1 |
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2004-04-28 21:11 tim |
2 |
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|
3 |
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* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
4 |
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unmatched c/fortran interface |
5 |
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|
6 |
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2004-04-28 18:09 tim |
7 |
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|
8 |
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* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
9 |
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keep the previous position of cantilever in SMD |
10 |
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|
11 |
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2004-04-28 17:34 tim |
12 |
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|
13 |
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* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
14 |
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libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
15 |
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in Molecule.cpp which initialize massRatio before creat the array. |
16 |
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fix two bugs in ZconsVisitor |
17 |
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|
18 |
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2004-04-28 17:06 gezelter |
19 |
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|
20 |
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* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
21 |
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Adding molecular cutoffs |
22 |
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|
23 |
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2004-04-28 16:39 gezelter |
24 |
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|
25 |
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* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
26 |
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fSimulation.h, force_globals.F90, simulation_module.F90: work on |
27 |
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molecular cutoffs |
28 |
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|
29 |
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2004-04-28 16:39 gezelter |
30 |
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|
31 |
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* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
32 |
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Globals |
33 |
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|
34 |
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2004-04-27 11:26 tim |
35 |
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|
36 |
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
37 |
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ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
38 |
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fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
39 |
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molecule and massRation into atom class |
40 |
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|
41 |
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2004-04-26 16:16 mmeineke |
42 |
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|
43 |
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* libBASS/Globals.cpp: modified the defaults for the system init |
44 |
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time and system init state. |
45 |
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|
46 |
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2004-04-26 09:29 gezelter |
47 |
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|
48 |
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* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
49 |
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calc_charge_charge.F90 |
50 |
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|
51 |
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2004-04-23 23:31 tim |
52 |
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|
53 |
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* ChangeLog, libmdtools/AtomVisitor.cpp, |
54 |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
55 |
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reaction field correction to charge-charge interaction |
56 |
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|
57 |
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2004-04-22 16:33 tim |
58 |
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|
59 |
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* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
60 |
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Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
61 |
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calculation of pressure tensor |
62 |
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|
63 |
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2004-04-22 09:55 tim |
64 |
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|
65 |
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
66 |
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another bug in InitFromFile. MPI verion of OOPSE is working again |
67 |
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|
68 |
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2004-04-21 22:29 tim |
69 |
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|
70 |
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* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
71 |
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InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
72 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
73 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
74 |
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DumpWriter |
75 |
+ |
|
76 |
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2004-04-21 00:32 tim |
77 |
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|
78 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
79 |
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libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
80 |
+ |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
81 |
+ |
useless files |
82 |
+ |
|
83 |
+ |
2004-04-20 11:56 tim |
84 |
+ |
|
85 |
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* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
86 |
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SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
87 |
+ |
velocitize at thermo |
88 |
+ |
|
89 |
+ |
2004-04-20 00:39 tim |
90 |
+ |
|
91 |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
92 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
93 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
94 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
95 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
96 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
97 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
98 |
+ |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
99 |
+ |
|
100 |
+ |
2004-04-19 17:13 gezelter |
101 |
+ |
|
102 |
+ |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
103 |
+ |
Thermo.cpp: Fixed a charge bug |
104 |
+ |
|
105 |
+ |
2004-04-19 15:54 tim |
106 |
+ |
|
107 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
108 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
109 |
+ |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
110 |
+ |
a bug in CompositeVisitor which cause the double counting problem |
111 |
+ |
|
112 |
+ |
2004-04-19 12:44 tim |
113 |
+ |
|
114 |
+ |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
115 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
116 |
+ |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
117 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
118 |
+ |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
119 |
+ |
Dump2XYZ is almost working except atoms in rigidbody are double |
120 |
+ |
counted |
121 |
+ |
|
122 |
+ |
2004-04-18 22:52 tim |
123 |
+ |
|
124 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
125 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
126 |
+ |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
127 |
+ |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
128 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
129 |
+ |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
130 |
+ |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
131 |
+ |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
132 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
133 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
134 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
135 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
136 |
+ |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
137 |
+ |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
138 |
+ |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
139 |
+ |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
140 |
+ |
implement of quickLate using visitor and composite pattern |
141 |
+ |
|
142 |
+ |
2004-04-15 17:15 tim |
143 |
+ |
|
144 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
145 |
+ |
exclude list |
146 |
+ |
|
147 |
+ |
2004-04-15 11:18 tim |
148 |
+ |
|
149 |
+ |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
150 |
+ |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
151 |
+ |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
152 |
+ |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
153 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
154 |
+ |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
155 |
+ |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
156 |
+ |
whole bunch of bugs :-) |
157 |
+ |
|
158 |
+ |
2004-04-14 12:20 chrisfen |
159 |
+ |
|
160 |
+ |
* forceFields/WATER.frc: Added the WATER.frc force field |
161 |
+ |
|
162 |
+ |
2004-04-14 11:32 gezelter |
163 |
+ |
|
164 |
+ |
* libmdtools/Molecule.cpp: fixed for get_potential |
165 |
+ |
|
166 |
+ |
2004-04-14 10:37 tim |
167 |
+ |
|
168 |
+ |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
169 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
170 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
171 |
+ |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
172 |
+ |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
173 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
174 |
+ |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
175 |
+ |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
176 |
+ |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
177 |
+ |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
178 |
+ |
Change DumpWriter and InitFromFile |
179 |
+ |
|
180 |
+ |
2004-04-13 11:26 gezelter |
181 |
+ |
|
182 |
+ |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
183 |
+ |
molecules can keep track of their own IntegrableObjects (and |
184 |
+ |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
185 |
+ |
RigidBodies (which was done incorrectly before). |
186 |
+ |
|
187 |
+ |
2004-04-13 11:25 gezelter |
188 |
+ |
|
189 |
+ |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
190 |
+ |
(will back out momentarily) |
191 |
+ |
|
192 |
+ |
2004-04-13 10:10 gezelter |
193 |
+ |
|
194 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
195 |
+ |
Those were old. |
196 |
+ |
|
197 |
+ |
2004-04-13 10:09 gezelter |
198 |
+ |
|
199 |
+ |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
200 |
+ |
to add IntegrableObjects |
201 |
+ |
|
202 |
+ |
2004-04-12 16:02 gezelter |
203 |
+ |
|
204 |
+ |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
205 |
+ |
|
206 |
+ |
2004-04-12 15:32 gezelter |
207 |
+ |
|
208 |
+ |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
209 |
+ |
test run |
210 |
+ |
|
211 |
+ |
2004-04-12 15:32 gezelter |
212 |
+ |
|
213 |
+ |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
214 |
+ |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
215 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
216 |
+ |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
217 |
+ |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
218 |
+ |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
219 |
+ |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
220 |
+ |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
221 |
+ |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
222 |
+ |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
223 |
+ |
(Somewhat extensive) |
224 |
+ |
|
225 |
+ |
2004-04-12 15:31 gezelter |
226 |
+ |
|
227 |
+ |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
228 |
+ |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
229 |
+ |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
230 |
+ |
Changes for RigidBody dynamics |
231 |
+ |
|
232 |
|
2004-03-17 09:22 tim |
233 |
|
|
234 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
235 |
|
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
236 |
|
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
237 |
|
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
238 |
< |
does not sound like a good choice, next commit will seperate SMD and |
238 |
> |
does not sound a good choice, next commit will seperate SMD and |
239 |
|
ZConstraint |
240 |
|
|
241 |
|
2004-03-16 14:22 tim |