1 |
tim |
1648 |
2004-10-25 17:46 tim |
2 |
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* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
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src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
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src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
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test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
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test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
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and Vector classes |
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10 |
tim |
1644 |
2004-10-25 12:03 tim |
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* ChangeLog, src/utils/GenericFactory.hpp, |
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test/utils/GenericFactoryTestCase.cpp, |
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test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
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GenericFactory Test Case. GenericFactory now can bed used to creat |
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ForcefieldFactory and IntegratorFactory etc. |
17 |
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2004-10-24 23:08 tim |
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* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
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brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
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brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
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get reconstructed |
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2004-10-24 02:55 tim |
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* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
28 |
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29 |
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2004-10-23 18:09 tim |
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31 |
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* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
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StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
33 |
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RigidBody.cpp: Refactoring in progress |
34 |
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35 |
tim |
1643 |
2004-10-22 18:09 tim |
36 |
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37 |
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* ChangeLog, src/brains/Snapshot.hpp, |
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src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
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test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
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test/brains/StuntDouble.hpp: more work in Snapshot |
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42 |
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2004-10-22 17:59 chrisfen |
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* src/: UseTheForce/LJFF.cpp, |
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UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
46 |
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god! It runs and conserves energy! |
47 |
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48 |
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2004-10-22 17:54 chrisfen |
49 |
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* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
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52 |
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2004-10-22 17:53 chrisfen |
53 |
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54 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
55 |
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UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
56 |
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UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
57 |
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brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
58 |
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breakey |
59 |
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60 |
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2004-10-22 17:53 chrisfen |
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62 |
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* make/Makefile.in: compiler flags |
63 |
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64 |
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2004-10-22 16:20 gezelter |
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66 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
67 |
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UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
68 |
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brains/fSimulation.h, types/AtomType.hpp, |
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types/DirectionalAtomType.hpp: fixey fixey |
70 |
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71 |
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2004-10-22 15:22 gezelter |
72 |
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73 |
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* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
74 |
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charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
75 |
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lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
76 |
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fortran files and c/Fortran interfaces |
77 |
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78 |
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2004-10-22 15:21 gezelter |
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80 |
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* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
81 |
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DirectionalAtomType.hpp, Makefile: More on AtomType and |
82 |
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DirectionalAtomType |
83 |
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84 |
tim |
1639 |
2004-10-22 09:47 gezelter |
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86 |
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* src/types/AtomType.hpp: Adding AtomType |
87 |
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88 |
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2004-10-21 16:31 tim |
89 |
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90 |
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* ChangeLog, src/brains/Snapshot.hpp, |
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src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
92 |
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src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
93 |
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src/math/Vector.hpp, src/math/Vector3.hpp, |
94 |
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test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
95 |
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Snapshot and SnapshotManager in progress |
96 |
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97 |
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2004-10-21 16:30 tim |
98 |
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99 |
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* test/brains/: BrainsTest.cpp, Makefile, |
100 |
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SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
101 |
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SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
102 |
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Snapshot and snapshotManager. |
103 |
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104 |
tim |
1630 |
2004-10-21 15:15 gezelter |
105 |
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106 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
107 |
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UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
108 |
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UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
109 |
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UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
110 |
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UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
111 |
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UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
112 |
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brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
113 |
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Fixey Fixey. |
114 |
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115 |
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2004-10-21 11:32 tim |
116 |
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117 |
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* src/utils/GenericData.cpp, src/utils/Makefile, |
118 |
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test/utils/Makefile, test/utils/UtilTest: remove some junk files |
119 |
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120 |
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2004-10-21 11:24 tim |
121 |
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122 |
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* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
123 |
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124 |
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2004-10-21 11:22 tim |
125 |
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126 |
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* ChangeLog, src/brains/SimSetup.cpp, |
127 |
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src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
128 |
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src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
129 |
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src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
130 |
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src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
131 |
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src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
132 |
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src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
133 |
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src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
134 |
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src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
135 |
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src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
136 |
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src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
137 |
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src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
138 |
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src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
139 |
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src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
140 |
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GenericData |
141 |
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142 |
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2004-10-21 10:25 chuckv |
143 |
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144 |
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* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
145 |
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module. |
146 |
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147 |
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2004-10-21 10:24 chuckv |
148 |
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149 |
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* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
150 |
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fortran lj module. |
151 |
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152 |
tim |
1625 |
2004-10-20 17:54 tim |
153 |
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154 |
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* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
155 |
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test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
156 |
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test/utils/PropertyMapTestCase.cpp, |
157 |
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test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
158 |
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GenericData and PropertyMap pass unit test. |
159 |
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160 |
tim |
1622 |
2004-10-20 16:52 gezelter |
161 |
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162 |
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* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
163 |
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DarkSide/sticky_interface.h: fixed a fortran name problem |
164 |
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165 |
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2004-10-20 16:38 tim |
166 |
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167 |
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* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
168 |
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GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
169 |
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UtilTest, UtilTest.cpp: adding generic data test case |
170 |
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171 |
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2004-10-20 16:16 chuckv |
172 |
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173 |
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* configure, ac-tools/aclocal.m4, |
174 |
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src/UseTheForce/DarkSide/Makefile, |
175 |
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src/UseTheForce/DarkSide/mpiSimulation.F90, |
176 |
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src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
177 |
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src/UseTheForce/DarkSide/simParallel.F90, |
178 |
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src/UseTheForce/DarkSide/simParallel_interface.h, |
179 |
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src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
180 |
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Fortran/C++ interface de-obfuscation project appears to be |
181 |
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complete! Woo hoo! |
182 |
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183 |
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2004-10-20 15:47 chuckv |
184 |
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185 |
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* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
186 |
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fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
187 |
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continues |
188 |
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189 |
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2004-10-20 15:46 chuckv |
190 |
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191 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
192 |
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UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
193 |
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UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
194 |
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UseTheForce/doForces_interface.h, |
195 |
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UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
196 |
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UseTheForce/DarkSide/atype_interface.h, |
197 |
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UseTheForce/DarkSide/eam_interface.h, |
198 |
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UseTheForce/DarkSide/gb_interface.h, |
199 |
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UseTheForce/DarkSide/mpiSimulation_interface.h, |
200 |
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UseTheForce/DarkSide/shapes_interface.h, |
201 |
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UseTheForce/DarkSide/simulation_interface.h, |
202 |
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UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
203 |
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brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
204 |
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de-obfuscation project (It is a very long story) |
205 |
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206 |
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2004-10-20 13:07 tim |
207 |
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208 |
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* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
209 |
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test/math/SquareMatrix3TestCase.cpp, |
210 |
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test/math/SquareMatrixTestCase.cpp, |
211 |
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test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
212 |
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213 |
tim |
1616 |
2004-10-20 00:52 tim |
214 |
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215 |
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* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
216 |
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SnapshotManager in design phase |
217 |
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218 |
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2004-10-19 23:54 gezelter |
219 |
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220 |
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* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
221 |
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problem prevented linking |
222 |
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223 |
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2004-10-19 23:54 gezelter |
224 |
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225 |
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* src/UseTheForce/Shapes_FF.cpp: fixed include |
226 |
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227 |
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2004-10-19 23:26 gezelter |
228 |
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229 |
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* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
230 |
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oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
231 |
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more fortran name mangling |
232 |
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233 |
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2004-10-19 23:23 gezelter |
234 |
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235 |
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* src/profiling/timing.F90: yet more fortran renaming |
236 |
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237 |
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2004-10-19 23:19 gezelter |
238 |
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239 |
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* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
240 |
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do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
241 |
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notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
242 |
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wrappers.F90: Fortran name cleanup continues |
243 |
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244 |
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2004-10-19 23:12 gezelter |
245 |
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246 |
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* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
247 |
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broken fortran stuff |
248 |
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249 |
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2004-10-19 23:02 gezelter |
250 |
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251 |
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* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
252 |
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atype_interface.h, atype_module.F90, atype_module_interface.h, |
253 |
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calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
254 |
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calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
255 |
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calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
256 |
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eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
257 |
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gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
258 |
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mpiSimulation_interface.h, mpiSimulation_module.F90, |
259 |
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mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
260 |
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shapes_interface.h, shapes_module.h, simulation.F90, |
261 |
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simulation_interface.h, simulation_module.F90, |
262 |
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simulation_module_interface.h, sticky.F90, sticky_interface.h, |
263 |
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sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
264 |
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name sanity on the fortran side |
265 |
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266 |
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2004-10-19 19:18 tim |
267 |
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268 |
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* test/math/SquareMatrix3TestCase.hpp: [no log message] |
269 |
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270 |
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2004-10-19 18:01 tim |
271 |
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272 |
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* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
273 |
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src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
274 |
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except diagonalize(), all of functions in math library pass the |
275 |
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test |
276 |
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277 |
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2004-10-19 17:43 chuckv |
278 |
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279 |
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* src/UseTheForce/do_Forces.h: Added correct prototypes for |
280 |
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C-fortran interface functions. |
281 |
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282 |
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2004-10-19 17:37 chuckv |
283 |
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284 |
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* src/UseTheForce/DarkSide/: atype_module_interface.h, |
285 |
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eam_module_inteface.h, gb_module_interface.h, |
286 |
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mpisimulation_module_interface.h, simulation_module_interface.h, |
287 |
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sticky_pair_module_interface.h: Added correct prototypes for |
288 |
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C-fortran interface functions. |
289 |
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290 |
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2004-10-19 16:28 tim |
291 |
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292 |
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* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
293 |
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src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
294 |
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test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
295 |
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test/math/RectMatrixTestCase.cpp, |
296 |
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test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
297 |
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test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
298 |
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bugs get fixed at math library |
299 |
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300 |
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2004-10-19 15:43 chuckv |
301 |
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302 |
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* src/UseTheForce/: DarkSide/atype_module_interface.h, |
303 |
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DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
304 |
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DarkSide/mpisimulation_module_interface.h, |
305 |
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DarkSide/simulation_module_interface.h, |
306 |
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DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
307 |
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DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
308 |
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DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
309 |
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DarkSide/simulation_module.F90, do_Forces.F90, |
310 |
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fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
311 |
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notifycutoffs_module_interface.h: Added new files for fortran |
312 |
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interface. |
313 |
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314 |
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2004-10-19 15:43 gezelter |
315 |
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316 |
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* src/UseTheForce/Makefile: regressing |
317 |
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318 |
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2004-10-19 15:40 gezelter |
319 |
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320 |
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* src/: UseTheForce/DarkSide/calc_shapes.F90, |
321 |
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UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
322 |
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working on shapes for portability |
323 |
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324 |
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2004-10-19 15:40 gezelter |
325 |
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326 |
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* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
327 |
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328 |
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2004-10-19 13:21 chrisfen |
329 |
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330 |
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* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
331 |
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findBegin |
332 |
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333 |
tim |
1603 |
2004-10-18 23:34 tim |
334 |
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335 |
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* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
336 |
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are fixed in Vector class |
337 |
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338 |
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2004-10-18 23:28 tim |
339 |
|
|
|
340 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
341 |
|
|
some bugs in RectMatrixTestCase |
342 |
|
|
|
343 |
|
|
2004-10-18 23:21 tim |
344 |
|
|
|
345 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
346 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
347 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
348 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
349 |
|
|
|
350 |
|
|
2004-10-18 18:13 tim |
351 |
|
|
|
352 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
353 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
354 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
355 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
356 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
357 |
|
|
tests on math library |
358 |
|
|
|
359 |
|
|
2004-10-18 16:03 tim |
360 |
|
|
|
361 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
362 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
363 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
364 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
365 |
|
|
more testing units |
366 |
|
|
|
367 |
|
|
2004-10-18 12:07 tim |
368 |
|
|
|
369 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
370 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
371 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
372 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
373 |
|
|
|
374 |
|
|
2004-10-18 11:30 gezelter |
375 |
|
|
|
376 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
377 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
378 |
|
|
\phi) |
379 |
|
|
|
380 |
|
|
2004-10-18 11:29 gezelter |
381 |
|
|
|
382 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
383 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
384 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
385 |
|
|
Shapes into OOPSE |
386 |
|
|
|
387 |
|
|
2004-10-18 10:21 gezelter |
388 |
|
|
|
389 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
390 |
|
|
|
391 |
|
|
2004-10-18 00:23 tim |
392 |
|
|
|
393 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
394 |
|
|
|
395 |
|
|
2004-10-18 00:23 tim |
396 |
|
|
|
397 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
398 |
|
|
test case |
399 |
|
|
|
400 |
tim |
1594 |
2004-10-16 20:19 tim |
401 |
|
|
|
402 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
403 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
404 |
|
|
progress |
405 |
|
|
|
406 |
|
|
2004-10-15 20:31 tim |
407 |
|
|
|
408 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
409 |
|
|
|
410 |
|
|
2004-10-15 16:11 tim |
411 |
|
|
|
412 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
413 |
|
|
IfstrstreamTestCase.hpp: adding test file |
414 |
|
|
|
415 |
|
|
2004-10-15 16:10 tim |
416 |
|
|
|
417 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
418 |
|
|
|
419 |
|
|
2004-10-15 15:42 tim |
420 |
|
|
|
421 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
422 |
|
|
|
423 |
|
|
2004-10-15 15:35 tim |
424 |
|
|
|
425 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
426 |
|
|
|
427 |
|
|
2004-10-15 15:34 tim |
428 |
|
|
|
429 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
430 |
|
|
namespace oopse |
431 |
|
|
|
432 |
|
|
2004-10-15 14:38 chuckv |
433 |
|
|
|
434 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
435 |
|
|
XLF and XLC. |
436 |
|
|
|
437 |
|
|
2004-10-15 13:28 tim |
438 |
|
|
|
439 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
440 |
|
|
adding ifstrstream test case |
441 |
|
|
|
442 |
|
|
2004-10-15 13:20 tim |
443 |
|
|
|
444 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
445 |
|
|
|
446 |
|
|
2004-10-15 13:18 tim |
447 |
|
|
|
448 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
449 |
|
|
|
450 |
|
|
2004-10-15 13:17 tim |
451 |
|
|
|
452 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
453 |
|
|
|
454 |
|
|
2004-10-15 13:16 tim |
455 |
|
|
|
456 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
457 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
458 |
|
|
|
459 |
|
|
2004-10-15 10:37 tim |
460 |
|
|
|
461 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
462 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
463 |
|
|
|
464 |
|
|
2004-10-15 10:20 tim |
465 |
|
|
|
466 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
467 |
|
|
|
468 |
|
|
2004-10-15 10:19 tim |
469 |
|
|
|
470 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
471 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
472 |
|
|
SquareMatrixTestCase class |
473 |
|
|
|
474 |
|
|
2004-10-15 02:52 tim |
475 |
|
|
|
476 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
477 |
|
|
|
478 |
|
|
2004-10-14 18:28 tim |
479 |
|
|
|
480 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
481 |
|
|
Vector.hpp: math library in progress |
482 |
|
|
|
483 |
|
|
2004-10-14 18:27 tim |
484 |
|
|
|
485 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
486 |
|
|
|
487 |
|
|
2004-10-13 18:53 tim |
488 |
|
|
|
489 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
490 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
491 |
|
|
|
492 |
|
|
2004-10-13 17:28 tim |
493 |
|
|
|
494 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
495 |
|
|
class |
496 |
|
|
|
497 |
|
|
2004-10-13 17:27 tim |
498 |
|
|
|
499 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
500 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
501 |
|
|
|
502 |
|
|
2004-10-13 17:24 tim |
503 |
|
|
|
504 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
505 |
|
|
|
506 |
|
|
2004-10-13 01:51 tim |
507 |
|
|
|
508 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
509 |
|
|
Vector3.hpp: refactory vector and matrix classes |
510 |
|
|
|
511 |
|
|
2004-10-13 01:50 tim |
512 |
|
|
|
513 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
514 |
|
|
|
515 |
|
|
2004-10-12 18:57 tim |
516 |
|
|
|
517 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
518 |
|
|
Matrix3x3d.hpp |
519 |
|
|
|
520 |
|
|
2004-10-12 14:08 tim |
521 |
|
|
|
522 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
523 |
|
|
|
524 |
|
|
2004-10-11 17:15 tim |
525 |
|
|
|
526 |
|
|
* src/: constraints/AbstractClasses.hpp, |
527 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
528 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
529 |
|
|
|
530 |
|
|
2004-10-11 16:54 tim |
531 |
|
|
|
532 |
|
|
* scripts/filepp: fix a bug in filepp |
533 |
|
|
|
534 |
|
|
2004-10-11 16:13 tim |
535 |
|
|
|
536 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
537 |
|
|
of compilers |
538 |
|
|
|
539 |
|
|
2004-10-11 16:10 tim |
540 |
|
|
|
541 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
542 |
|
|
c/c++ now |
543 |
|
|
|
544 |
|
|
2004-10-11 13:40 tim |
545 |
|
|
|
546 |
|
|
* make/Makefile.in: remove -module from F90Options |
547 |
|
|
|
548 |
|
|
2004-10-11 13:01 tim |
549 |
|
|
|
550 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
551 |
|
|
target directory |
552 |
|
|
|
553 |
|
|
2004-10-11 10:43 gezelter |
554 |
|
|
|
555 |
|
|
* make/Makefile.in: fixed makefile.in |
556 |
|
|
|
557 |
|
|
2004-10-11 09:51 tim |
558 |
|
|
|
559 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
560 |
|
|
machine |
561 |
|
|
|
562 |
|
|
2004-10-11 09:26 tim |
563 |
|
|
|
564 |
|
|
* forceFields/Makefile: add Makefile |
565 |
|
|
|
566 |
|
|
2004-10-11 09:23 tim |
567 |
|
|
|
568 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
569 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
570 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
571 |
|
|
directory |
572 |
|
|
|
573 |
|
|
2004-10-11 09:23 tim |
574 |
|
|
|
575 |
|
|
* samples/argon/Makefile: remove argon.dump and argon.eor from |
576 |
|
|
Makefile |
577 |
|
|
|
578 |
|
|
2004-10-09 01:01 tim |
579 |
|
|
|
580 |
|
|
* samples/: alkane/Makefile.in, argon/Makefile.in, |
581 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
582 |
|
|
Remove some Makefile.in |
583 |
|
|
|
584 |
|
|
2004-10-08 18:15 tim |
585 |
|
|
|
586 |
|
|
* make/Makefile.in: [no log message] |
587 |
|
|
|
588 |
|
|
2004-10-08 17:51 tim |
589 |
|
|
|
590 |
|
|
* make/Makefile.in: fix make install |
591 |
|
|
|
592 |
|
|
2004-10-08 17:10 tim |
593 |
|
|
|
594 |
|
|
* make/Makefile.in: adding make install |
595 |
|
|
|
596 |
|
|
2004-10-08 17:04 tim |
597 |
|
|
|
598 |
|
|
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
599 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
600 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
601 |
|
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
602 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
603 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
604 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
605 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
606 |
|
|
|
607 |
|
|
2004-10-06 18:03 gezelter |
608 |
|
|
|
609 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
610 |
|
|
stuff |
611 |
|
|
|
612 |
|
|
2004-10-06 18:03 gezelter |
613 |
|
|
|
614 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
615 |
|
|
make/Doxyfile, src/applications/getopt.c, |
616 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
617 |
|
|
build fixes |
618 |
|
|
|
619 |
|
|
2004-10-06 17:20 tim |
620 |
|
|
|
621 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
622 |
|
|
|
623 |
|
|
2004-10-06 17:19 tim |
624 |
|
|
|
625 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
626 |
|
|
and suffix |
627 |
|
|
|
628 |
|
|
2004-10-06 16:27 gezelter |
629 |
|
|
|
630 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
631 |
|
|
OOPSE-2.0 directory structure yet |
632 |
|
|
|
633 |
|
|
2004-10-06 16:27 gezelter |
634 |
|
|
|
635 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
636 |
|
|
|
637 |
gezelter |
1536 |
2004-10-06 16:22 gezelter |
638 |
gezelter |
1490 |
|
639 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
640 |
|
|
make/Makefile.in: cleaning up build process |
641 |
gezelter |
1490 |
|
642 |
tim |
1594 |
2004-10-06 15:01 chrisfen |
643 |
|
|
|
644 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
645 |
|
|
restraints more intelligent - no longer gives uninformative seg |
646 |
|
|
faults |
647 |
|
|
|
648 |
|
|
2004-10-06 14:55 gezelter |
649 |
|
|
|
650 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
651 |
|
|
|
652 |
gezelter |
1536 |
2004-10-06 14:51 gezelter |
653 |
gezelter |
1490 |
|
654 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
655 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
656 |
gezelter |
1490 |
|
657 |
tim |
1594 |
2004-10-06 13:53 tim |
658 |
|
|
|
659 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
660 |
|
|
|
661 |
|
|
2004-10-06 13:18 tim |
662 |
|
|
|
663 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
664 |
|
|
combine all of the static libraries to a big library |
665 |
|
|
|
666 |
|
|
2004-10-05 17:57 tim |
667 |
|
|
|
668 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
669 |
|
|
|
670 |
|
|
2004-10-05 14:37 tim |
671 |
|
|
|
672 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
673 |
|
|
UseTheForce/mpiSimulation_module.F90, |
674 |
|
|
UseTheForce/DarkSide/Makefile, |
675 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
676 |
|
|
mpiSimulation_module to DarkSide |
677 |
|
|
|
678 |
|
|
2004-10-05 14:35 tim |
679 |
|
|
|
680 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
681 |
|
|
library instead of shared library |
682 |
|
|
|
683 |
|
|
2004-10-05 09:14 tim |
684 |
|
|
|
685 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
686 |
|
|
to filepp |
687 |
|
|
|
688 |
|
|
2004-10-04 15:56 tim |
689 |
|
|
|
690 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
691 |
|
|
|
692 |
|
|
2004-10-04 11:24 gezelter |
693 |
|
|
|
694 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
695 |
|
|
|
696 |
|
|
2004-10-04 11:06 gezelter |
697 |
|
|
|
698 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
699 |
|
|
|
700 |
|
|
2004-10-04 10:27 gezelter |
701 |
|
|
|
702 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
703 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
704 |
|
|
shapes |
705 |
|
|
|
706 |
|
|
2004-10-01 23:40 tim |
707 |
|
|
|
708 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
709 |
|
|
|
710 |
|
|
2004-10-01 23:22 tim |
711 |
|
|
|
712 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
713 |
|
|
|
714 |
|
|
2004-10-01 16:59 tim |
715 |
|
|
|
716 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
717 |
|
|
|
718 |
gezelter |
1536 |
2004-10-01 16:22 gezelter |
719 |
gezelter |
1490 |
|
720 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
721 |
|
|
few minor build changes |
722 |
gezelter |
1490 |
|
723 |
tim |
1594 |
2004-10-01 16:11 tim |
724 |
|
|
|
725 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
726 |
|
|
|
727 |
|
|
2004-09-30 10:41 tim |
728 |
|
|
|
729 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
730 |
|
|
remove object files belong to current package. turn off silent |
731 |
|
|
mode |
732 |
|
|
|
733 |
|
|
2004-09-29 16:55 tim |
734 |
|
|
|
735 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
736 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
737 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
738 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
739 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
740 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
741 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
742 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
743 |
|
|
|
744 |
|
|
2004-09-29 16:54 tim |
745 |
|
|
|
746 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
747 |
|
|
script |
748 |
|
|
|
749 |
|
|
2004-09-29 16:32 tim |
750 |
|
|
|
751 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
752 |
|
|
|
753 |
|
|
2004-09-29 13:37 tim |
754 |
|
|
|
755 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
756 |
|
|
|
757 |
gezelter |
1536 |
2004-09-29 12:57 gezelter |
758 |
gezelter |
1490 |
|
759 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
760 |
gezelter |
1490 |
|
761 |
tim |
1594 |
2004-09-29 12:56 gezelter |
762 |
|
|
|
763 |
tim |
1603 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
764 |
tim |
1594 |
|
765 |
gezelter |
1536 |
2004-09-29 12:46 tim |
766 |
gezelter |
1490 |
|
767 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
768 |
gezelter |
1490 |
|
769 |
tim |
1594 |
2004-09-29 12:12 tim |
770 |
|
|
|
771 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
772 |
|
|
|
773 |
gezelter |
1536 |
2004-09-29 10:58 gezelter |
774 |
gezelter |
1490 |
|
775 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
776 |
gezelter |
1490 |
|
777 |
tim |
1594 |
2004-09-29 10:00 tim |
778 |
|
|
|
779 |
|
|
* make/Makefile: add print statment to rules |
780 |
|
|
|
781 |
|
|
2004-09-29 09:59 tim |
782 |
|
|
|
783 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
784 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
785 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
786 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
787 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
788 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
789 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
790 |
|
|
|
791 |
|
|
2004-09-28 21:55 tim |
792 |
|
|
|
793 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
794 |
|
|
which cause headache in bulding libutils |
795 |
|
|
|
796 |
|
|
2004-09-28 18:24 tim |
797 |
|
|
|
798 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
799 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
800 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
801 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
802 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
803 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
804 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
805 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
806 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
807 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
808 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
809 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
810 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
811 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
812 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
813 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
814 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
815 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
816 |
|
|
change directory structure of application. Every executable file is |
817 |
|
|
replaced in seperate directory |
818 |
|
|
|
819 |
|
|
2004-09-28 17:15 gezelter |
820 |
|
|
|
821 |
|
|
* lib/dummy: Keep that lib around, please. |
822 |
|
|
|
823 |
gezelter |
1536 |
2004-09-28 17:14 gezelter |
824 |
gezelter |
1490 |
|
825 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
826 |
|
|
starting a configure version |
827 |
gezelter |
1490 |
|
828 |
tim |
1594 |
2004-09-28 16:08 tim |
829 |
|
|
|
830 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
831 |
|
|
UseTheForce/DarkSide/Makefile, |
832 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
833 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
834 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
835 |
|
|
around to solve dependency problem |
836 |
|
|
|
837 |
gezelter |
1536 |
2004-09-28 15:43 tim |
838 |
gezelter |
1490 |
|
839 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
840 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
841 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
842 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
843 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
844 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
845 |
|
|
src/utils/Makefile: [no log message] |
846 |
gezelter |
1490 |
|
847 |
tim |
1594 |
2004-09-28 15:41 tim |
848 |
|
|
|
849 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
850 |
|
|
problem |
851 |
|
|
|
852 |
|
|
2004-09-28 11:13 tim |
853 |
|
|
|
854 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
855 |
|
|
src/io/Makefile: add yacc and lex rules |
856 |
|
|
|
857 |
|
|
2004-09-27 15:24 tim |
858 |
|
|
|
859 |
|
|
* make/Makefile: adding include path to F90Options |
860 |
|
|
|
861 |
|
|
2004-09-27 15:13 tim |
862 |
|
|
|
863 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
864 |
|
|
|
865 |
|
|
2004-09-24 11:27 tim |
866 |
|
|
|
867 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
868 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
869 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
870 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
871 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
872 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
873 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
874 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
875 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
876 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
877 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
878 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
879 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
880 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
881 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
882 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
883 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
884 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
885 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
886 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
887 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
888 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
889 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
890 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
891 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
892 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
893 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
894 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
895 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
896 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
897 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
898 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
899 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
900 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
901 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
902 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
903 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
904 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
905 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
906 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
907 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
908 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
909 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
910 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
911 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
912 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
913 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
914 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
915 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
916 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
917 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
918 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
919 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
920 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
921 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
922 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
923 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
924 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
925 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
926 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
927 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
928 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
929 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
930 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
931 |
|
|
|
932 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
933 |
gezelter |
1490 |
|
934 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
935 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
936 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
937 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
938 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
939 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
940 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
941 |
|
|
src/UseTheForce/fForceField.h, |
942 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
943 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
944 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
945 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
946 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
947 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
948 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
949 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
950 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
951 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
952 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
953 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
954 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
955 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
956 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
957 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
958 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
959 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
960 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
961 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
962 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
963 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
964 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
965 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
966 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
967 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
968 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
969 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
970 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
971 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
972 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
973 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
974 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
975 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
976 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
977 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
978 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
979 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
980 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
981 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
982 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
983 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
984 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
985 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
986 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
987 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
988 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
989 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
990 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
991 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
992 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
993 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
994 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
995 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
996 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
997 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
998 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
999 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
1000 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1001 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
1002 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1003 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
1004 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
1005 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1006 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1007 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
1008 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1009 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
1010 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
1011 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
1012 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
1013 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
1014 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
1015 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
1016 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
1017 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
1018 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
1019 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
1020 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
1021 |
|
|
src/utils/simError.c, src/utils/simError.h, |
1022 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
1023 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1024 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1025 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
1026 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
1027 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
1028 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1029 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
1030 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
1031 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
1032 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
1033 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
1034 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
1035 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
1036 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1037 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1038 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1039 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1040 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1041 |
|
|
src/applications/LatticeCreator.cpp, |
1042 |
|
|
src/applications/LatticeCreator.hpp, |
1043 |
|
|
src/applications/LatticeFactory.cpp, |
1044 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1045 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
1046 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1047 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
1048 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
1049 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1050 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1051 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1052 |
|
|
src/applications/simpleBuilder.ggo, |
1053 |
|
|
src/applications/simpleBuilderCmd.c, |
1054 |
|
|
src/integrators/AbstractClasses.hpp, |
1055 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1056 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1057 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1058 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1059 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
1060 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1061 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1062 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1063 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1064 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1065 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1066 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1067 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1068 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1069 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1070 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1071 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1072 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1073 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1074 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1075 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1076 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1077 |
|
|
samples/argon/500.in, samples/argon/500.md, |
1078 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
1079 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1080 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
1081 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1082 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1083 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1084 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1085 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1086 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1087 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1088 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1089 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1090 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1091 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1092 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1093 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1094 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1095 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1096 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1097 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1098 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1099 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1100 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1101 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1102 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1103 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1104 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1105 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
1106 |
gezelter |
1490 |
|
1107 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
1108 |
gezelter |
1490 |
|
1109 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
1110 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
1111 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
1112 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
1113 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
1114 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
1115 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
1116 |
|
|
src/UseTheForce/fForceField.h, |
1117 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
1118 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
1119 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
1120 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
1121 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
1122 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
1123 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
1124 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
1125 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
1126 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
1127 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
1128 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
1129 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
1130 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
1131 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
1132 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
1133 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
1134 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
1135 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
1136 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
1137 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
1138 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
1139 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
1140 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
1141 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
1142 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
1143 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1144 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
1145 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
1146 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
1147 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
1148 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
1149 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
1150 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
1151 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
1152 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
1153 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
1154 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
1155 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1156 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1157 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1158 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
1159 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
1160 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
1161 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
1162 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
1163 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1164 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
1165 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1166 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1167 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
1168 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
1169 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
1170 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
1171 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
1172 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
1173 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
1174 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
1175 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1176 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
1177 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1178 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
1179 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
1180 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1181 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1182 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
1183 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1184 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
1185 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
1186 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
1187 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
1188 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
1189 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
1190 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
1191 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
1192 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
1193 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
1194 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
1195 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
1196 |
|
|
src/utils/simError.c, src/utils/simError.h, |
1197 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
1198 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1199 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1200 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
1201 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
1202 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
1203 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1204 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
1205 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
1206 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
1207 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
1208 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
1209 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
1210 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
1211 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1212 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1213 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1214 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1215 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1216 |
|
|
src/applications/LatticeCreator.cpp, |
1217 |
|
|
src/applications/LatticeCreator.hpp, |
1218 |
|
|
src/applications/LatticeFactory.cpp, |
1219 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1220 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
1221 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1222 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
1223 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
1224 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1225 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1226 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1227 |
|
|
src/applications/simpleBuilder.ggo, |
1228 |
|
|
src/applications/simpleBuilderCmd.c, |
1229 |
|
|
src/integrators/AbstractClasses.hpp, |
1230 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1231 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1232 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1233 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1234 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
1235 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1236 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1237 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1238 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1239 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1240 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1241 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1242 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1243 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1244 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1245 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1246 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1247 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1248 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1249 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1250 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1251 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1252 |
|
|
samples/argon/500.in, samples/argon/500.md, |
1253 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
1254 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1255 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
1256 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1257 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1258 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1259 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1260 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1261 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1262 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1263 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1264 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1265 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1266 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1267 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1268 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1269 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1270 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1271 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1272 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1273 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1274 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1275 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1276 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1277 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1278 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1279 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1280 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
1281 |
gezelter |
1490 |
|