1 |
+ |
2004-04-22 16:33 tim |
2 |
+ |
|
3 |
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* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
4 |
+ |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
5 |
+ |
calculation of pressure tensor |
6 |
+ |
|
7 |
+ |
2004-04-22 09:55 tim |
8 |
+ |
|
9 |
+ |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
10 |
+ |
another bug in InitFromFile. MPI verion of OOPSE is working again |
11 |
+ |
|
12 |
+ |
2004-04-21 22:29 tim |
13 |
+ |
|
14 |
+ |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
15 |
+ |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
16 |
+ |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
17 |
+ |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
18 |
+ |
DumpWriter |
19 |
+ |
|
20 |
+ |
2004-04-21 00:32 tim |
21 |
+ |
|
22 |
+ |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
23 |
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libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
24 |
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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 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
36 |
+ |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
37 |
+ |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
38 |
+ |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
39 |
+ |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
40 |
+ |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
41 |
+ |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
42 |
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utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
43 |
+ |
|
44 |
+ |
2004-04-19 17:13 gezelter |
45 |
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|
46 |
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* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
47 |
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Thermo.cpp: Fixed a charge bug |
48 |
+ |
|
49 |
+ |
2004-04-19 15:54 tim |
50 |
+ |
|
51 |
+ |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
52 |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
53 |
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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 |
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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 |
+ |
counted |
65 |
+ |
|
66 |
+ |
2004-04-18 22:52 tim |
67 |
+ |
|
68 |
+ |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
69 |
+ |
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 |
+ |
|
86 |
+ |
2004-04-15 17:15 tim |
87 |
+ |
|
88 |
+ |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
89 |
+ |
exclude list |
90 |
+ |
|
91 |
+ |
2004-04-15 11:18 tim |
92 |
+ |
|
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 |
+ |
|
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, |