1 |
tim |
1677 |
2004-10-28 14:06 tim |
2 |
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* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
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src/applications/simpleBuilder/simpleBuilder.cpp, |
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src/utils/next_combination.hpp, test/utils/Makefile, |
6 |
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test/utils/NextCombinationTestCase.cpp, |
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test/utils/ReplaceWildCardTestCase.cpp, |
8 |
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test/utils/next_combination.hpp: STL next_permutation like |
9 |
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next_combination is working |
10 |
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11 |
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2004-10-28 12:22 chrisfen |
12 |
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13 |
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* src/UseTheForce/WATER.cpp: fix of setDipoles |
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15 |
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2004-10-28 12:20 gezelter |
16 |
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17 |
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* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
18 |
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shapeFile |
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20 |
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2004-10-28 12:20 gezelter |
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* samples/shape/linear.md: forgot the orientation line |
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24 |
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2004-10-28 11:56 gezelter |
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26 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
27 |
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UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
28 |
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UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
29 |
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declaration foo |
30 |
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31 |
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2004-10-28 11:55 gezelter |
32 |
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* samples/lipid/5x5.md: uncommented .in line |
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35 |
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2004-10-28 10:42 tim |
36 |
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37 |
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* test/utils/: Makefile, NextCombinationTestCase.cpp, |
38 |
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NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
39 |
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in progress |
40 |
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41 |
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2004-10-28 10:15 tim |
42 |
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43 |
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* test/utils/: NextCombinationTestCase.cpp, |
44 |
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NextCombinationTestCase.hpp: adding next_combination test case |
45 |
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46 |
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2004-10-28 10:02 tim |
47 |
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48 |
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* test/utils/next_combination.hpp: STL Compatible combination |
49 |
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sequence generator |
50 |
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51 |
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2004-10-28 01:23 tim |
52 |
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53 |
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* test/utils/: GenerateCombination.hpp, |
54 |
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ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
55 |
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56 |
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2004-10-28 01:16 tim |
57 |
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58 |
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* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
59 |
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next_combination function. |
60 |
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61 |
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2004-10-27 22:27 tim |
62 |
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63 |
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* test/utils/ReplaceWildCard.hpp: no message |
64 |
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65 |
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2004-10-27 22:14 tim |
66 |
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67 |
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* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
68 |
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ReplaceWildCard(recursive version) is working, need refactoring. An |
69 |
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iterative version is on the way |
70 |
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71 |
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2004-10-27 21:28 tim |
72 |
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73 |
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* test/utils/: Makefile, ReplaceWildCard.hpp, |
74 |
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ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
75 |
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76 |
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2004-10-27 21:08 tim |
77 |
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78 |
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* test/utils/: ReplaceWildCardTestCase.cpp, |
79 |
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ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
80 |
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81 |
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2004-10-27 18:17 tim |
82 |
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83 |
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* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
84 |
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test |
85 |
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86 |
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2004-10-27 01:25 tim |
87 |
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88 |
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* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
89 |
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char matching is on the way |
90 |
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91 |
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2004-10-27 01:07 tim |
92 |
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93 |
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* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
94 |
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95 |
tim |
1674 |
2004-10-26 22:00 gezelter |
96 |
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97 |
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* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
98 |
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99 |
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2004-10-26 21:20 gezelter |
100 |
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101 |
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* src/UseTheForce/ForceFields.hpp: subclass foo |
102 |
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103 |
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2004-10-26 21:16 gezelter |
104 |
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105 |
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* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
106 |
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string conversion |
107 |
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108 |
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2004-10-26 19:01 gezelter |
109 |
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110 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
111 |
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UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
112 |
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brains/SimSetup.hpp: char* -> string |
113 |
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114 |
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2004-10-26 17:25 gezelter |
115 |
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116 |
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* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
117 |
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Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
118 |
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ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
119 |
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isXXX |
120 |
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121 |
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2004-10-26 17:25 gezelter |
122 |
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123 |
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* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
124 |
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define name collision |
125 |
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126 |
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2004-10-26 17:24 gezelter |
127 |
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128 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
129 |
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UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
130 |
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UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
131 |
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UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
132 |
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UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
133 |
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forcefield refactoring for shapes |
134 |
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135 |
tim |
1677 |
2004-10-26 17:24 gezelter |
136 |
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137 |
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* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
138 |
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Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
139 |
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linear.md, linear.shape, toluene.shape: adding sample shape |
140 |
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directory |
141 |
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142 |
tim |
1674 |
2004-10-26 17:19 tim |
143 |
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144 |
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* ChangeLog, src/brains/DataStorage.cpp, |
145 |
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src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
146 |
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test/brains/DataStorageTestCase.cpp, |
147 |
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test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
148 |
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DataStorage passes unit test |
149 |
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150 |
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2004-10-26 13:03 chrisfen |
151 |
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152 |
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* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
153 |
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Changes to help advance shapes |
154 |
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155 |
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2004-10-26 13:02 chrisfen |
156 |
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157 |
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* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
158 |
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Shapes force field reader |
159 |
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160 |
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2004-10-26 12:28 tim |
161 |
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162 |
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* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
163 |
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SnapshotTestCase in progress |
164 |
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165 |
tim |
1648 |
2004-10-25 17:46 tim |
166 |
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167 |
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* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
168 |
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src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
169 |
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src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
170 |
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test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
171 |
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test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
172 |
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and Vector classes |
173 |
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174 |
tim |
1644 |
2004-10-25 12:03 tim |
175 |
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176 |
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* ChangeLog, src/utils/GenericFactory.hpp, |
177 |
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test/utils/GenericFactoryTestCase.cpp, |
178 |
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test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
179 |
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GenericFactory Test Case. GenericFactory now can bed used to creat |
180 |
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ForcefieldFactory and IntegratorFactory etc. |
181 |
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182 |
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2004-10-24 23:08 tim |
183 |
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184 |
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* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
185 |
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brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
186 |
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brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
187 |
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get reconstructed |
188 |
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189 |
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2004-10-24 02:55 tim |
190 |
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191 |
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* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
192 |
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193 |
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2004-10-23 18:09 tim |
194 |
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195 |
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* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
196 |
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StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
197 |
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RigidBody.cpp: Refactoring in progress |
198 |
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199 |
tim |
1643 |
2004-10-22 18:09 tim |
200 |
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201 |
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* ChangeLog, src/brains/Snapshot.hpp, |
202 |
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src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
203 |
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test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
204 |
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test/brains/StuntDouble.hpp: more work in Snapshot |
205 |
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206 |
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2004-10-22 17:59 chrisfen |
207 |
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208 |
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* src/: UseTheForce/LJFF.cpp, |
209 |
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UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
210 |
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god! It runs and conserves energy! |
211 |
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212 |
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2004-10-22 17:54 chrisfen |
213 |
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214 |
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* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
215 |
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216 |
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2004-10-22 17:53 chrisfen |
217 |
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218 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
219 |
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UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
220 |
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UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
221 |
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brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
222 |
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breakey |
223 |
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224 |
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2004-10-22 17:53 chrisfen |
225 |
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226 |
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* make/Makefile.in: compiler flags |
227 |
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228 |
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2004-10-22 16:20 gezelter |
229 |
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230 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
231 |
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UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
232 |
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brains/fSimulation.h, types/AtomType.hpp, |
233 |
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types/DirectionalAtomType.hpp: fixey fixey |
234 |
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235 |
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2004-10-22 15:22 gezelter |
236 |
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237 |
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* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
238 |
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charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
239 |
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lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
240 |
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fortran files and c/Fortran interfaces |
241 |
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242 |
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2004-10-22 15:21 gezelter |
243 |
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244 |
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* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
245 |
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DirectionalAtomType.hpp, Makefile: More on AtomType and |
246 |
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DirectionalAtomType |
247 |
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248 |
tim |
1639 |
2004-10-22 09:47 gezelter |
249 |
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250 |
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* src/types/AtomType.hpp: Adding AtomType |
251 |
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252 |
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2004-10-21 16:31 tim |
253 |
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254 |
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* ChangeLog, src/brains/Snapshot.hpp, |
255 |
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src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
256 |
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src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
257 |
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src/math/Vector.hpp, src/math/Vector3.hpp, |
258 |
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test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
259 |
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Snapshot and SnapshotManager in progress |
260 |
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261 |
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2004-10-21 16:30 tim |
262 |
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263 |
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* test/brains/: BrainsTest.cpp, Makefile, |
264 |
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SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
265 |
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SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
266 |
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Snapshot and snapshotManager. |
267 |
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268 |
tim |
1630 |
2004-10-21 15:15 gezelter |
269 |
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270 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
271 |
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UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
272 |
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UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
273 |
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UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
274 |
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UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
275 |
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UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
276 |
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brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
277 |
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Fixey Fixey. |
278 |
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279 |
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2004-10-21 11:32 tim |
280 |
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281 |
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* src/utils/GenericData.cpp, src/utils/Makefile, |
282 |
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test/utils/Makefile, test/utils/UtilTest: remove some junk files |
283 |
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284 |
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2004-10-21 11:24 tim |
285 |
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286 |
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* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
287 |
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288 |
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2004-10-21 11:22 tim |
289 |
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290 |
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* ChangeLog, src/brains/SimSetup.cpp, |
291 |
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src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
292 |
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src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
293 |
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src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
294 |
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src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
295 |
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src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
296 |
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src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
297 |
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src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
298 |
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src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
299 |
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src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
300 |
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src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
301 |
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src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
302 |
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src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
303 |
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src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
304 |
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GenericData |
305 |
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306 |
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2004-10-21 10:25 chuckv |
307 |
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308 |
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* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
309 |
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module. |
310 |
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311 |
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2004-10-21 10:24 chuckv |
312 |
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313 |
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* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
314 |
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fortran lj module. |
315 |
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316 |
tim |
1625 |
2004-10-20 17:54 tim |
317 |
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318 |
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* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
319 |
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test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
320 |
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test/utils/PropertyMapTestCase.cpp, |
321 |
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test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
322 |
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GenericData and PropertyMap pass unit test. |
323 |
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324 |
tim |
1622 |
2004-10-20 16:52 gezelter |
325 |
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326 |
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* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
327 |
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DarkSide/sticky_interface.h: fixed a fortran name problem |
328 |
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329 |
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2004-10-20 16:38 tim |
330 |
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331 |
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* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
332 |
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GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
333 |
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UtilTest, UtilTest.cpp: adding generic data test case |
334 |
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335 |
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2004-10-20 16:16 chuckv |
336 |
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337 |
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* configure, ac-tools/aclocal.m4, |
338 |
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src/UseTheForce/DarkSide/Makefile, |
339 |
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src/UseTheForce/DarkSide/mpiSimulation.F90, |
340 |
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src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
341 |
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src/UseTheForce/DarkSide/simParallel.F90, |
342 |
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src/UseTheForce/DarkSide/simParallel_interface.h, |
343 |
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src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
344 |
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Fortran/C++ interface de-obfuscation project appears to be |
345 |
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complete! Woo hoo! |
346 |
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347 |
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2004-10-20 15:47 chuckv |
348 |
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349 |
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* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
350 |
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fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
351 |
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continues |
352 |
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353 |
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2004-10-20 15:46 chuckv |
354 |
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355 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
356 |
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UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
357 |
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UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
358 |
|
|
UseTheForce/doForces_interface.h, |
359 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
360 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
361 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
362 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
363 |
|
|
UseTheForce/DarkSide/mpiSimulation_interface.h, |
364 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
365 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
366 |
|
|
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
367 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
368 |
|
|
de-obfuscation project (It is a very long story) |
369 |
|
|
|
370 |
|
|
2004-10-20 13:07 tim |
371 |
|
|
|
372 |
|
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
373 |
|
|
test/math/SquareMatrix3TestCase.cpp, |
374 |
|
|
test/math/SquareMatrixTestCase.cpp, |
375 |
|
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
376 |
|
|
|
377 |
tim |
1616 |
2004-10-20 00:52 tim |
378 |
|
|
|
379 |
|
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
380 |
|
|
SnapshotManager in design phase |
381 |
|
|
|
382 |
|
|
2004-10-19 23:54 gezelter |
383 |
|
|
|
384 |
|
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
385 |
|
|
problem prevented linking |
386 |
|
|
|
387 |
|
|
2004-10-19 23:54 gezelter |
388 |
|
|
|
389 |
|
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
390 |
|
|
|
391 |
|
|
2004-10-19 23:26 gezelter |
392 |
|
|
|
393 |
|
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
394 |
|
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
395 |
|
|
more fortran name mangling |
396 |
|
|
|
397 |
|
|
2004-10-19 23:23 gezelter |
398 |
|
|
|
399 |
|
|
* src/profiling/timing.F90: yet more fortran renaming |
400 |
|
|
|
401 |
|
|
2004-10-19 23:19 gezelter |
402 |
|
|
|
403 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
404 |
|
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
405 |
|
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
406 |
|
|
wrappers.F90: Fortran name cleanup continues |
407 |
|
|
|
408 |
|
|
2004-10-19 23:12 gezelter |
409 |
|
|
|
410 |
|
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
411 |
|
|
broken fortran stuff |
412 |
|
|
|
413 |
|
|
2004-10-19 23:02 gezelter |
414 |
|
|
|
415 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
416 |
|
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
417 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
418 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
419 |
|
|
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
420 |
|
|
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
421 |
|
|
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
422 |
|
|
mpiSimulation_interface.h, mpiSimulation_module.F90, |
423 |
|
|
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
424 |
|
|
shapes_interface.h, shapes_module.h, simulation.F90, |
425 |
|
|
simulation_interface.h, simulation_module.F90, |
426 |
|
|
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
427 |
|
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
428 |
|
|
name sanity on the fortran side |
429 |
|
|
|
430 |
|
|
2004-10-19 19:18 tim |
431 |
|
|
|
432 |
|
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
433 |
|
|
|
434 |
|
|
2004-10-19 18:01 tim |
435 |
|
|
|
436 |
|
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
437 |
|
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
438 |
|
|
except diagonalize(), all of functions in math library pass the |
439 |
|
|
test |
440 |
|
|
|
441 |
|
|
2004-10-19 17:43 chuckv |
442 |
|
|
|
443 |
|
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
444 |
|
|
C-fortran interface functions. |
445 |
|
|
|
446 |
|
|
2004-10-19 17:37 chuckv |
447 |
|
|
|
448 |
|
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
449 |
|
|
eam_module_inteface.h, gb_module_interface.h, |
450 |
|
|
mpisimulation_module_interface.h, simulation_module_interface.h, |
451 |
|
|
sticky_pair_module_interface.h: Added correct prototypes for |
452 |
|
|
C-fortran interface functions. |
453 |
|
|
|
454 |
|
|
2004-10-19 16:28 tim |
455 |
|
|
|
456 |
|
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
457 |
|
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
458 |
|
|
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
459 |
|
|
test/math/RectMatrixTestCase.cpp, |
460 |
|
|
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
461 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
462 |
|
|
bugs get fixed at math library |
463 |
|
|
|
464 |
|
|
2004-10-19 15:43 chuckv |
465 |
|
|
|
466 |
|
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
467 |
|
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
468 |
|
|
DarkSide/mpisimulation_module_interface.h, |
469 |
|
|
DarkSide/simulation_module_interface.h, |
470 |
|
|
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
471 |
|
|
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
472 |
|
|
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
473 |
|
|
DarkSide/simulation_module.F90, do_Forces.F90, |
474 |
|
|
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
475 |
|
|
notifycutoffs_module_interface.h: Added new files for fortran |
476 |
|
|
interface. |
477 |
|
|
|
478 |
|
|
2004-10-19 15:43 gezelter |
479 |
|
|
|
480 |
|
|
* src/UseTheForce/Makefile: regressing |
481 |
|
|
|
482 |
|
|
2004-10-19 15:40 gezelter |
483 |
|
|
|
484 |
|
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
485 |
|
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
486 |
|
|
working on shapes for portability |
487 |
|
|
|
488 |
|
|
2004-10-19 15:40 gezelter |
489 |
|
|
|
490 |
|
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
491 |
|
|
|
492 |
|
|
2004-10-19 13:21 chrisfen |
493 |
|
|
|
494 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
495 |
|
|
findBegin |
496 |
|
|
|
497 |
tim |
1603 |
2004-10-18 23:34 tim |
498 |
|
|
|
499 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
500 |
|
|
are fixed in Vector class |
501 |
|
|
|
502 |
|
|
2004-10-18 23:28 tim |
503 |
|
|
|
504 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
505 |
|
|
some bugs in RectMatrixTestCase |
506 |
|
|
|
507 |
|
|
2004-10-18 23:21 tim |
508 |
|
|
|
509 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
510 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
511 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
512 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
513 |
|
|
|
514 |
|
|
2004-10-18 18:13 tim |
515 |
|
|
|
516 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
517 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
518 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
519 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
520 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
521 |
|
|
tests on math library |
522 |
|
|
|
523 |
|
|
2004-10-18 16:03 tim |
524 |
|
|
|
525 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
526 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
527 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
528 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
529 |
|
|
more testing units |
530 |
|
|
|
531 |
|
|
2004-10-18 12:07 tim |
532 |
|
|
|
533 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
534 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
535 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
536 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
537 |
|
|
|
538 |
|
|
2004-10-18 11:30 gezelter |
539 |
|
|
|
540 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
541 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
542 |
|
|
\phi) |
543 |
|
|
|
544 |
|
|
2004-10-18 11:29 gezelter |
545 |
|
|
|
546 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
547 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
548 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
549 |
|
|
Shapes into OOPSE |
550 |
|
|
|
551 |
|
|
2004-10-18 10:21 gezelter |
552 |
|
|
|
553 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
554 |
|
|
|
555 |
|
|
2004-10-18 00:23 tim |
556 |
|
|
|
557 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
558 |
|
|
|
559 |
|
|
2004-10-18 00:23 tim |
560 |
|
|
|
561 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
562 |
|
|
test case |
563 |
|
|
|
564 |
tim |
1594 |
2004-10-16 20:19 tim |
565 |
|
|
|
566 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
567 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
568 |
|
|
progress |
569 |
|
|
|
570 |
|
|
2004-10-15 20:31 tim |
571 |
|
|
|
572 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
573 |
|
|
|
574 |
|
|
2004-10-15 16:11 tim |
575 |
|
|
|
576 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
577 |
|
|
IfstrstreamTestCase.hpp: adding test file |
578 |
|
|
|
579 |
|
|
2004-10-15 16:10 tim |
580 |
|
|
|
581 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
582 |
|
|
|
583 |
|
|
2004-10-15 15:42 tim |
584 |
|
|
|
585 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
586 |
|
|
|
587 |
|
|
2004-10-15 15:35 tim |
588 |
|
|
|
589 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
590 |
|
|
|
591 |
|
|
2004-10-15 15:34 tim |
592 |
|
|
|
593 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
594 |
|
|
namespace oopse |
595 |
|
|
|
596 |
|
|
2004-10-15 14:38 chuckv |
597 |
|
|
|
598 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
599 |
|
|
XLF and XLC. |
600 |
|
|
|
601 |
|
|
2004-10-15 13:28 tim |
602 |
|
|
|
603 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
604 |
|
|
adding ifstrstream test case |
605 |
|
|
|
606 |
|
|
2004-10-15 13:20 tim |
607 |
|
|
|
608 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
609 |
|
|
|
610 |
|
|
2004-10-15 13:18 tim |
611 |
|
|
|
612 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
613 |
|
|
|
614 |
|
|
2004-10-15 13:17 tim |
615 |
|
|
|
616 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
617 |
|
|
|
618 |
|
|
2004-10-15 13:16 tim |
619 |
|
|
|
620 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
621 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
622 |
|
|
|
623 |
|
|
2004-10-15 10:37 tim |
624 |
|
|
|
625 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
626 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
627 |
|
|
|
628 |
|
|
2004-10-15 10:20 tim |
629 |
|
|
|
630 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
631 |
|
|
|
632 |
|
|
2004-10-15 10:19 tim |
633 |
|
|
|
634 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
635 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
636 |
|
|
SquareMatrixTestCase class |
637 |
|
|
|
638 |
|
|
2004-10-15 02:52 tim |
639 |
|
|
|
640 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
641 |
|
|
|
642 |
|
|
2004-10-14 18:28 tim |
643 |
|
|
|
644 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
645 |
|
|
Vector.hpp: math library in progress |
646 |
|
|
|
647 |
|
|
2004-10-14 18:27 tim |
648 |
|
|
|
649 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
650 |
|
|
|
651 |
|
|
2004-10-13 18:53 tim |
652 |
|
|
|
653 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
654 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
655 |
|
|
|
656 |
|
|
2004-10-13 17:28 tim |
657 |
|
|
|
658 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
659 |
|
|
class |
660 |
|
|
|
661 |
|
|
2004-10-13 17:27 tim |
662 |
|
|
|
663 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
664 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
665 |
|
|
|
666 |
|
|
2004-10-13 17:24 tim |
667 |
|
|
|
668 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
669 |
|
|
|
670 |
|
|
2004-10-13 01:51 tim |
671 |
|
|
|
672 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
673 |
|
|
Vector3.hpp: refactory vector and matrix classes |
674 |
|
|
|
675 |
|
|
2004-10-13 01:50 tim |
676 |
|
|
|
677 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
678 |
|
|
|
679 |
|
|
2004-10-12 18:57 tim |
680 |
|
|
|
681 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
682 |
|
|
Matrix3x3d.hpp |
683 |
|
|
|
684 |
|
|
2004-10-12 14:08 tim |
685 |
|
|
|
686 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
687 |
|
|
|
688 |
|
|
2004-10-11 17:15 tim |
689 |
|
|
|
690 |
|
|
* src/: constraints/AbstractClasses.hpp, |
691 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
692 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
693 |
|
|
|
694 |
|
|
2004-10-11 16:54 tim |
695 |
|
|
|
696 |
|
|
* scripts/filepp: fix a bug in filepp |
697 |
|
|
|
698 |
|
|
2004-10-11 16:13 tim |
699 |
|
|
|
700 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
701 |
|
|
of compilers |
702 |
|
|
|
703 |
|
|
2004-10-11 16:10 tim |
704 |
|
|
|
705 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
706 |
|
|
c/c++ now |
707 |
|
|
|
708 |
|
|
2004-10-11 13:40 tim |
709 |
|
|
|
710 |
|
|
* make/Makefile.in: remove -module from F90Options |
711 |
|
|
|
712 |
|
|
2004-10-11 13:01 tim |
713 |
|
|
|
714 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
715 |
|
|
target directory |
716 |
|
|
|
717 |
|
|
2004-10-11 10:43 gezelter |
718 |
|
|
|
719 |
|
|
* make/Makefile.in: fixed makefile.in |
720 |
|
|
|
721 |
|
|
2004-10-11 09:51 tim |
722 |
|
|
|
723 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
724 |
|
|
machine |
725 |
|
|
|
726 |
|
|
2004-10-11 09:26 tim |
727 |
|
|
|
728 |
|
|
* forceFields/Makefile: add Makefile |
729 |
|
|
|
730 |
|
|
2004-10-11 09:23 tim |
731 |
|
|
|
732 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
733 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
734 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
735 |
|
|
directory |
736 |
|
|
|
737 |
|
|
2004-10-11 09:23 tim |
738 |
|
|
|
739 |
|
|
* samples/argon/Makefile: remove argon.dump and argon.eor from |
740 |
|
|
Makefile |
741 |
|
|
|
742 |
|
|
2004-10-09 01:01 tim |
743 |
|
|
|
744 |
|
|
* samples/: alkane/Makefile.in, argon/Makefile.in, |
745 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
746 |
|
|
Remove some Makefile.in |
747 |
|
|
|
748 |
|
|
2004-10-08 18:15 tim |
749 |
|
|
|
750 |
|
|
* make/Makefile.in: [no log message] |
751 |
|
|
|
752 |
|
|
2004-10-08 17:51 tim |
753 |
|
|
|
754 |
|
|
* make/Makefile.in: fix make install |
755 |
|
|
|
756 |
|
|
2004-10-08 17:10 tim |
757 |
|
|
|
758 |
|
|
* make/Makefile.in: adding make install |
759 |
|
|
|
760 |
|
|
2004-10-08 17:04 tim |
761 |
|
|
|
762 |
|
|
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
763 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
764 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
765 |
|
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
766 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
767 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
768 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
769 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
770 |
|
|
|
771 |
|
|
2004-10-06 18:03 gezelter |
772 |
|
|
|
773 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
774 |
|
|
stuff |
775 |
|
|
|
776 |
|
|
2004-10-06 18:03 gezelter |
777 |
|
|
|
778 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
779 |
|
|
make/Doxyfile, src/applications/getopt.c, |
780 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
781 |
|
|
build fixes |
782 |
|
|
|
783 |
|
|
2004-10-06 17:20 tim |
784 |
|
|
|
785 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
786 |
|
|
|
787 |
|
|
2004-10-06 17:19 tim |
788 |
|
|
|
789 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
790 |
|
|
and suffix |
791 |
|
|
|
792 |
|
|
2004-10-06 16:27 gezelter |
793 |
|
|
|
794 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
795 |
|
|
OOPSE-2.0 directory structure yet |
796 |
|
|
|
797 |
|
|
2004-10-06 16:27 gezelter |
798 |
|
|
|
799 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
800 |
|
|
|
801 |
gezelter |
1536 |
2004-10-06 16:22 gezelter |
802 |
gezelter |
1490 |
|
803 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
804 |
|
|
make/Makefile.in: cleaning up build process |
805 |
gezelter |
1490 |
|
806 |
tim |
1594 |
2004-10-06 15:01 chrisfen |
807 |
|
|
|
808 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
809 |
|
|
restraints more intelligent - no longer gives uninformative seg |
810 |
|
|
faults |
811 |
|
|
|
812 |
|
|
2004-10-06 14:55 gezelter |
813 |
|
|
|
814 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
815 |
|
|
|
816 |
gezelter |
1536 |
2004-10-06 14:51 gezelter |
817 |
gezelter |
1490 |
|
818 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
819 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
820 |
gezelter |
1490 |
|
821 |
tim |
1594 |
2004-10-06 13:53 tim |
822 |
|
|
|
823 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
824 |
|
|
|
825 |
|
|
2004-10-06 13:18 tim |
826 |
|
|
|
827 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
828 |
|
|
combine all of the static libraries to a big library |
829 |
|
|
|
830 |
|
|
2004-10-05 17:57 tim |
831 |
|
|
|
832 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
833 |
|
|
|
834 |
|
|
2004-10-05 14:37 tim |
835 |
|
|
|
836 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
837 |
|
|
UseTheForce/mpiSimulation_module.F90, |
838 |
|
|
UseTheForce/DarkSide/Makefile, |
839 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
840 |
|
|
mpiSimulation_module to DarkSide |
841 |
|
|
|
842 |
|
|
2004-10-05 14:35 tim |
843 |
|
|
|
844 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
845 |
|
|
library instead of shared library |
846 |
|
|
|
847 |
|
|
2004-10-05 09:14 tim |
848 |
|
|
|
849 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
850 |
|
|
to filepp |
851 |
|
|
|
852 |
|
|
2004-10-04 15:56 tim |
853 |
|
|
|
854 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
855 |
|
|
|
856 |
|
|
2004-10-04 11:24 gezelter |
857 |
|
|
|
858 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
859 |
|
|
|
860 |
|
|
2004-10-04 11:06 gezelter |
861 |
|
|
|
862 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
863 |
|
|
|
864 |
|
|
2004-10-04 10:27 gezelter |
865 |
|
|
|
866 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
867 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
868 |
|
|
shapes |
869 |
|
|
|
870 |
|
|
2004-10-01 23:40 tim |
871 |
|
|
|
872 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
873 |
|
|
|
874 |
|
|
2004-10-01 23:22 tim |
875 |
|
|
|
876 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
877 |
|
|
|
878 |
|
|
2004-10-01 16:59 tim |
879 |
|
|
|
880 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
881 |
|
|
|
882 |
gezelter |
1536 |
2004-10-01 16:22 gezelter |
883 |
gezelter |
1490 |
|
884 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
885 |
|
|
few minor build changes |
886 |
gezelter |
1490 |
|
887 |
tim |
1594 |
2004-10-01 16:11 tim |
888 |
|
|
|
889 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
890 |
|
|
|
891 |
|
|
2004-09-30 10:41 tim |
892 |
|
|
|
893 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
894 |
|
|
remove object files belong to current package. turn off silent |
895 |
|
|
mode |
896 |
|
|
|
897 |
|
|
2004-09-29 16:55 tim |
898 |
|
|
|
899 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
900 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
901 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
902 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
903 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
904 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
905 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
906 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
907 |
|
|
|
908 |
|
|
2004-09-29 16:54 tim |
909 |
|
|
|
910 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
911 |
|
|
script |
912 |
|
|
|
913 |
|
|
2004-09-29 16:32 tim |
914 |
|
|
|
915 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
916 |
|
|
|
917 |
|
|
2004-09-29 13:37 tim |
918 |
|
|
|
919 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
920 |
|
|
|
921 |
gezelter |
1536 |
2004-09-29 12:57 gezelter |
922 |
gezelter |
1490 |
|
923 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
924 |
gezelter |
1490 |
|
925 |
tim |
1594 |
2004-09-29 12:56 gezelter |
926 |
|
|
|
927 |
tim |
1603 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
928 |
tim |
1594 |
|
929 |
gezelter |
1536 |
2004-09-29 12:46 tim |
930 |
gezelter |
1490 |
|
931 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
932 |
gezelter |
1490 |
|
933 |
tim |
1594 |
2004-09-29 12:12 tim |
934 |
|
|
|
935 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
936 |
|
|
|
937 |
gezelter |
1536 |
2004-09-29 10:58 gezelter |
938 |
gezelter |
1490 |
|
939 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
940 |
gezelter |
1490 |
|
941 |
tim |
1594 |
2004-09-29 10:00 tim |
942 |
|
|
|
943 |
|
|
* make/Makefile: add print statment to rules |
944 |
|
|
|
945 |
|
|
2004-09-29 09:59 tim |
946 |
|
|
|
947 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
948 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
949 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
950 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
951 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
952 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
953 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
954 |
|
|
|
955 |
|
|
2004-09-28 21:55 tim |
956 |
|
|
|
957 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
958 |
|
|
which cause headache in bulding libutils |
959 |
|
|
|
960 |
|
|
2004-09-28 18:24 tim |
961 |
|
|
|
962 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
963 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
964 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
965 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
966 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
967 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
968 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
969 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
970 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
971 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
972 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
973 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
974 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
975 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
976 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
977 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
978 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
979 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
980 |
|
|
change directory structure of application. Every executable file is |
981 |
|
|
replaced in seperate directory |
982 |
|
|
|
983 |
|
|
2004-09-28 17:15 gezelter |
984 |
|
|
|
985 |
|
|
* lib/dummy: Keep that lib around, please. |
986 |
|
|
|
987 |
gezelter |
1536 |
2004-09-28 17:14 gezelter |
988 |
gezelter |
1490 |
|
989 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
990 |
|
|
starting a configure version |
991 |
gezelter |
1490 |
|
992 |
tim |
1594 |
2004-09-28 16:08 tim |
993 |
|
|
|
994 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
995 |
|
|
UseTheForce/DarkSide/Makefile, |
996 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
997 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
998 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
999 |
|
|
around to solve dependency problem |
1000 |
|
|
|
1001 |
gezelter |
1536 |
2004-09-28 15:43 tim |
1002 |
gezelter |
1490 |
|
1003 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
1004 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
1005 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
1006 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
1007 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
1008 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
1009 |
|
|
src/utils/Makefile: [no log message] |
1010 |
gezelter |
1490 |
|
1011 |
tim |
1594 |
2004-09-28 15:41 tim |
1012 |
|
|
|
1013 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
1014 |
|
|
problem |
1015 |
|
|
|
1016 |
|
|
2004-09-28 11:13 tim |
1017 |
|
|
|
1018 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
1019 |
|
|
src/io/Makefile: add yacc and lex rules |
1020 |
|
|
|
1021 |
|
|
2004-09-27 15:24 tim |
1022 |
|
|
|
1023 |
|
|
* make/Makefile: adding include path to F90Options |
1024 |
|
|
|
1025 |
|
|
2004-09-27 15:13 tim |
1026 |
|
|
|
1027 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
1028 |
|
|
|
1029 |
|
|
2004-09-24 11:27 tim |
1030 |
|
|
|
1031 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
1032 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
1033 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
1034 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
1035 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
1036 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
1037 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
1038 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
1039 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
1040 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
1041 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
1042 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
1043 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
1044 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
1045 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
1046 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
1047 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
1048 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1049 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
1050 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
1051 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
1052 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
1053 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
1054 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
1055 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
1056 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
1057 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
1058 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
1059 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
1060 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
1061 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
1062 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
1063 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
1064 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
1065 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
1066 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
1067 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
1068 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
1069 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
1070 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
1071 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
1072 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
1073 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
1074 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
1075 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
1076 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
1077 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
1078 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
1079 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
1080 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
1081 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
1082 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
1083 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
1084 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
1085 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
1086 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
1087 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
1088 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
1089 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
1090 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
1091 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
1092 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
1093 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
1094 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
1095 |
|
|
|
1096 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
1097 |
gezelter |
1490 |
|
1098 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
1099 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
1100 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
1101 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
1102 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
1103 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
1104 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
1105 |
|
|
src/UseTheForce/fForceField.h, |
1106 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
1107 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
1108 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
1109 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
1110 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
1111 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
1112 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
1113 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
1114 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
1115 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
1116 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
1117 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
1118 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
1119 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
1120 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
1121 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
1122 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
1123 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
1124 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
1125 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
1126 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
1127 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
1128 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
1129 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
1130 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
1131 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
1132 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1133 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
1134 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
1135 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
1136 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
1137 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
1138 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
1139 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
1140 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
1141 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
1142 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
1143 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
1144 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1145 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1146 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1147 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
1148 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
1149 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
1150 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
1151 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
1152 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1153 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
1154 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1155 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1156 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
1157 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
1158 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
1159 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
1160 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
1161 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
1162 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
1163 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
1164 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1165 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
1166 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1167 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
1168 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
1169 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1170 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1171 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
1172 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1173 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
1174 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
1175 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
1176 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
1177 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
1178 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
1179 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
1180 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
1181 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
1182 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
1183 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
1184 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
1185 |
|
|
src/utils/simError.c, src/utils/simError.h, |
1186 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
1187 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1188 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1189 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
1190 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
1191 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
1192 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1193 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
1194 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
1195 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
1196 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
1197 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
1198 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
1199 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
1200 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1201 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1202 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1203 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1204 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1205 |
|
|
src/applications/LatticeCreator.cpp, |
1206 |
|
|
src/applications/LatticeCreator.hpp, |
1207 |
|
|
src/applications/LatticeFactory.cpp, |
1208 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1209 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
1210 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1211 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
1212 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
1213 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1214 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1215 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1216 |
|
|
src/applications/simpleBuilder.ggo, |
1217 |
|
|
src/applications/simpleBuilderCmd.c, |
1218 |
|
|
src/integrators/AbstractClasses.hpp, |
1219 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1220 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1221 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1222 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1223 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
1224 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1225 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1226 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1227 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1228 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1229 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1230 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1231 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1232 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1233 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1234 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1235 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1236 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1237 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1238 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1239 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1240 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1241 |
|
|
samples/argon/500.in, samples/argon/500.md, |
1242 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
1243 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1244 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
1245 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1246 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1247 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1248 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1249 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1250 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1251 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1252 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1253 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1254 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1255 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1256 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1257 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1258 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1259 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1260 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1261 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1262 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1263 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1264 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1265 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1266 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1267 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1268 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1269 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
1270 |
gezelter |
1490 |
|
1271 |
gezelter |
1536 |
2004-09-23 23:16 gezelter |
1272 |
gezelter |
1490 |
|
1273 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
1274 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
1275 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
1276 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
1277 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
1278 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
1279 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
1280 |
|
|
src/UseTheForce/fForceField.h, |
1281 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
1282 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
1283 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
1284 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
1285 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
1286 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
1287 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
1288 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
1289 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
1290 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
1291 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
1292 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
1293 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
1294 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
1295 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
1296 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
1297 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
1298 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
1299 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
1300 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
1301 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
1302 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
1303 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
1304 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
1305 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
1306 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
1307 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1308 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
1309 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
1310 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
1311 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
1312 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
1313 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
1314 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
1315 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
1316 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
1317 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
1318 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
1319 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1320 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1321 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1322 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
1323 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
1324 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
1325 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
1326 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
1327 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1328 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
1329 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1330 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1331 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
1332 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
1333 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
1334 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
1335 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
1336 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
1337 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
1338 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
1339 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1340 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
1341 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1342 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
1343 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
1344 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1345 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1346 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
1347 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1348 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
1349 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
1350 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
1351 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
1352 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
1353 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
1354 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
1355 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
1356 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
1357 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
1358 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
1359 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
1360 |
|
|
src/utils/simError.c, src/utils/simError.h, |
1361 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
1362 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1363 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1364 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
1365 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
1366 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
1367 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1368 |
tim |
1603 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
1369 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
1370 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
1371 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
1372 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
1373 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
1374 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
1375 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1376 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1377 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1378 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1379 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1380 |
|
|
src/applications/LatticeCreator.cpp, |
1381 |
|
|
src/applications/LatticeCreator.hpp, |
1382 |
|
|
src/applications/LatticeFactory.cpp, |
1383 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1384 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
1385 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1386 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
1387 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
1388 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1389 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1390 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1391 |
|
|
src/applications/simpleBuilder.ggo, |
1392 |
|
|
src/applications/simpleBuilderCmd.c, |
1393 |
|
|
src/integrators/AbstractClasses.hpp, |
1394 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1395 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1396 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1397 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1398 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
1399 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1400 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1401 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1402 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1403 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1404 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1405 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1406 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1407 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1408 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1409 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1410 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1411 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1412 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1413 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1414 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1415 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
1416 |
|
|
samples/argon/500.in, samples/argon/500.md, |
1417 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
1418 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1419 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
1420 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1421 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1422 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1423 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1424 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1425 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1426 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1427 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1428 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1429 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1430 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1431 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1432 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1433 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1434 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1435 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1436 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1437 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1438 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1439 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1440 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1441 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1442 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1443 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1444 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
1445 |
gezelter |
1490 |
|