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2003-09-10 16:28 mmeineke |
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2004-04-27 11:26 tim |
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3 |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
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work on getting gofR working. |
3 |
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
4 |
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ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
5 |
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fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
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molecule and massRation into atom class |
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2003-09-09 16:50 mmeineke |
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2004-04-26 16:16 mmeineke |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
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beginings of the GofR pair correlation. |
10 |
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* libBASS/Globals.cpp: modified the defaults for the system init |
11 |
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time and system init state. |
12 |
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|
13 |
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2004-04-26 09:29 gezelter |
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|
15 |
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* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
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calc_charge_charge.F90 |
17 |
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|
18 |
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2004-04-23 23:31 tim |
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|
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* ChangeLog, libmdtools/AtomVisitor.cpp, |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
22 |
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reaction field correction to charge-charge interaction |
23 |
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|
24 |
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2004-04-22 16:33 tim |
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|
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* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
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Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
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calculation of pressure tensor |
29 |
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|
30 |
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2004-04-22 09:55 tim |
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|
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
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another bug in InitFromFile. MPI verion of OOPSE is working again |
34 |
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|
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2004-04-21 22:29 tim |
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|
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* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
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InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
39 |
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SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
40 |
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bugs in MPI version of InitfromFile and one unmatch MPI command in |
41 |
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DumpWriter |
42 |
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|
43 |
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2004-04-21 00:32 tim |
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|
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* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
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libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
47 |
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utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
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useless files |
49 |
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|
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2004-04-20 11:56 tim |
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|
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* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
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SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
54 |
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velocitize at thermo |
55 |
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|
56 |
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2004-04-20 00:39 tim |
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|
58 |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
60 |
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libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
61 |
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libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
62 |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
63 |
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libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
64 |
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utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
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utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
66 |
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|
67 |
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2004-04-19 17:13 gezelter |
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|
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* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
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Thermo.cpp: Fixed a charge bug |
71 |
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|
72 |
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2004-04-19 15:54 tim |
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|
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* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
76 |
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libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
77 |
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a bug in CompositeVisitor which cause the double counting problem |
78 |
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|
79 |
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2004-04-19 12:44 tim |
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|
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* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
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libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
83 |
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libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
84 |
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libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
85 |
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libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
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Dump2XYZ is almost working except atoms in rigidbody are double |
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counted |
88 |
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|
89 |
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2004-04-18 22:52 tim |
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|
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
93 |
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libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
94 |
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libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
95 |
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libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
96 |
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libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
97 |
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libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
98 |
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libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
99 |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
100 |
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libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
101 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
102 |
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libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
103 |
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libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
104 |
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libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
105 |
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libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
106 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
107 |
> |
implement of quickLate using visitor and composite pattern |
108 |
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|
109 |
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2004-04-15 17:15 tim |
110 |
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|
111 |
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* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
112 |
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exclude list |
113 |
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|
114 |
> |
2004-04-15 11:18 tim |
115 |
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|
116 |
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* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
117 |
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libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
118 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
119 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
120 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
121 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
122 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
123 |
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whole bunch of bugs :-) |
124 |
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|
125 |
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2004-04-14 12:20 chrisfen |
126 |
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|
127 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
128 |
> |
|
129 |
> |
2004-04-14 11:32 gezelter |
130 |
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|
131 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
132 |
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|
133 |
> |
2004-04-14 10:37 tim |
134 |
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|
135 |
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* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
136 |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
137 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
138 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
139 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
140 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
141 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
142 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
143 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
144 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
145 |
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Change DumpWriter and InitFromFile |
146 |
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|
147 |
> |
2004-04-13 11:26 gezelter |
148 |
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|
149 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
150 |
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molecules can keep track of their own IntegrableObjects (and |
151 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
152 |
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RigidBodies (which was done incorrectly before). |
153 |
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|
154 |
> |
2004-04-13 11:25 gezelter |
155 |
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|
156 |
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* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
157 |
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(will back out momentarily) |
158 |
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|
159 |
> |
2004-04-13 10:10 gezelter |
160 |
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|
161 |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
162 |
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Those were old. |
163 |
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|
164 |
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2004-04-13 10:09 gezelter |
165 |
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|
166 |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
167 |
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to add IntegrableObjects |
168 |
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|
169 |
> |
2004-04-12 16:02 gezelter |
170 |
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|
171 |
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* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
172 |
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|
173 |
> |
2004-04-12 15:32 gezelter |
174 |
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|
175 |
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* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
176 |
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test run |
177 |
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|
178 |
> |
2004-04-12 15:32 gezelter |
179 |
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|
180 |
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* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
181 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
182 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
183 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
184 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
185 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
186 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
187 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
188 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
189 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
190 |
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(Somewhat extensive) |
191 |
> |
|
192 |
> |
2004-04-12 15:31 gezelter |
193 |
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|
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> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
195 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
196 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
197 |
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Changes for RigidBody dynamics |
198 |
> |
|
199 |
> |
2004-03-17 09:22 tim |
200 |
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|
201 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
202 |
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libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
203 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
204 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
205 |
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does not sound a good choice, next commit will seperate SMD and |
206 |
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ZConstraint |
207 |
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|
208 |
> |
2004-03-16 14:22 tim |
209 |
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|
210 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
211 |
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libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
212 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
213 |
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libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
214 |
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now can support sequential moving. Refactorying is needed to |
215 |
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support SMD in ZConstraint |
216 |
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|
217 |
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2004-03-02 15:32 tim |
218 |
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|
219 |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
220 |
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StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
221 |
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support large file |
222 |
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|
223 |
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2004-03-01 16:17 tim |
224 |
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|
225 |
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* utils/zsub.cpp: Fix a couple of bugs in zsub |
226 |
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|
227 |
> |
2004-03-01 15:01 tim |
228 |
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|
229 |
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* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
230 |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
231 |
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libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
232 |
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utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
233 |
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utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
234 |
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program which can be used to replace atom type for zconstraint into |
235 |
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OOPSE |
236 |
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|
237 |
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2004-02-24 11:36 tim |
238 |
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|
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
240 |
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libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
241 |
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message] |
242 |
> |
|
243 |
> |
2004-02-24 10:49 tim |
244 |
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|
245 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
246 |
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Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
247 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
248 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
249 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
250 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
251 |
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SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
252 |
> |
|
253 |
> |
2004-02-24 10:44 tim |
254 |
> |
|
255 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
256 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
257 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
258 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
259 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
260 |
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compose to implement Minimizer both versions are working |
261 |
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|
262 |
> |
2004-02-17 14:23 tim |
263 |
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|
264 |
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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
265 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
266 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
267 |
> |
libmdtools/MinimizerParameterSet.hpp, |
268 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
269 |
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to remove the constraint force along bond direction |
270 |
> |
|
271 |
> |
2004-02-10 16:33 tim |
272 |
> |
|
273 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
274 |
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libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
275 |
> |
single version of energy minimization is working. |
276 |
> |
|
277 |
> |
2004-02-09 15:38 mmeineke |
278 |
> |
|
279 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
280 |
> |
the massive memory overusage by OOPSE |
281 |
> |
|
282 |
> |
2004-02-09 09:48 chrisfen |
283 |
> |
|
284 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
285 |
> |
hardwired LJ_rcut |
286 |
> |
|
287 |
> |
2004-02-06 19:14 tim |
288 |
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|
289 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
290 |
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message] |
291 |
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|
292 |
> |
2004-02-06 16:37 tim |
293 |
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|
294 |
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* ChangeLog, libBASS/Globals.cpp, |
295 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
296 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
297 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
298 |
> |
energy minimization for argon is working, need to add constraint |
299 |
> |
|
300 |
> |
2004-02-06 14:05 tim |
301 |
> |
|
302 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
303 |
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one more file into Makefile.in |
304 |
> |
|
305 |
> |
2004-02-06 13:58 tim |
306 |
> |
|
307 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
308 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
309 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
310 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
311 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
312 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
313 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
314 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
315 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
316 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
317 |
> |
some lines into global.cpp to make it work with energy minimization |
318 |
> |
|
319 |
> |
2004-02-04 17:26 tim |
320 |
> |
|
321 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
322 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
323 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
324 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
325 |
> |
Single version of conjugate gradient with golden search linesearch |
326 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
327 |
> |
|
328 |
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2004-02-03 17:54 tim |
329 |
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|
330 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
331 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
332 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
333 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
334 |
> |
|
335 |
> |
2004-02-03 15:47 tim |
336 |
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|
337 |
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* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
338 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
339 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
340 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
341 |
> |
SteepestDescent.hpp: [no log message] |
342 |
> |
|
343 |
> |
2004-02-03 15:43 tim |
344 |
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|
345 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
346 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
347 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
348 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
349 |
> |
constraint class |
350 |
> |
|
351 |
> |
2004-02-03 12:10 tim |
352 |
> |
|
353 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
354 |
> |
|
355 |
> |
2004-02-03 10:21 tim |
356 |
> |
|
357 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
358 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
359 |
> |
|
360 |
> |
2004-02-02 15:29 tim |
361 |
> |
|
362 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
363 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
364 |
> |
Adding GoldenSection and Brent LineSearch Method |
365 |
> |
|
366 |
> |
2004-01-30 16:47 tim |
367 |
> |
|
368 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
369 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
370 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
371 |
> |
MinimizerBase instead of a functor to do line seach |
372 |
> |
|
373 |
> |
2004-01-30 10:00 chrisfen |
374 |
> |
|
375 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
376 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
377 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
378 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
379 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
380 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
381 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
382 |
> |
has a working WATER.cpp forcefield and parser. This involved |
383 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
384 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
385 |
> |
This will be removed on the next commit... |
386 |
> |
|
387 |
> |
2004-01-29 18:00 gezelter |
388 |
> |
|
389 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
390 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
391 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
392 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
393 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
394 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
395 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
396 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
397 |
> |
member list fixes for rigid bodies |
398 |
> |
|
399 |
> |
2004-01-29 16:44 tim |
400 |
> |
|
401 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
402 |
> |
MinimizerParameterSet class. |
403 |
> |
|
404 |
> |
2004-01-28 17:44 tim |
405 |
> |
|
406 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
407 |
> |
NLModel0 and NLModel1 |
408 |
> |
|
409 |
> |
2004-01-28 15:40 tim |
410 |
> |
|
411 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
412 |
> |
of NLModel |
413 |
> |
|
414 |
> |
2004-01-27 15:34 gezelter |
415 |
> |
|
416 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
417 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
418 |
> |
|
419 |
> |
2004-01-27 15:34 gezelter |
420 |
> |
|
421 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
422 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
423 |
> |
stuff |
424 |
> |
|
425 |
> |
2004-01-27 14:39 gezelter |
426 |
> |
|
427 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
428 |
> |
|
429 |
> |
2004-01-27 14:39 gezelter |
430 |
> |
|
431 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
432 |
> |
|
433 |
> |
2004-01-27 14:38 gezelter |
434 |
> |
|
435 |
> |
* samples/argon/argon.bass: Longer run time to test argon |
436 |
> |
|
437 |
> |
2004-01-27 14:38 gezelter |
438 |
> |
|
439 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
440 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
441 |
> |
morning |
442 |
> |
|
443 |
> |
2004-01-27 14:37 gezelter |
444 |
> |
|
445 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
446 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
447 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
448 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
449 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
450 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
451 |
> |
do new rigidBody scheme |
452 |
> |
|
453 |
> |
2004-01-27 14:15 tim |
454 |
> |
|
455 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
456 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
457 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
458 |
> |
constraint for Nonlinear Optimization Model |
459 |
> |
|
460 |
> |
2004-01-26 17:01 gezelter |
461 |
> |
|
462 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
463 |
> |
Euler angles for orientation instead of unit vectors required |
464 |
> |
changes in MoLocator |
465 |
> |
|
466 |
> |
2004-01-26 16:53 gezelter |
467 |
> |
|
468 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
469 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
470 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
471 |
> |
euler angles |
472 |
> |
|
473 |
> |
2004-01-26 16:52 gezelter |
474 |
> |
|
475 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
476 |
> |
|
477 |
> |
2004-01-26 16:45 gezelter |
478 |
> |
|
479 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
480 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
481 |
> |
the ability to set orientation using a unit vector |
482 |
> |
|
483 |
> |
2004-01-26 16:26 gezelter |
484 |
> |
|
485 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
486 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
487 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
488 |
> |
ability to set orientation using a unit vector |
489 |
> |
|
490 |
> |
2004-01-26 13:52 gezelter |
491 |
> |
|
492 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
493 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
494 |
> |
|
495 |
> |
2004-01-22 12:34 chrisfen |
496 |
> |
|
497 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
498 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
499 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
500 |
> |
|
501 |
> |
2004-01-21 17:16 tim |
502 |
> |
|
503 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
504 |
> |
NLOPModel.hpp: constraint class in energy minimization |
505 |
> |
|
506 |
> |
2004-01-20 15:34 tim |
507 |
> |
|
508 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
509 |
> |
|
510 |
> |
2004-01-20 15:32 tim |
511 |
> |
|
512 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
513 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
514 |
> |
|
515 |
> |
2004-01-19 16:17 gezelter |
516 |
> |
|
517 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
518 |
> |
more user-friendly |
519 |
> |
|
520 |
> |
2004-01-19 13:51 chrisfen |
521 |
> |
|
522 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
523 |
> |
|
524 |
> |
2004-01-19 13:36 tim |
525 |
> |
|
526 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
527 |
> |
time, status time, thermal time and reset time are not divisible by |
528 |
> |
dt |
529 |
> |
|
530 |
> |
2004-01-19 11:10 gezelter |
531 |
> |
|
532 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
533 |
> |
won't complain |
534 |
> |
|
535 |
> |
2004-01-19 11:10 gezelter |
536 |
> |
|
537 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
538 |
> |
|
539 |
> |
2004-01-19 11:09 gezelter |
540 |
> |
|
541 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
542 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
543 |
> |
in mpiSimulation.cpp |
544 |
> |
|
545 |
> |
2004-01-19 11:08 gezelter |
546 |
> |
|
547 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
548 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
549 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
550 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
551 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
552 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
553 |
> |
|
554 |
> |
2004-01-16 16:55 tim |
555 |
> |
|
556 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
557 |
> |
eor file |
558 |
> |
|
559 |
> |
2004-01-16 16:51 mmeineke |
560 |
> |
|
561 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
562 |
> |
write eor files |
563 |
> |
|
564 |
> |
2004-01-16 10:01 mmeineke |
565 |
> |
|
566 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
567 |
> |
initialization of the AtomStruct |
568 |
> |
|
569 |
> |
2004-01-15 16:57 chuckv |
570 |
> |
|
571 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
572 |
> |
|
573 |
> |
2004-01-15 10:51 gezelter |
574 |
> |
|
575 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
576 |
> |
|
577 |
> |
2004-01-15 09:22 gezelter |
578 |
> |
|
579 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
580 |
> |
|
581 |
> |
2004-01-14 23:33 gezelter |
582 |
> |
|
583 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
584 |
> |
|
585 |
> |
2004-01-14 20:14 gezelter |
586 |
> |
|
587 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
588 |
> |
notifyCutoffs.F90: More work for adding charges |
589 |
> |
|
590 |
> |
2004-01-14 17:41 gezelter |
591 |
> |
|
592 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
593 |
> |
src/Makefile.in: autoconf fixes |
594 |
> |
|
595 |
> |
2004-01-14 11:28 mmeineke |
596 |
> |
|
597 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
598 |
> |
|
599 |
> |
2004-01-14 10:48 gezelter |
600 |
> |
|
601 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
602 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
603 |
> |
changes for icc8 |
604 |
> |
|
605 |
> |
2004-01-13 18:01 gezelter |
606 |
> |
|
607 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
608 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
609 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
610 |
> |
Changes for adding direct charge-charge interactions (with |
611 |
> |
switching function) |
612 |
> |
|
613 |
> |
2004-01-13 17:34 gezelter |
614 |
> |
|
615 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
616 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
617 |
> |
direct charge-charge interactions |
618 |
> |
|
619 |
> |
2004-01-13 17:11 tim |
620 |
> |
|
621 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
622 |
> |
|
623 |
> |
2004-01-13 16:22 tim |
624 |
> |
|
625 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
626 |
> |
|
627 |
> |
2004-01-13 15:35 tim |
628 |
> |
|
629 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
630 |
> |
eor file whenever it is used instead of rewinding it |
631 |
> |
|
632 |
> |
2004-01-13 15:04 tim |
633 |
> |
|
634 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
635 |
> |
of writeFrame |
636 |
> |
|
637 |
> |
2004-01-13 10:46 tim |
638 |
> |
|
639 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
640 |
> |
Merge the code of writeFinal and writeDump; |
641 |
> |
Adding sortingIndex into DumpWriter; |
642 |
> |
Fix a bug of writing last frame twice in integrator |
643 |
> |
|
644 |
> |
2004-01-12 17:54 tim |
645 |
> |
|
646 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
647 |
> |
a bug in copying string |
648 |
> |
|
649 |
> |
2004-01-12 15:37 tim |
650 |
> |
|
651 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
652 |
> |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
653 |
> |
master nodes |
654 |
> |
|
655 |
> |
2004-01-10 04:46 tim |
656 |
> |
|
657 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
658 |
> |
roll it back fix a bug of copying string to a pointer Still have |
659 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
660 |
> |
|
661 |
> |
2004-01-09 21:15 tim |
662 |
> |
|
663 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
664 |
> |
|
665 |
> |
2004-01-09 15:29 gezelter |
666 |
> |
|
667 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
668 |
> |
|
669 |
> |
2004-01-08 17:25 chuckv |
670 |
> |
|
671 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
672 |
> |
|
673 |
> |
2004-01-08 13:59 gezelter |
674 |
> |
|
675 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
676 |
> |
case |
677 |
> |
|
678 |
> |
2004-01-08 13:13 mmeineke |
679 |
> |
|
680 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
681 |
> |
state bug. |
682 |
> |
|
683 |
> |
2004-01-08 13:05 gezelter |
684 |
> |
|
685 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
686 |
> |
|
687 |
> |
2004-01-08 12:57 mmeineke |
688 |
> |
|
689 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
690 |
> |
exstended state bug |
691 |
> |
|
692 |
> |
2004-01-08 12:40 gezelter |
693 |
> |
|
694 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
695 |
> |
|
696 |
> |
2004-01-08 10:44 mmeineke |
697 |
> |
|
698 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
699 |
> |
XS state info flag |
700 |
> |
|
701 |
> |
2004-01-07 14:26 tim |
702 |
> |
|
703 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
704 |
> |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
705 |
> |
sending message from master node to itself in DumpWriter.cpp and |
706 |
> |
InitializeFromFile.cpp |
707 |
> |
|
708 |
> |
2004-01-06 14:49 chuckv |
709 |
> |
|
710 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
711 |
> |
performance fixes in the dipole dipole and reaction field code |
712 |
> |
|
713 |
> |
2004-01-06 13:54 chuckv |
714 |
> |
|
715 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
716 |
> |
little more sane |
717 |
> |
|
718 |
> |
2004-01-05 17:49 chuckv |
719 |
> |
|
720 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
721 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
722 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
723 |
> |
performance by reducing spurious function calls |
724 |
> |
|
725 |
> |
2004-01-05 17:18 chuckv |
726 |
> |
|
727 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
728 |
> |
|
729 |
> |
2004-01-05 17:18 chuckv |
730 |
> |
|
731 |
> |
* configure, ac-tools/configure.in: mpich mucking |
732 |
> |
|
733 |
> |
2004-01-05 17:12 chuckv |
734 |
> |
|
735 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
736 |
> |
|
737 |
> |
2004-01-05 16:00 chuckv |
738 |
> |
|
739 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
740 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
741 |
> |
lookup |
742 |
> |
|
743 |
> |
2003-12-29 14:56 chuckv |
744 |
> |
|
745 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
746 |
> |
third-party directory for code not written by us. Also added |
747 |
> |
Mersenne Twister random number generator code. This will eventually |
748 |
> |
replace sprng as the random number generator used by OOPSE. |
749 |
> |
|
750 |
> |
2003-12-22 16:26 chuckv |
751 |
> |
|
752 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
753 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
754 |
> |
Fixes to profile code. |
755 |
> |
|
756 |
> |
2003-12-19 15:36 mmeineke |
757 |
> |
|
758 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
759 |
> |
timing.F90, timing.f90: More profiling fixes. |
760 |
> |
|
761 |
> |
2003-12-19 15:19 chuckv |
762 |
> |
|
763 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
764 |
> |
|
765 |
> |
2003-12-19 15:17 chuckv |
766 |
> |
|
767 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
768 |
> |
|
769 |
> |
2003-12-19 13:53 mmeineke |
770 |
> |
|
771 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
772 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
773 |
> |
the code |
774 |
> |
|
775 |
> |
2003-12-19 12:25 mmeineke |
776 |
> |
|
777 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
778 |
> |
some profiling routines |
779 |
> |
|
780 |
> |
2003-12-19 10:12 mmeineke |
781 |
> |
|
782 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
783 |
> |
and GofRomega |
784 |
|
|
785 |
< |
added identification of identI in matchI. |
785 |
> |
additional work on randomBilayer |
786 |
> |
|
787 |
> |
2003-12-19 10:12 mmeineke |
788 |
> |
|
789 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
790 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
791 |
> |
GofRomega |
792 |
> |
|
793 |
> |
2003-12-18 16:47 mmeineke |
794 |
> |
|
795 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
796 |
> |
some profile functionality |
797 |
> |
|
798 |
> |
2003-12-18 15:46 chuckv |
799 |
> |
|
800 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
801 |
> |
Added functions for simple profiling in fortran. |
802 |
> |
|
803 |
> |
2003-12-17 15:13 chuckv |
804 |
> |
|
805 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
806 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
807 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
808 |
> |
zeros the array between scatters so half of the sum was being lost. |
809 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
810 |
> |
nlocal. |
811 |
> |
|
812 |
> |
2003-12-16 15:49 mmeineke |
813 |
> |
|
814 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
815 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
816 |
> |
gofRomega. both need to be debugged and tested. |
817 |
> |
|
818 |
> |
2003-12-12 10:42 gezelter |
819 |
> |
|
820 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
821 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
822 |
> |
gradients (to do minimizations) |
823 |
> |
|
824 |
> |
2003-12-12 10:33 mmeineke |
825 |
> |
|
826 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
827 |
> |
header |
828 |
> |
|
829 |
> |
2003-12-10 11:52 mmeineke |
830 |
> |
|
831 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
832 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
833 |
> |
randomBilayer to the build. Also move the random bilayer builder |
834 |
> |
from bilayerSys to randomBilayer |
835 |
> |
|
836 |
> |
2003-11-25 10:44 mmeineke |
837 |
> |
|
838 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
839 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
840 |
> |
TB3 in DUFF.frc |
841 |
> |
|
842 |
> |
2003-11-21 15:09 mmeineke |
843 |
> |
|
844 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
845 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
846 |
> |
message in SimInfo. Added a more informative error message in |
847 |
> |
InitializeFromFile |
848 |
> |
|
849 |
> |
2003-11-21 15:07 mmeineke |
850 |
> |
|
851 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
852 |
> |
ing in the GofR,CosTheta |
853 |
> |
|
854 |
> |
2003-11-21 14:31 chrisfen |
855 |
> |
|
856 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
857 |
> |
a bug in SimInfo ordering of radii |
858 |
> |
|
859 |
> |
2003-11-11 12:20 mmeineke |
860 |
> |
|
861 |
> |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
862 |
> |
a min function. |
863 |
> |
|
864 |
> |
2003-11-10 16:50 mmeineke |
865 |
> |
|
866 |
> |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
867 |
> |
reordered the rcut/ecr/boxSize initialization |
868 |
> |
|
869 |
> |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
870 |
> |
now exit when it runs into rcut or ecr. |
871 |
> |
|
872 |
> |
2003-11-07 16:46 chuckv |
873 |
> |
|
874 |
> |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
875 |
> |
oopseMPI_module.F90: Added support for compiling fortran without |
876 |
> |
use of mpich modules. We use mpif.h instead.: |
877 |
> |
|
878 |
> |
2003-11-07 12:09 mmeineke |
879 |
> |
|
880 |
> |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
881 |
> |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
882 |
> |
the atom loop in the NPT family of integrators. |
883 |
> |
|
884 |
> |
2003-11-06 17:01 mmeineke |
885 |
> |
|
886 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
887 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
888 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
889 |
> |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
890 |
> |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
891 |
> |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
892 |
> |
* useIntiTime => useInitialTime |
893 |
> |
|
894 |
> |
2003-11-06 14:24 mmeineke |
895 |
> |
|
896 |
> |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
897 |
> |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
898 |
> |
parse_tree.h: fixed the includes in the Make.dep |
899 |
> |
|
900 |
> |
2003-11-06 14:11 mmeineke |
901 |
> |
|
902 |
> |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
903 |
> |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
904 |
> |
new-templateless branch to the main trunk. |
905 |
> |
|
906 |
> |
bug Fixes include: * fixed the switching function from ortho to |
907 |
> |
non-ortho box. !!!!! THis was responsible for all of the |
908 |
> |
sudden deaths we saw. * some formating in the string when we |
909 |
> |
write out the extended system state. * added NPT.cpp to the |
910 |
> |
makefile.in |
911 |
> |
|
912 |
> |
2003-11-06 13:20 mmeineke |
913 |
> |
|
914 |
> |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
915 |
> |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
916 |
> |
bug. The box was not switching between orthorhombic and |
917 |
> |
non-orthorhombic wrapping correctly. we added a fabs() to |
918 |
> |
the check.which should fix it. |
919 |
> |
|
920 |
> |
2003-11-05 14:16 mmeineke |
921 |
> |
|
922 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
923 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
924 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
925 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
926 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
927 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
928 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
929 |
> |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
930 |
> |
some work on trying to find the compression bug |
931 |
> |
|
932 |
> |
2003-11-03 17:07 mmeineke |
933 |
> |
|
934 |
> |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
935 |
> |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
936 |
> |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
937 |
> |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
938 |
> |
most of standard template library from OOPSE. |
939 |
> |
|
940 |
> |
2003-10-31 16:06 mmeineke |
941 |
> |
|
942 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
943 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
944 |
> |
SimSetup.cpp: started work on template removal. |
945 |
> |
|
946 |
> |
2003-10-31 13:28 mmeineke |
947 |
> |
|
948 |
> |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
949 |
> |
added template stuff to the Maikefile template |
950 |
> |
|
951 |
> |
little changes to some printf format statements |
952 |
> |
|
953 |
> |
2003-10-31 13:28 mmeineke |
954 |
> |
|
955 |
> |
* libBASS/Makefile.in: added template stuff to the Maikefile |
956 |
> |
template |
957 |
> |
|
958 |
> |
2003-10-30 13:59 gezelter |
959 |
> |
|
960 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
961 |
> |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
962 |
> |
rList problems |
963 |
> |
|
964 |
> |
2003-10-30 09:11 gezelter |
965 |
> |
|
966 |
> |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
967 |
> |
queried before q0 was allocated. |
968 |
> |
|
969 |
> |
2003-10-29 15:41 mmeineke |
970 |
> |
|
971 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
972 |
> |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
973 |
> |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
974 |
> |
in bass.l |
975 |
> |
|
976 |
> |
fixed a little bug in the first time step, regarding the setting of |
977 |
> |
ecr and est in fortran |
978 |
> |
|
979 |
> |
2003-10-29 15:40 mmeineke |
980 |
> |
|
981 |
> |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
982 |
> |
|
983 |
> |
2003-10-29 12:55 mmeineke |
984 |
> |
|
985 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
986 |
> |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
987 |
> |
rcut is setup, as well as additional debugging comments. |
988 |
> |
|
989 |
> |
2003-10-29 09:28 gezelter |
990 |
> |
|
991 |
> |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
992 |
> |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
993 |
> |
templates |
994 |
> |
|
995 |
> |
2003-10-28 22:16 gezelter |
996 |
> |
|
997 |
> |
* src/Makefile.in: Refixed broken makefile |
998 |
> |
|
999 |
> |
2003-10-28 22:06 gezelter |
1000 |
> |
|
1001 |
> |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1002 |
> |
fixes |
1003 |
> |
|
1004 |
> |
2003-10-28 19:19 tim |
1005 |
> |
|
1006 |
> |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1007 |
> |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1008 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1009 |
> |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1010 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1011 |
> |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1012 |
> |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
1013 |
> |
file. |
1014 |
> |
|
1015 |
> |
2003-10-28 17:25 mmeineke |
1016 |
> |
|
1017 |
> |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1018 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1019 |
> |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1020 |
> |
how c calls fortran. All function pointers and fortran calls are |
1021 |
> |
rigidly typecast now. |
1022 |
> |
|
1023 |
> |
2003-10-28 15:42 gezelter |
1024 |
> |
|
1025 |
> |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1026 |
> |
Portability fixes |
1027 |
> |
|
1028 |
> |
2003-10-28 15:09 gezelter |
1029 |
> |
|
1030 |
> |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1031 |
> |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1032 |
> |
src/Makefile.in: Compatibility fixes |
1033 |
> |
|
1034 |
> |
2003-10-28 12:08 mmeineke |
1035 |
> |
|
1036 |
> |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1037 |
> |
started work on template removal |
1038 |
> |
|
1039 |
> |
2003-10-28 12:04 gezelter |
1040 |
> |
|
1041 |
> |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1042 |
> |
trying to understand extern "C" stuff for pointers |
1043 |
> |
|
1044 |
> |
2003-10-28 11:20 gezelter |
1045 |
> |
|
1046 |
> |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1047 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1048 |
> |
|
1049 |
> |
2003-10-28 11:03 gezelter |
1050 |
> |
|
1051 |
> |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1052 |
> |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1053 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1054 |
> |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1055 |
> |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1056 |
> |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1057 |
> |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1058 |
> |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1059 |
> |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1060 |
> |
more portable c header stuff Also, mod file fixes and portability |
1061 |
> |
changes Some fortran changes will need to be reversed. |
1062 |
> |
|
1063 |
> |
2003-10-28 11:03 gezelter |
1064 |
> |
|
1065 |
> |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1066 |
> |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1067 |
> |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1068 |
> |
portable c header stuff Also, mod file fixes and portability |
1069 |
> |
changes |
1070 |
> |
|
1071 |
> |
2003-10-28 11:02 gezelter |
1072 |
> |
|
1073 |
> |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1074 |
> |
stuff |
1075 |
> |
|
1076 |
> |
2003-10-27 18:00 gezelter |
1077 |
> |
|
1078 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1079 |
> |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1080 |
> |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1081 |
> |
|
1082 |
> |
2003-10-27 17:08 mmeineke |
1083 |
> |
|
1084 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1085 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1086 |
> |
added routines for the sysbuilder to work with simSetup |
1087 |
> |
|
1088 |
> |
remved the QuickBass routines, and had all parsing go through |
1089 |
> |
SimSetup. LatticeBilayer is in complete working order now. |
1090 |
> |
|
1091 |
> |
2003-10-27 17:07 mmeineke |
1092 |
> |
|
1093 |
> |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1094 |
> |
routines for the sysbuilder to work with simSetup |
1095 |
> |
|
1096 |
> |
2003-10-27 11:20 gezelter |
1097 |
> |
|
1098 |
> |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1099 |
> |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1100 |
> |
|
1101 |
> |
2003-10-24 17:17 mmeineke |
1102 |
> |
|
1103 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1104 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1105 |
> |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1106 |
> |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1107 |
> |
overhauled latticeBilayer into its own program. Removed sysBuild |
1108 |
> |
from the Makefile |
1109 |
> |
|
1110 |
> |
2003-10-24 12:36 gezelter |
1111 |
> |
|
1112 |
> |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1113 |
> |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1114 |
> |
builder |
1115 |
> |
|
1116 |
> |
2003-10-24 12:35 gezelter |
1117 |
> |
|
1118 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1119 |
> |
merge problem |
1120 |
> |
|
1121 |
> |
2003-10-23 14:57 mmeineke |
1122 |
> |
|
1123 |
> |
* samples/metals/Makefile.in: added eam ForceField files to the |
1124 |
> |
init |
1125 |
> |
|
1126 |
> |
fixed an eam mpi parmeter setup bug |
1127 |
> |
|
1128 |
> |
added the init file to the makefile |
1129 |
> |
|
1130 |
> |
2003-10-23 14:57 mmeineke |
1131 |
> |
|
1132 |
> |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1133 |
> |
to the init |
1134 |
> |
|
1135 |
> |
fixed an eam mpi parmeter setup bug |
1136 |
> |
|
1137 |
> |
2003-10-23 14:57 mmeineke |
1138 |
> |
|
1139 |
> |
* forceFields/Makefile.in: added eam ForceField files to the init |
1140 |
> |
|
1141 |
> |
2003-10-22 16:17 mmeineke |
1142 |
> |
|
1143 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1144 |
> |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1145 |
> |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1146 |
> |
no box skew allowed. |
1147 |
> |
|
1148 |
> |
2003-10-21 14:33 mmeineke |
1149 |
> |
|
1150 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1151 |
> |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1152 |
> |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1153 |
> |
* useInitTime = false: sets the origin time to 0.0 regardless |
1154 |
> |
of the time stamp in the .init file * default=> useInitTime = |
1155 |
> |
true; |
1156 |
> |
|
1157 |
> |
2003-10-17 16:19 mmeineke |
1158 |
> |
|
1159 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1160 |
> |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1161 |
> |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1162 |
> |
to the build list for both configure and configure.in |
1163 |
> |
|
1164 |
> |
fixed a number of bugs in the staticProps code. gofr is now |
1165 |
> |
working. |
1166 |
> |
|
1167 |
> |
2003-10-17 16:18 mmeineke |
1168 |
> |
|
1169 |
> |
* ac-tools/configure.in: added the staticProps directory to the |
1170 |
> |
build list for both configure and configure.in |
1171 |
> |
|
1172 |
> |
2003-10-17 16:17 mmeineke |
1173 |
> |
|
1174 |
> |
* configure: added the staticProps directory to the build list |
1175 |
> |
|
1176 |
> |
2003-10-16 14:16 mmeineke |
1177 |
> |
|
1178 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1179 |
> |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1180 |
> |
use linked lists instead of a vector. |
1181 |
> |
|
1182 |
> |
Fixed the makefile to build DumpReader.cpp |
1183 |
> |
|
1184 |
> |
Removed a comment output in Exclude.cpp |
1185 |
> |
|
1186 |
> |
Modified DumpWriter and Integrator to write an eor file every time |
1187 |
> |
a frame is written. This lets the .eor file represent the last |
1188 |
> |
written frame of a simulation. |
1189 |
> |
|
1190 |
> |
2003-10-10 12:10 mmeineke |
1191 |
> |
|
1192 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1193 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1194 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1195 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1196 |
> |
over to staticProps |
1197 |
> |
|
1198 |
> |
2003-10-09 17:09 mmeineke |
1199 |
> |
|
1200 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1201 |
> |
a position where it will compile and run first runs. |
1202 |
> |
|
1203 |
> |
2003-10-04 13:46 chuckv |
1204 |
> |
|
1205 |
> |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1206 |
> |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1207 |
> |
|
1208 |
> |
2003-10-04 13:08 chuckv |
1209 |
> |
|
1210 |
> |
* samples/metals/init_au.in: added Au init file for eam. |
1211 |
> |
|
1212 |
> |
2003-10-03 17:11 mmeineke |
1213 |
> |
|
1214 |
> |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1215 |
> |
entahlpy from the statwriter and thermo. |
1216 |
> |
|
1217 |
> |
2003-10-03 17:02 mmeineke |
1218 |
> |
|
1219 |
> |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1220 |
> |
statements in simError |
1221 |
> |
|
1222 |
> |
added a function to get the maxCutoff |
1223 |
> |
|
1224 |
> |
2003-10-03 17:01 mmeineke |
1225 |
> |
|
1226 |
> |
* libBASS/simError.c: changed the formating ogf the error |
1227 |
> |
statements in simError |
1228 |
> |
|
1229 |
> |
2003-09-30 11:00 mmeineke |
1230 |
> |
|
1231 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1232 |
> |
f90Flags so they are no longer overwritten by the compiler. |
1233 |
> |
|
1234 |
> |
2003-09-29 17:06 mmeineke |
1235 |
> |
|
1236 |
> |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1237 |
> |
for conifig.in |
1238 |
> |
|
1239 |
> |
fixed wrappers to extern "C" |
1240 |
> |
|
1241 |
> |
2003-09-29 17:06 mmeineke |
1242 |
> |
|
1243 |
> |
* ac-tools/configure.in: added mpif90 mod check back same for |
1244 |
> |
conifig.in |
1245 |
> |
|
1246 |
> |
2003-09-29 17:05 mmeineke |
1247 |
> |
|
1248 |
> |
* configure: added mpif90 mod check back |
1249 |
> |
|
1250 |
> |
2003-09-29 16:16 mmeineke |
1251 |
> |
|
1252 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1253 |
> |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1254 |
> |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1255 |
> |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1256 |
> |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1257 |
> |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1258 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1259 |
> |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1260 |
> |
found with SUN's SUNWspro.s1s7 |
1261 |
> |
|
1262 |
> |
2003-09-29 12:38 mmeineke |
1263 |
> |
|
1264 |
> |
* libmdtools/GenericData.hpp: light change in syntax. no |
1265 |
> |
signifigant change. |
1266 |
> |
|
1267 |
> |
2003-09-25 16:17 mmeineke |
1268 |
> |
|
1269 |
> |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1270 |
> |
additional remarks from icc -w3 (extra verbose output) |
1271 |
> |
|
1272 |
> |
2003-09-25 14:27 mmeineke |
1273 |
> |
|
1274 |
> |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1275 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1276 |
> |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1277 |
> |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1278 |
> |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1279 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1280 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1281 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1282 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1283 |
> |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1284 |
> |
gcc -Wall and g++ -Wall |
1285 |
> |
|
1286 |
> |
2003-09-25 13:54 gezelter |
1287 |
> |
|
1288 |
> |
* configure, ac-tools/configure.in: fixed a bug in configure |
1289 |
> |
|
1290 |
> |
2003-09-25 11:42 gezelter |
1291 |
> |
|
1292 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1293 |
> |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1294 |
> |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1295 |
> |
fixes for configure |
1296 |
> |
|
1297 |
> |
2003-09-24 14:34 mmeineke |
1298 |
> |
|
1299 |
> |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1300 |
> |
that it is called before the first Statistics are written. |
1301 |
> |
|
1302 |
> |
2003-09-23 15:36 gezelter |
1303 |
> |
|
1304 |
> |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1305 |
> |
bunch of Make.dep files to CVS |
1306 |
> |
|
1307 |
> |
2003-09-23 15:34 mmeineke |
1308 |
> |
|
1309 |
> |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1310 |
> |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1311 |
> |
|
1312 |
> |
Some small syntax cleaning in NPTfm and SimSetup |
1313 |
> |
|
1314 |
> |
2003-09-22 18:07 tim |
1315 |
> |
|
1316 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1317 |
> |
SimInfo.hpp: fix bug in calculating maxCutoff |
1318 |
> |
|
1319 |
> |
2003-09-22 16:23 mmeineke |
1320 |
> |
|
1321 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1322 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1323 |
> |
Converted NPTf to work with the NPT base class. |
1324 |
> |
|
1325 |
> |
Removed NPTfm and NPTim from cvs |
1326 |
> |
|
1327 |
> |
2003-09-19 15:00 mmeineke |
1328 |
> |
|
1329 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1330 |
> |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1331 |
> |
class. NPTi is up to date. NPTf is not. |
1332 |
> |
|
1333 |
> |
2003-09-19 11:03 mmeineke |
1334 |
> |
|
1335 |
> |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1336 |
> |
makefile |
1337 |
> |
|
1338 |
> |
2003-09-19 11:01 gezelter |
1339 |
> |
|
1340 |
> |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1341 |
> |
|
1342 |
> |
2003-09-19 11:01 gezelter |
1343 |
> |
|
1344 |
> |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1345 |
> |
(nearly) conserved quantities for both NPTi and NPTf |
1346 |
> |
|
1347 |
> |
2003-09-19 10:20 mmeineke |
1348 |
> |
|
1349 |
> |
* utils/Makefile.in: fixed a typo in the makefile. |
1350 |
> |
|
1351 |
> |
2003-09-19 09:55 gezelter |
1352 |
> |
|
1353 |
> |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1354 |
> |
samples/water/ssd.bass: [no log message] |
1355 |
> |
|
1356 |
> |
2003-09-19 09:22 tim |
1357 |
> |
|
1358 |
> |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1359 |
> |
|
1360 |
> |
2003-09-17 09:22 mmeineke |
1361 |
> |
|
1362 |
> |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1363 |
> |
work with constraints. |
1364 |
> |
|
1365 |
> |
2003-09-16 15:02 tim |
1366 |
> |
|
1367 |
> |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1368 |
> |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1369 |
> |
|
1370 |
> |
fixed conserved quantity in NPT (Still some small bug) |
1371 |
> |
|
1372 |
> |
NPTi appears very stable. |
1373 |
> |
|
1374 |
> |
2003-09-15 11:52 tim |
1375 |
> |
|
1376 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1377 |
> |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1378 |
> |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1379 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1380 |
> |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1381 |
> |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1382 |
> |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1383 |
> |
statWriter fix bug of vector wrapping at NPTi |
1384 |
> |
|
1385 |
> |
2003-09-12 11:20 gezelter |
1386 |
> |
|
1387 |
> |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1388 |
> |
Makefile.in |
1389 |
|
|
1390 |
+ |
2003-09-12 11:20 gezelter |
1391 |
+ |
|
1392 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1393 |
+ |
|
1394 |
|
2003-09-09 15:35 mmeineke |
1395 |
|
|
1396 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1464 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
1465 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1466 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
86 |
– |
|
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. |
1467 |
|
|
1468 |
|
2003-08-27 14:23 tim |
1469 |
|
|
1736 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1737 |
|
works..... |
1738 |
|
|
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) |
370 |
– |
|
1739 |
|
2003-08-08 12:48 mmeineke |
1740 |
|
|
1741 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
1792 |
|
2003-07-29 11:32 mmeineke |
1793 |
|
|
1794 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1795 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1796 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
429 |
< |
src/Makefile: working on the props code |
1795 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1796 |
> |
working on the props code |
1797 |
|
|
1798 |
|
2003-07-29 11:32 mmeineke |
1799 |
|
|
2920 |
|
|
2921 |
|
2003-03-25 09:29 mmeineke |
2922 |
|
|
2923 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2923 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2924 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2925 |
|
|
2926 |
|
2003-03-25 09:29 mmeineke |
2930 |
|
|
2931 |
|
2003-03-24 20:07 gezelter |
2932 |
|
|
2933 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
2933 |
> |
* samples/Makefile: moving tests to samples |
2934 |
|
|
2935 |
|
2003-03-24 20:06 gezelter |
2936 |
|
|
2937 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
2938 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
2939 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
2940 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
2941 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
2942 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
2943 |
< |
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 |
2937 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2938 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2939 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2940 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2941 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2942 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2943 |
> |
samples |
2944 |
|
|
2945 |
|
2003-03-24 19:51 gezelter |
2946 |
|
|
2948 |
|
|
2949 |
|
2003-03-24 19:46 gezelter |
2950 |
|
|
2951 |
< |
* 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 |
2951 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2952 |
|
|
2953 |
|
2003-03-24 16:55 gezelter |
2954 |
|
|
2965 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2966 |
|
do_Forces.F90: little bug fixes here and there |
2967 |
|
|
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 |
– |
|
2968 |
|
2003-03-24 10:26 mmeineke |
2969 |
|
|
2970 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
3074 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3075 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3076 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3077 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3078 |
< |
revision |
3077 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3078 |
> |
Tree |
3079 |
|
|
3080 |
|
2003-03-21 12:42 mmeineke |
3081 |
|
|
3132 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
3133 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
3134 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
3135 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
3136 |
< |
Tree |
3135 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
3136 |
> |
revision |
3137 |
|
|