |
> |
|
889 |
> |
2003-11-06 13:20 mmeineke |
890 |
> |
|
891 |
> |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
892 |
> |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
893 |
> |
bug. The box was not switching between orthorhombic and |
894 |
> |
non-orthorhombic wrapping correctly. we added a fabs() to |
895 |
> |
the check.which should fix it. |
896 |
> |
|
897 |
> |
2003-11-05 14:16 mmeineke |
898 |
> |
|
899 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
900 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
901 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
902 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
903 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
904 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
905 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
906 |
> |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
907 |
> |
some work on trying to find the compression bug |
908 |
> |
|
909 |
> |
2003-11-03 17:07 mmeineke |
910 |
> |
|
911 |
> |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
912 |
> |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
913 |
> |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
914 |
> |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
915 |
> |
most of standard template library from OOPSE. |
916 |
> |
|
917 |
> |
2003-10-31 16:06 mmeineke |
918 |
> |
|
919 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
920 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
921 |
> |
SimSetup.cpp: started work on template removal. |
922 |
> |
|
923 |
> |
2003-10-31 13:28 mmeineke |
924 |
> |
|
925 |
> |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
926 |
> |
added template stuff to the Maikefile template |
927 |
> |
|
928 |
> |
little changes to some printf format statements |
929 |
> |
|
930 |
> |
2003-10-31 13:28 mmeineke |
931 |
> |
|
932 |
> |
* libBASS/Makefile.in: added template stuff to the Maikefile |
933 |
> |
template |
934 |
> |
|
935 |
> |
2003-10-30 13:59 gezelter |
936 |
> |
|
937 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
938 |
> |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
939 |
> |
rList problems |
940 |
> |
|
941 |
> |
2003-10-30 09:11 gezelter |
942 |
> |
|
943 |
> |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
944 |
> |
queried before q0 was allocated. |
945 |
> |
|
946 |
> |
2003-10-29 15:41 mmeineke |
947 |
> |
|
948 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
949 |
> |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
950 |
> |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
951 |
> |
in bass.l |
952 |
> |
|
953 |
> |
fixed a little bug in the first time step, regarding the setting of |
954 |
> |
ecr and est in fortran |
955 |
> |
|
956 |
> |
2003-10-29 15:40 mmeineke |
957 |
> |
|
958 |
> |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
959 |
> |
|
960 |
> |
2003-10-29 12:55 mmeineke |
961 |
> |
|
962 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
963 |
> |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
964 |
> |
rcut is setup, as well as additional debugging comments. |
965 |
> |
|
966 |
> |
2003-10-29 09:28 gezelter |
967 |
> |
|
968 |
> |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
969 |
> |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
970 |
> |
templates |
971 |
> |
|
972 |
> |
2003-10-28 22:16 gezelter |
973 |
> |
|
974 |
> |
* src/Makefile.in: Refixed broken makefile |
975 |
> |
|
976 |
> |
2003-10-28 22:06 gezelter |
977 |
> |
|
978 |
> |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
979 |
> |
fixes |
980 |
> |
|
981 |
> |
2003-10-28 19:19 tim |
982 |
> |
|
983 |
> |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
984 |
> |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
985 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
986 |
> |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
987 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
988 |
> |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
989 |
> |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
990 |
> |
file. |
991 |
> |
|
992 |
> |
2003-10-28 17:25 mmeineke |
993 |
> |
|
994 |
> |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
995 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
996 |
> |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
997 |
> |
how c calls fortran. All function pointers and fortran calls are |
998 |
> |
rigidly typecast now. |
999 |
> |
|
1000 |
> |
2003-10-28 15:42 gezelter |
1001 |
> |
|
1002 |
> |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1003 |
> |
Portability fixes |
1004 |
> |
|
1005 |
> |
2003-10-28 15:09 gezelter |
1006 |
> |
|
1007 |
> |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1008 |
> |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1009 |
> |
src/Makefile.in: Compatibility fixes |
1010 |
> |
|
1011 |
> |
2003-10-28 12:08 mmeineke |
1012 |
> |
|
1013 |
> |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1014 |
> |
started work on template removal |
1015 |
> |
|
1016 |
> |
2003-10-28 12:04 gezelter |
1017 |
> |
|
1018 |
> |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1019 |
> |
trying to understand extern "C" stuff for pointers |
1020 |
> |
|
1021 |
> |
2003-10-28 11:20 gezelter |
1022 |
> |
|
1023 |
> |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1024 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1025 |
> |
|
1026 |
> |
2003-10-28 11:03 gezelter |
1027 |
> |
|
1028 |
> |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1029 |
> |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1030 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1031 |
> |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1032 |
> |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1033 |
> |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1034 |
> |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1035 |
> |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1036 |
> |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1037 |
> |
more portable c header stuff Also, mod file fixes and portability |
1038 |
> |
changes Some fortran changes will need to be reversed. |
1039 |
> |
|
1040 |
> |
2003-10-28 11:03 gezelter |
1041 |
> |
|
1042 |
> |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1043 |
> |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1044 |
> |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1045 |
> |
portable c header stuff Also, mod file fixes and portability |
1046 |
> |
changes |
1047 |
> |
|
1048 |
> |
2003-10-28 11:02 gezelter |
1049 |
> |
|
1050 |
> |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1051 |
> |
stuff |
1052 |
> |
|
1053 |
> |
2003-10-27 18:00 gezelter |
1054 |
> |
|
1055 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1056 |
> |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1057 |
> |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1058 |
> |
|
1059 |
> |
2003-10-27 17:08 mmeineke |
1060 |
> |
|
1061 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1062 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1063 |
> |
added routines for the sysbuilder to work with simSetup |
1064 |
> |
|
1065 |
> |
remved the QuickBass routines, and had all parsing go through |
1066 |
> |
SimSetup. LatticeBilayer is in complete working order now. |
1067 |
> |
|
1068 |
> |
2003-10-27 17:07 mmeineke |
1069 |
> |
|
1070 |
> |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1071 |
> |
routines for the sysbuilder to work with simSetup |
1072 |
> |
|
1073 |
> |
2003-10-27 11:20 gezelter |
1074 |
> |
|
1075 |
> |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1076 |
> |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1077 |
> |
|
1078 |
> |
2003-10-24 17:17 mmeineke |
1079 |
> |
|
1080 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1081 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1082 |
> |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1083 |
> |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1084 |
> |
overhauled latticeBilayer into its own program. Removed sysBuild |
1085 |
> |
from the Makefile |
1086 |
> |
|
1087 |
> |
2003-10-24 12:36 gezelter |
1088 |
> |
|
1089 |
> |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1090 |
> |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1091 |
> |
builder |
1092 |
> |
|
1093 |
> |
2003-10-24 12:35 gezelter |
1094 |
> |
|
1095 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1096 |
> |
merge problem |
1097 |
> |
|
1098 |
> |
2003-10-23 14:57 mmeineke |
1099 |
> |
|
1100 |
> |
* samples/metals/Makefile.in: added eam ForceField files to the |
1101 |
> |
init |
1102 |
> |
|
1103 |
> |
fixed an eam mpi parmeter setup bug |
1104 |
> |
|
1105 |
> |
added the init file to the makefile |
1106 |
> |
|
1107 |
> |
2003-10-23 14:57 mmeineke |
1108 |
> |
|
1109 |
> |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1110 |
> |
to the init |
1111 |
> |
|
1112 |
> |
fixed an eam mpi parmeter setup bug |
1113 |
> |
|
1114 |
> |
2003-10-23 14:57 mmeineke |
1115 |
> |
|
1116 |
> |
* forceFields/Makefile.in: added eam ForceField files to the init |
1117 |
> |
|
1118 |
> |
2003-10-22 16:17 mmeineke |
1119 |
> |
|
1120 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1121 |
> |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1122 |
> |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1123 |
> |
no box skew allowed. |
1124 |
> |
|
1125 |
> |
2003-10-21 14:33 mmeineke |
1126 |
> |
|
1127 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1128 |
> |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1129 |
> |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1130 |
> |
* useInitTime = false: sets the origin time to 0.0 regardless |
1131 |
> |
of the time stamp in the .init file * default=> useInitTime = |
1132 |
> |
true; |
1133 |
> |
|
1134 |
> |
2003-10-17 16:19 mmeineke |
1135 |
> |
|
1136 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1137 |
> |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1138 |
> |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1139 |
> |
to the build list for both configure and configure.in |
1140 |
> |
|
1141 |
> |
fixed a number of bugs in the staticProps code. gofr is now |
1142 |
> |
working. |
1143 |
> |
|
1144 |
> |
2003-10-17 16:18 mmeineke |
1145 |
> |
|
1146 |
> |
* ac-tools/configure.in: added the staticProps directory to the |
1147 |
> |
build list for both configure and configure.in |
1148 |
> |
|
1149 |
> |
2003-10-17 16:17 mmeineke |
1150 |
> |
|
1151 |
> |
* configure: added the staticProps directory to the build list |
1152 |
> |
|
1153 |
> |
2003-10-16 14:16 mmeineke |
1154 |
> |
|
1155 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1156 |
> |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1157 |
> |
use linked lists instead of a vector. |
1158 |
> |
|
1159 |
> |
Fixed the makefile to build DumpReader.cpp |
1160 |
> |
|
1161 |
> |
Removed a comment output in Exclude.cpp |
1162 |
> |
|
1163 |
> |
Modified DumpWriter and Integrator to write an eor file every time |
1164 |
> |
a frame is written. This lets the .eor file represent the last |
1165 |
> |
written frame of a simulation. |
1166 |
> |
|
1167 |
> |
2003-10-10 12:10 mmeineke |
1168 |
> |
|
1169 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1170 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1171 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1172 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1173 |
> |
over to staticProps |
1174 |
> |
|
1175 |
> |
2003-10-09 17:09 mmeineke |
1176 |
> |
|
1177 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1178 |
> |
a position where it will compile and run first runs. |
1179 |
> |
|
1180 |
> |
2003-10-04 13:46 chuckv |
1181 |
> |
|
1182 |
> |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1183 |
> |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1184 |
> |
|
1185 |
> |
2003-10-04 13:08 chuckv |
1186 |
> |
|
1187 |
> |
* samples/metals/init_au.in: added Au init file for eam. |
1188 |
> |
|
1189 |
> |
2003-10-03 17:11 mmeineke |
1190 |
> |
|
1191 |
> |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1192 |
> |
entahlpy from the statwriter and thermo. |
1193 |
> |
|
1194 |
> |
2003-10-03 17:02 mmeineke |
1195 |
> |
|
1196 |
> |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1197 |
> |
statements in simError |
1198 |
> |
|
1199 |
> |
added a function to get the maxCutoff |
1200 |
> |
|
1201 |
> |
2003-10-03 17:01 mmeineke |
1202 |
> |
|
1203 |
> |
* libBASS/simError.c: changed the formating ogf the error |
1204 |
> |
statements in simError |
1205 |
> |
|
1206 |
> |
2003-09-30 11:00 mmeineke |
1207 |
> |
|
1208 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1209 |
> |
f90Flags so they are no longer overwritten by the compiler. |
1210 |
> |
|
1211 |
> |
2003-09-29 17:06 mmeineke |
1212 |
> |
|
1213 |
> |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1214 |
> |
for conifig.in |
1215 |
> |
|
1216 |
> |
fixed wrappers to extern "C" |
1217 |
> |
|
1218 |
> |
2003-09-29 17:06 mmeineke |
1219 |
> |
|
1220 |
> |
* ac-tools/configure.in: added mpif90 mod check back same for |
1221 |
> |
conifig.in |
1222 |
> |
|
1223 |
> |
2003-09-29 17:05 mmeineke |
1224 |
> |
|
1225 |
> |
* configure: added mpif90 mod check back |
1226 |
> |
|
1227 |
> |
2003-09-29 16:16 mmeineke |
1228 |
> |
|
1229 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1230 |
> |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1231 |
> |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1232 |
> |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1233 |
> |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1234 |
> |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1235 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1236 |
> |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1237 |
> |
found with SUN's SUNWspro.s1s7 |
1238 |
> |
|
1239 |
> |
2003-09-29 12:38 mmeineke |
1240 |
> |
|
1241 |
> |
* libmdtools/GenericData.hpp: light change in syntax. no |
1242 |
> |
signifigant change. |
1243 |
> |
|
1244 |
> |
2003-09-25 16:17 mmeineke |
1245 |
> |
|
1246 |
> |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1247 |
> |
additional remarks from icc -w3 (extra verbose output) |
1248 |
> |
|
1249 |
> |
2003-09-25 14:27 mmeineke |
1250 |
> |
|
1251 |
> |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1252 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1253 |
> |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1254 |
> |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1255 |
> |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1256 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1257 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1258 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1259 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1260 |
> |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1261 |
> |
gcc -Wall and g++ -Wall |
1262 |
> |
|
1263 |
> |
2003-09-25 13:54 gezelter |
1264 |
> |
|
1265 |
> |
* configure, ac-tools/configure.in: fixed a bug in configure |
1266 |
> |
|
1267 |
> |
2003-09-25 11:42 gezelter |
1268 |
> |
|
1269 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1270 |
> |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1271 |
> |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1272 |
> |
fixes for configure |
1273 |
> |
|
1274 |
> |
2003-09-24 14:34 mmeineke |
1275 |
> |
|
1276 |
> |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1277 |
> |
that it is called before the first Statistics are written. |
1278 |
> |
|
1279 |
> |
2003-09-23 15:36 gezelter |
1280 |
> |
|
1281 |
> |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1282 |
> |
bunch of Make.dep files to CVS |
1283 |
> |
|
1284 |
> |
2003-09-23 15:34 mmeineke |
1285 |
> |
|
1286 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1287 |
> |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1288 |
> |
|
1289 |
> |
Some small syntax cleaning in NPTfm and SimSetup |
1290 |
> |
|
1291 |
> |
2003-09-22 18:07 tim |
1292 |
> |
|
1293 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1294 |
> |
SimInfo.hpp: fix bug in calculating maxCutoff |
1295 |
> |
|
1296 |
> |
2003-09-22 16:23 mmeineke |
1297 |
> |
|
1298 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1299 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1300 |
> |
Converted NPTf to work with the NPT base class. |
1301 |
> |
|
1302 |
> |
Removed NPTfm and NPTim from cvs |
1303 |
> |
|
1304 |
> |
2003-09-19 15:00 mmeineke |
1305 |
> |
|
1306 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1307 |
> |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1308 |
> |
class. NPTi is up to date. NPTf is not. |
1309 |
> |
|
1310 |
> |
2003-09-19 11:03 mmeineke |
1311 |
> |
|
1312 |
> |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1313 |
> |
makefile |
1314 |
> |
|
1315 |
> |
2003-09-19 11:01 gezelter |
1316 |
> |
|
1317 |
> |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1318 |
> |
|
1319 |
> |
2003-09-19 11:01 gezelter |
1320 |
> |
|
1321 |
> |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1322 |
> |
(nearly) conserved quantities for both NPTi and NPTf |
1323 |
> |
|
1324 |
> |
2003-09-19 10:20 mmeineke |
1325 |
> |
|
1326 |
> |
* utils/Makefile.in: fixed a typo in the makefile. |
1327 |
> |
|
1328 |
> |
2003-09-19 09:55 gezelter |
1329 |
> |
|
1330 |
> |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1331 |
> |
samples/water/ssd.bass: [no log message] |
1332 |
> |
|
1333 |
> |
2003-09-19 09:22 tim |
1334 |
> |
|
1335 |
> |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1336 |
> |
|
1337 |
> |
2003-09-17 09:22 mmeineke |
1338 |
> |
|
1339 |
> |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1340 |
> |
work with constraints. |
1341 |
> |
|
1342 |
> |
2003-09-16 15:02 tim |
1343 |
> |
|
1344 |
> |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1345 |
> |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1346 |
> |
|
1347 |
> |
fixed conserved quantity in NPT (Still some small bug) |
1348 |
> |
|
1349 |
> |
NPTi appears very stable. |
1350 |
> |
|
1351 |
> |
2003-09-15 11:52 tim |
1352 |
> |
|
1353 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1354 |
> |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1355 |
> |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1356 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1357 |
> |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1358 |
> |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1359 |
> |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1360 |
> |
statWriter fix bug of vector wrapping at NPTi |
1361 |
> |
|
1362 |
> |
2003-09-12 11:20 gezelter |
1363 |
> |
|
1364 |
> |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1365 |
> |
Makefile.in |
1366 |
> |
|
1367 |
> |
2003-09-12 11:20 gezelter |
1368 |
> |
|
1369 |
> |
* ChangeLog: Entered changes for configure into ChangeLog |
1370 |
|
|
1371 |
|
2003-09-09 15:35 mmeineke |
1372 |
|
|
1442 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1443 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
1444 |
|
|
87 |
– |
2003-08-28 11:59 mmeineke |
88 |
– |
|
89 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
90 |
– |
added the first functional parts of the PairCorrType Abstract |
91 |
– |
classes. |
92 |
– |
|
1445 |
|
2003-08-27 14:23 tim |
1446 |
|
|
1447 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
1712 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1713 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1714 |
|
works..... |
363 |
– |
|
364 |
– |
2003-08-08 13:32 mmeineke |
365 |
– |
|
366 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
367 |
– |
moved frameCount's functionality into DumpReader. also split props |
368 |
– |
into staticProps and dynamicProps. (currently only have |
369 |
– |
staticProps) |
1715 |
|
|
1716 |
|
2003-08-08 12:48 mmeineke |
1717 |
|
|
1769 |
|
2003-07-29 11:32 mmeineke |
1770 |
|
|
1771 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1772 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1773 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
429 |
< |
src/Makefile: working on the props code |
1772 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1773 |
> |
working on the props code |
1774 |
|
|
1775 |
|
2003-07-29 11:32 mmeineke |
1776 |
|
|
2897 |
|
|
2898 |
|
2003-03-25 09:29 mmeineke |
2899 |
|
|
2900 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2900 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2901 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2902 |
|
|
2903 |
|
2003-03-25 09:29 mmeineke |
2907 |
|
|
2908 |
|
2003-03-24 20:07 gezelter |
2909 |
|
|
2910 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
2910 |
> |
* samples/Makefile: moving tests to samples |
2911 |
|
|
2912 |
|
2003-03-24 20:06 gezelter |
2913 |
|
|
2914 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
2915 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
2916 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
2917 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
2918 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
2919 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
2920 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
1577 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
1578 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
1579 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
1580 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
1581 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
1582 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
1583 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
1584 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
1585 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
1586 |
< |
tests/water/water.mdl: moved tests to samples |
2914 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2915 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2916 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2917 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2918 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2919 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2920 |
> |
samples |
2921 |
|
|
2922 |
|
2003-03-24 19:51 gezelter |
2923 |
|
|
2925 |
|
|
2926 |
|
2003-03-24 19:46 gezelter |
2927 |
|
|
2928 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
1595 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
1596 |
< |
Added makefiles in tests directories |
2928 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2929 |
|
|
2930 |
|
2003-03-24 16:55 gezelter |
2931 |
|
|
2942 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2943 |
|
do_Forces.F90: little bug fixes here and there |
2944 |
|
|
1613 |
– |
2003-03-24 11:04 mmeineke |
1614 |
– |
|
1615 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
1616 |
– |
test simulation |
1617 |
– |
|
1618 |
– |
2003-03-24 11:02 mmeineke |
1619 |
– |
|
1620 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
1621 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
1622 |
– |
water/water.mdl: [no log message] |
1623 |
– |
|
1624 |
– |
2003-03-24 11:02 mmeineke |
1625 |
– |
|
1626 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
1627 |
– |
some test bass files for experimenting with |
1628 |
– |
|
2945 |
|
2003-03-24 10:26 mmeineke |
2946 |
|
|
2947 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |