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chrisfen |
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2007-05-01 10:59 chuckv |
2 |
chrisfen |
3038 |
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3 |
chrisfen |
3131 |
* samples/bond-order/: Readme.txt, surface_icosahedron.md: Added md |
4 |
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file for half of a icosahedron. |
5 |
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6 |
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2007-04-20 11:15 chrisfen |
7 |
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* src/: UseTheForce/doForces.F90, |
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UseTheForce/doForces_interface.F90, |
10 |
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UseTheForce/doForces_interface.h, UseTheForce/DarkSide/LJ.F90, |
11 |
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brains/SimInfo.cpp, brains/SimInfo.hpp, |
12 |
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hydrodynamics/Ellipsoid.cpp, integrators/LDForceManager.cpp, |
13 |
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restraints/Restraints.cpp, types/TorsionStamp.hpp: SF Lennard-Jones |
14 |
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was added for everyones' enjoyment. The behavior is tethered to |
15 |
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the electrostaticSummationMethod keyword. |
16 |
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17 |
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2007-04-11 16:27 chuckv |
18 |
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19 |
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* src/applications/staticProps/: BOPofR.cpp, BOPofR.hpp, Makefile, |
20 |
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StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
21 |
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StaticPropsCmd.h: Added Bond Order Parameter as a function of |
22 |
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radius. |
23 |
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24 |
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2007-04-09 11:24 gezelter |
25 |
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26 |
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* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: more changes for |
27 |
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atomic virials and Lennard-Jones force switching |
28 |
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29 |
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2007-04-06 14:53 gezelter |
30 |
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* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/LJ.F90, |
32 |
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UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp, |
33 |
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brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
34 |
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brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
35 |
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brains/fSimulation.h, integrators/LDForceManager.cpp, |
36 |
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integrators/LDForceManager.hpp, |
37 |
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integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
38 |
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io/Globals.hpp, primitives/RigidBody.cpp, primitives/RigidBody.hpp: |
39 |
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Massive update to do virials (both atomic and cutoff-group) |
40 |
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correctly. The rigid body constraint contributions had been |
41 |
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missing and this was masked by the use of cutoff groups... |
42 |
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43 |
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2007-03-07 15:07 gezelter |
44 |
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45 |
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* samples/water/ice_surfaces/secondary_prism.md: Adding a starter |
46 |
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file for the secondary prism {1,1,-2,0} face. |
47 |
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48 |
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2007-03-07 11:29 gezelter |
49 |
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50 |
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* samples/water/ice_surfaces/: basal.md, prism2.md, water.md: |
51 |
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adding new ice surface files |
52 |
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53 |
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2007-03-05 16:01 chrisfen |
54 |
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55 |
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* src/applications/utilities/waterBoxer: forgot a tolerance for |
56 |
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simple cubic lattice magic number determination |
57 |
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58 |
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2007-02-27 16:53 chuckv |
59 |
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60 |
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* src/UseTheForce/DarkSide/electrostatic.F90: Fixed conversion bug |
61 |
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in self_self, when adding self energy to mypot, energy needs to be |
62 |
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converted by pre11. |
63 |
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64 |
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2007-02-25 20:45 chuckv |
65 |
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66 |
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* src/: UseTheForce/DarkSide/neighborLists_interface.h, |
67 |
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brains/SimInfo.cpp: Fixed a bug in NeighborListNeighbors. |
68 |
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69 |
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2007-02-02 10:55 chuckv |
70 |
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71 |
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* src/integrators/LDForceManager.cpp: Spherical boundary |
72 |
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conditions. |
73 |
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74 |
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2007-01-22 14:27 gezelter |
75 |
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76 |
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* src/applications/utilities/: md-solvator, waterBoxer: fixed a bug |
77 |
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in waterBoxer |
78 |
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79 |
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2007-01-16 14:18 chuckv |
80 |
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81 |
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* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: Support for |
82 |
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printPosOnly in Dump2XYZ. |
83 |
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84 |
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2007-01-16 14:17 chuckv |
85 |
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86 |
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* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
87 |
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Dump2XYZCmd.c, Dump2XYZCmd.h: Added printPosOnly to Dump2XYZ as a |
88 |
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userbase(BETH) request. |
89 |
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90 |
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2007-01-11 13:46 gezelter |
91 |
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92 |
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* src/applications/utilities/md-solvator: adding md-solvator |
93 |
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94 |
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2007-01-08 19:42 gezelter |
95 |
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96 |
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* src/applications/utilities/waterBoxer: Added the ability of |
97 |
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waterBoxer to deal with non-cubical boxes. |
98 |
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99 |
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2007-01-08 13:32 chuckv |
100 |
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101 |
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* src/applications/dynamicProps/: ThetaCorrFunc.cpp, |
102 |
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ThetaCorrFunc.hpp: Added thetacorr functions to dynamic props. |
103 |
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104 |
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2007-01-08 13:29 chuckv |
105 |
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106 |
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* src/UseTheForce/DarkSide/simParallel.F90: Added more error |
107 |
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reporting to simParallel. |
108 |
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109 |
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2007-01-03 12:46 chuckv |
110 |
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111 |
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* src/: applications/dynamicProps/DynamicProps.cpp, |
112 |
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applications/dynamicProps/DynamicProps.ggo, |
113 |
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applications/dynamicProps/DynamicPropsCmd.c, |
114 |
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applications/dynamicProps/DynamicPropsCmd.h, |
115 |
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applications/dynamicProps/Makefile, |
116 |
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applications/dynamicProps/RadialRCorrFunc.cpp, |
117 |
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applications/dynamicProps/RadialRCorrFunc.hpp, brains/Snapshot.cpp, |
118 |
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brains/Snapshot.hpp, io/DumpReader.cpp, primitives/StuntDouble.hpp: |
119 |
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Changes to add thetacorr to dynamic props and fixes to radial |
120 |
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rcorr. |
121 |
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122 |
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2007-01-02 20:40 chuckv |
123 |
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124 |
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* src/applications/dynamicProps/Makefile: Remove snapshotcentroid |
125 |
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from makefile. |
126 |
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127 |
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2007-01-02 20:40 chuckv |
128 |
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129 |
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* src/applications/dynamicProps/: RadialRCorrFunc.cpp, |
130 |
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RadialRCorrFunc.hpp, SnapshotCentroid.cpp, SnapshotCentroid.hpp: |
131 |
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Removeing snapshot centroid and adding support for COM calculaton |
132 |
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from snapshot. |
133 |
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134 |
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2007-01-02 12:42 chuckv |
135 |
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136 |
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* src/applications/utilities/mdSplit: More changes to mdsplit. |
137 |
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138 |
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2007-01-02 12:30 chuckv |
139 |
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140 |
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* src/applications/utilities/mdSplit: Breaking more mdsplit |
141 |
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stuff.... |
142 |
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143 |
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2007-01-02 12:12 chuckv |
144 |
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145 |
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* src/applications/utilities/mdSplit: Changed how mdsplit gets file |
146 |
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names. Full path is now removed from name. |
147 |
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148 |
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2006-12-29 13:57 gezelter |
149 |
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150 |
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* src/brains/: BlockSnapshotManager.cpp, BlockSnapshotManager.hpp: |
151 |
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Fixing an implementation problem |
152 |
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153 |
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2006-12-29 13:51 gezelter |
154 |
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155 |
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* src/brains/BlockSnapshotManager.hpp: BSM has to talk to reader |
156 |
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about center of mass properties |
157 |
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158 |
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2006-12-29 13:43 gezelter |
159 |
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160 |
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* src/: applications/dynamicProps/TimeCorrFunc.hpp, |
161 |
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brains/DataStorage.cpp, brains/DataStorage.hpp, |
162 |
|
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brains/Snapshot.cpp, brains/Snapshot.hpp, io/DumpReader.cpp, |
163 |
|
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io/DumpReader.hpp: Adding the ability to compute Center of Mass |
164 |
|
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properties on reading in a dump file. DumpReader must be told if |
165 |
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it needs to do this, however. |
166 |
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167 |
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2006-12-29 12:21 chuckv |
168 |
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169 |
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* src/brains/: SimInfo.cpp, SimInfo.hpp: Added function to |
170 |
|
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calculate volume based on ellipsoid definded by radius of gyration. |
171 |
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172 |
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2006-12-21 12:50 gezelter |
173 |
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174 |
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* samples/bond-order/: Readme.txt, bcc.md, icosahedron.md, sc.md, |
175 |
|
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tet.md: new ideal structures |
176 |
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177 |
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2006-12-20 18:20 gezelter |
178 |
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|
179 |
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* samples/bond-order/: Ag_Cu_bulkslab_lattice.md, Readme.txt, |
180 |
|
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bcc.md, fcc.md, hcp.md, icosahedron.md, metals.md, tet.md: Added a |
181 |
|
|
bunch of bond order parameter test cases. |
182 |
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183 |
|
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2006-12-20 13:03 gezelter |
184 |
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185 |
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* src/applications/staticProps/BondOrderParameter.cpp: bug fixing |
186 |
|
|
Wigner 3-j import to C++ |
187 |
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188 |
|
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2006-12-19 07:45 gezelter |
189 |
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190 |
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* configure, ac-tools/configure.in, src/math/Makefile, |
191 |
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src/math/Makefile.in: fixed a configuration error |
192 |
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193 |
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2006-12-14 11:38 chuckv |
194 |
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|
195 |
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* src/applications/dynamicProps/: DynamicProps.cpp, |
196 |
|
|
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, |
197 |
|
|
RadialRCorrFunc.hpp: Code to run radial rcorr. |
198 |
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|
199 |
|
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2006-12-14 11:32 chuckv |
200 |
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|
201 |
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* src/math/: ConvexHull.cpp, ConvexHull.hpp, Makefile: Added |
202 |
|
|
preliminary support for CGAL and computation of convex hull. |
203 |
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|
204 |
|
|
2006-12-05 17:05 chuckv |
205 |
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|
206 |
|
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* src/applications/dynamicProps/: Makefile, RadialRCorrFunc.cpp, |
207 |
|
|
RadialRCorrFunc.hpp, SnapshotCentroid.cpp, SnapshotCentroid.hpp: |
208 |
|
|
Adding support for radial rcorr. |
209 |
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|
210 |
|
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2006-12-04 16:17 chuckv |
211 |
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212 |
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* src/: UseTheForce/DarkSide/Makefile, |
213 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
214 |
|
|
UseTheForce/DarkSide/neighborLists_interface.F90, |
215 |
|
|
UseTheForce/DarkSide/neighborLists_interface.h, brains/SimInfo.cpp, |
216 |
|
|
io/Globals.cpp, io/Globals.hpp: Added interface to change number of |
217 |
|
|
neighbors in calculating neighbor list. |
218 |
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|
219 |
|
|
2006-11-21 12:44 gezelter |
220 |
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|
221 |
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* src/applications/staticProps/BondOrderParameter.cpp: fixes for |
222 |
|
|
BOP |
223 |
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|
224 |
|
|
2006-11-20 15:12 chuckv |
225 |
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|
226 |
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* src/applications/staticProps/Makefile: Fix to makefile. |
227 |
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228 |
|
|
2006-11-17 11:45 chuckv |
229 |
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|
230 |
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* src/applications/staticProps/RhoR.cpp: Histogram bin change. |
231 |
|
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|
232 |
|
|
2006-11-10 10:45 chuckv |
233 |
|
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|
234 |
|
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* src/applications/staticProps/: Makefile, RhoR.cpp, RhoR.hpp, |
235 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
236 |
|
|
StaticPropsCmd.h: Added support for nanoparticle density profile. |
237 |
|
|
|
238 |
|
|
2006-11-03 14:02 gezelter |
239 |
|
|
|
240 |
|
|
* src/applications/staticProps/BondOrderParameter.cpp: possible fix |
241 |
|
|
for unnormalized BO |
242 |
|
|
|
243 |
|
|
2006-11-01 14:22 chrisfen |
244 |
|
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|
245 |
|
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* src/brains/SimInfo.cpp: user selected dampingAlpha now gets set |
246 |
|
|
|
247 |
|
|
2006-10-29 14:41 chrisfen |
248 |
|
|
|
249 |
|
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* src/UseTheForce/DarkSide/electrostatic.F90: returned to half |
250 |
|
|
self-term values |
251 |
|
|
|
252 |
|
|
2006-10-23 13:27 chuckv |
253 |
|
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|
254 |
|
|
* src/applications/nanoRodBuilder/GeometryBuilder.hpp: Support for |
255 |
|
|
OOPSE RealType. |
256 |
|
|
|
257 |
|
|
2006-10-23 11:21 gezelter |
258 |
|
|
|
259 |
|
|
* make/Makefile.in: fixes for CGAL |
260 |
|
|
|
261 |
|
|
2006-10-23 11:11 chuckv |
262 |
|
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|
263 |
|
|
* configure, ac-tools/configure.in, |
264 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp: Changes to |
265 |
|
|
nanorod builder for new dump format. Changes to configure to test |
266 |
|
|
for new version of cgal. |
267 |
|
|
|
268 |
|
|
2006-10-20 08:40 gezelter |
269 |
|
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|
270 |
|
|
* src/: brains/Register.cpp, openbabel/amberformat.hpp, |
271 |
|
|
openbabel/fingerprintformat.hpp, openbabel/gromos96format.hpp, |
272 |
|
|
openbabel/pdbformat.hpp, openbabel/povrayformat.hpp, |
273 |
|
|
openbabel/smilesformat.hpp, openbabel/tinkerformat.hpp, |
274 |
|
|
openbabel/xyzformat.hpp: fixes for open babel |
275 |
|
|
|
276 |
|
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2006-10-20 07:59 gezelter |
277 |
|
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|
278 |
|
|
* make/Makefile.in, samples/builders/runMe, |
279 |
|
|
src/applications/thermalizer/Makefile, |
280 |
|
|
src/applications/thermalizer/thermalizer.cpp, |
281 |
|
|
src/applications/thermalizer/thermalizer.ggo, |
282 |
|
|
src/applications/thermalizer/thermalizerCmd.c, |
283 |
|
|
src/applications/thermalizer/thermalizerCmd.h, |
284 |
|
|
src/applications/velocitizer/Makefile, |
285 |
|
|
src/applications/velocitizer/velocitizer.cpp, |
286 |
|
|
src/applications/velocitizer/velocitizer.ggo, |
287 |
|
|
src/applications/velocitizer/velocitizerCmd.c, |
288 |
|
|
src/applications/velocitizer/velocitizerCmd.h: more openbabel |
289 |
|
|
updates, also changing velocitizer to thermalizer to avoid a |
290 |
|
|
filename collision on case-insensitve file systems |
291 |
|
|
|
292 |
|
|
2006-10-19 13:50 gezelter |
293 |
|
|
|
294 |
|
|
* src/openbabel/: amberformat.hpp, fingerprintformat.hpp, |
295 |
|
|
gromos96format.hpp, pdbformat.hpp, povrayformat.hpp, |
296 |
|
|
smilesformat.hpp, tinkerformat.hpp, xyzformat.hpp: Updating |
297 |
|
|
OpenBabel to version 2.0.2. These files aren't used anymore |
298 |
|
|
|
299 |
|
|
2006-10-19 13:49 gezelter |
300 |
|
|
|
301 |
|
|
* forceFields/SMARTS_InteLigand.txt, |
302 |
|
|
forceFields/SMARTS_InteLigand_051110.txt, forceFields/atomtyp.txt, |
303 |
|
|
forceFields/extable.txt, forceFields/phmodel.txt, |
304 |
|
|
forceFields/resdata.txt, forceFields/types.txt, src/config.h.in, |
305 |
|
|
src/openbabel/amberformat.cpp, src/openbabel/chains.cpp, |
306 |
|
|
src/openbabel/chains.hpp, src/openbabel/data.cpp, |
307 |
|
|
src/openbabel/dlhandler.hpp, src/openbabel/fingerprint.cpp, |
308 |
|
|
src/openbabel/fingerprint.hpp, src/openbabel/fingerprintformat.cpp, |
309 |
|
|
src/openbabel/gromos96format.cpp, src/openbabel/kekulize.cpp, |
310 |
|
|
src/openbabel/matrix3x3.cpp, src/openbabel/matrix3x3.hpp, |
311 |
|
|
src/openbabel/mol.cpp, src/openbabel/mol.hpp, |
312 |
|
|
src/openbabel/obconversion.cpp, src/openbabel/obconversion.hpp, |
313 |
|
|
src/openbabel/oberror.cpp, src/openbabel/obiter.cpp, |
314 |
|
|
src/openbabel/obutil.cpp, src/openbabel/obutil.hpp, |
315 |
|
|
src/openbabel/parsmart.cpp, src/openbabel/parsmart.hpp, |
316 |
|
|
src/openbabel/patty.cpp, src/openbabel/pdbformat.cpp, |
317 |
|
|
src/openbabel/phmodel.cpp, src/openbabel/povrayformat.cpp, |
318 |
|
|
src/openbabel/rotor.cpp, src/openbabel/smilesformat.cpp, |
319 |
|
|
src/openbabel/tinkerformat.cpp, src/openbabel/typer.cpp, |
320 |
|
|
src/openbabel/vector3.cpp, src/openbabel/vector3.hpp, |
321 |
|
|
src/openbabel/xyzformat.cpp, src/openbabel/zipstream.hpp, |
322 |
|
|
src/openbabel/zipstreamimpl.hpp: updated OpenBabel to version 2.0.2 |
323 |
|
|
|
324 |
|
|
2006-10-19 12:51 gezelter |
325 |
|
|
|
326 |
|
|
* src/openbabel/oopseformat.cpp: Slight changes to oopseformat to |
327 |
|
|
allow importing of openbabel's perceived atom types into OOPSE md |
328 |
|
|
files |
329 |
|
|
|
330 |
|
|
2006-10-19 08:57 gezelter |
331 |
|
|
|
332 |
|
|
* make/Makefile.in, samples/builders/Makefile, |
333 |
|
|
samples/builders/runMe, src/Makefile, src/applications/Makefile, |
334 |
|
|
src/applications/velocitizer/Makefile, |
335 |
|
|
src/applications/velocitizer/velocitizer.cpp, |
336 |
|
|
src/applications/velocitizer/velocitizer.ggo, |
337 |
|
|
src/applications/velocitizer/velocitizerCmd.c, |
338 |
|
|
src/applications/velocitizer/velocitizerCmd.h, |
339 |
|
|
src/integrators/Velocitizer.cpp: Added velocitizer utility program, |
340 |
|
|
added samples of its use to the builder samples. |
341 |
|
|
|
342 |
|
|
2006-10-18 14:58 gezelter |
343 |
|
|
|
344 |
|
|
* src/: applications/staticProps/BondOrderParameter.cpp, |
345 |
|
|
applications/staticProps/DensityPlot.cpp, |
346 |
|
|
applications/staticProps/GofAngle2.cpp, |
347 |
|
|
applications/staticProps/GofR.cpp, |
348 |
|
|
applications/staticProps/GofRAngle.cpp, |
349 |
|
|
applications/staticProps/GofXyz.cpp, |
350 |
|
|
applications/staticProps/Hxy.cpp, |
351 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
352 |
|
|
applications/staticProps/RhoZ.cpp, |
353 |
|
|
applications/staticProps/SCDOrderParameter.cpp, |
354 |
|
|
applications/staticProps/SCDOrderParameter.hpp, |
355 |
|
|
applications/staticProps/StaticAnalyser.hpp, brains/SimInfo.cpp, |
356 |
|
|
io/Globals.cpp, io/Globals.hpp: fixing a wrapVector problem in |
357 |
|
|
staticProps, also making Shifted force and electrostatic damping |
358 |
|
|
the default behavior |
359 |
|
|
|
360 |
|
|
2006-10-18 12:35 gezelter |
361 |
|
|
|
362 |
|
|
* src/applications/: nanoparticleBuilder/nanoparticleBuilder.cpp, |
363 |
|
|
nanoparticleBuilder/nanoparticleBuilder.ggo, |
364 |
|
|
nanoparticleBuilder/nanoparticleBuilderCmd.c, |
365 |
|
|
nanoparticleBuilder/nanoparticleBuilderCmd.h, |
366 |
|
|
randomBuilder/randomBuilder.cpp: bug fixes for vacancies |
367 |
|
|
|
368 |
|
|
2006-10-18 12:34 gezelter |
369 |
|
|
|
370 |
|
|
* samples/builders/: bimetallic.md, gold.md, metals.md, runMe: |
371 |
|
|
Adding samples for builders |
372 |
|
|
|
373 |
|
|
2006-10-17 10:51 gezelter |
374 |
|
|
|
375 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: bug |
376 |
|
|
fixes |
377 |
|
|
|
378 |
|
|
2006-10-17 08:24 gezelter |
379 |
|
|
|
380 |
|
|
* src/: |
381 |
|
|
applications/nanoparticleBuilder/shapedLatticeSpherical.cpp, |
382 |
|
|
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: bugfixing |
383 |
|
|
shapedLattice to have crystal origin at one of the occupied lattice |
384 |
|
|
sites |
385 |
|
|
|
386 |
|
|
2006-10-15 11:02 chuckv |
387 |
|
|
|
388 |
|
|
* src/applications/utilities/mdSplit: More typos... |
389 |
|
|
|
390 |
|
|
2006-10-15 10:59 chuckv |
391 |
|
|
|
392 |
|
|
* src/applications/utilities/mdSplit: Typo in mdSplit. |
393 |
|
|
|
394 |
|
|
2006-10-15 10:02 chuckv |
395 |
|
|
|
396 |
|
|
* src/applications/utilities/mdSplit: Fixed printing of OOPSE |
397 |
|
|
version at header and trailer. |
398 |
|
|
|
399 |
|
|
2006-10-14 13:21 gezelter |
400 |
|
|
|
401 |
|
|
* samples/argon/500.md, |
402 |
|
|
src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
403 |
|
|
src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp, |
404 |
|
|
src/applications/nanoparticleBuilder/shapedLatticeSpherical.hpp, |
405 |
|
|
src/lattice/shapedLattice.cpp, src/lattice/shapedLattice.hpp: fixed |
406 |
|
|
a few bugs |
407 |
|
|
|
408 |
|
|
2006-10-13 13:16 chuckv |
409 |
|
|
|
410 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
411 |
|
|
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
412 |
|
|
nanoparticleBuilderCmd.h: Changed nanoparticle builder for new dump |
413 |
|
|
syntax. |
414 |
|
|
|
415 |
|
|
2006-10-11 12:24 chrisfen |
416 |
|
|
|
417 |
|
|
* src/applications/utilities/solvator: now the -n command works |
418 |
|
|
|
419 |
|
|
2006-10-10 11:34 gezelter |
420 |
|
|
|
421 |
|
|
* samples/builders/one_component.md, samples/builders/runMe, |
422 |
|
|
src/applications/randomBuilder/randomBuilder.cpp, |
423 |
|
|
src/applications/randomBuilder/randomBuilder.ggo, |
424 |
|
|
src/applications/randomBuilder/randomBuilderCmd.c, |
425 |
|
|
src/applications/randomBuilder/randomBuilderCmd.h, |
426 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
427 |
|
|
src/applications/simpleBuilder/simpleBuilder.ggo, |
428 |
|
|
src/applications/simpleBuilder/simpleBuilderCmd.c, |
429 |
|
|
src/applications/simpleBuilder/simpleBuilderCmd.h: fixing missing |
430 |
|
|
lattice arguments, adding a builder sample |
431 |
|
|
|
432 |
|
|
2006-10-10 08:55 gezelter |
433 |
|
|
|
434 |
|
|
* make/Makefile.in, samples/builders/Makefile, |
435 |
|
|
samples/builders/lj.md, samples/builders/runMe, |
436 |
|
|
samples/builders/three_component.md: adding builder samples |
437 |
|
|
|
438 |
|
|
2006-10-10 07:52 gezelter |
439 |
|
|
|
440 |
|
|
* src/applications/randomBuilder/randomBuilder.cpp: nearly complete |
441 |
|
|
rewrite of randomBuilder |
442 |
|
|
|
443 |
|
|
2006-10-10 07:36 chrisfen |
444 |
|
|
|
445 |
|
|
* ChangeLog, configure, ac-tools/configure.in, |
446 |
|
|
src/applications/utilities/affineScale: oops with the affineScale |
447 |
|
|
|
448 |
|
|
2006-10-10 07:08 chrisfen |
449 |
|
|
|
450 |
chrisfen |
3038 |
* src/applications/utilities/: affineScale, affineScale.in, |
451 |
|
|
solvator, solvator.in, waterBoxer, waterBoxer.in: who needs .in |
452 |
|
|
files for perl? using env |
453 |
|
|
|
454 |
chrisfen |
3131 |
2006-10-09 19:44 gezelter |
455 |
chrisfen |
3038 |
|
456 |
|
|
* src/: applications/randomBuilder/randomBuilder.cpp, |
457 |
|
|
applications/randomBuilder/randomBuilder.ggo, |
458 |
|
|
applications/randomBuilder/randomBuilderCmd.c, |
459 |
|
|
applications/randomBuilder/randomBuilderCmd.h, utils/MoLocator.cpp: |
460 |
|
|
fixing bugs in randomBuilder |
461 |
|
|
|
462 |
chrisfen |
3131 |
2006-10-09 15:16 gezelter |
463 |
chrisfen |
3038 |
|
464 |
|
|
* samples/argon/lj.md, |
465 |
|
|
src/applications/randomBuilder/randomBuilder.cpp, |
466 |
|
|
src/applications/simpleBuilder/Makefile, |
467 |
|
|
src/applications/simpleBuilder/randomBuilder.cpp, |
468 |
|
|
src/applications/simpleBuilder/randomBuilder.ggo, |
469 |
|
|
src/applications/simpleBuilder/randomBuilderCmd.c, |
470 |
|
|
src/applications/simpleBuilder/randomBuilderCmd.h: Fixing the |
471 |
|
|
builders to prepare for OOPSE-4 release |
472 |
|
|
|
473 |
chrisfen |
3131 |
2006-10-06 14:29 chuckv |
474 |
chrisfen |
3038 |
|
475 |
|
|
* src/applications/utilities/mdSplit: Added utility to split dump |
476 |
|
|
file frames into md files. |
477 |
|
|
|
478 |
chrisfen |
3131 |
2006-10-03 15:39 chrisfen |
479 |
chrisfen |
3038 |
|
480 |
|
|
* src/applications/utilities/Makefile: forgot to adjust the |
481 |
|
|
makefile |
482 |
|
|
|
483 |
chrisfen |
3131 |
2006-10-03 15:38 chrisfen |
484 |
chrisfen |
3038 |
|
485 |
|
|
* src/applications/utilities/: solvator.in, waterBoxer.in: added |
486 |
|
|
solvator and adjusted waterBoxer |
487 |
|
|
|
488 |
chrisfen |
3131 |
2006-10-02 16:54 chrisfen |
489 |
chrisfen |
3038 |
|
490 |
|
|
* src/applications/utilities/waterBoxer.in: improvements to |
491 |
|
|
waterBoxer |
492 |
|
|
|
493 |
chrisfen |
3131 |
2006-10-02 16:27 chrisfen |
494 |
chrisfen |
3038 |
|
495 |
|
|
* src/applications/utilities/waterBoxer.in: fixed a bug in |
496 |
|
|
waterBoxer for invalid water names |
497 |
|
|
|
498 |
chrisfen |
3131 |
2006-09-26 14:55 gezelter |
499 |
chrisfen |
3038 |
|
500 |
|
|
* AUTHORS, README: Starting cleanup for 4.0 release |
501 |
|
|
|
502 |
chrisfen |
3131 |
2006-09-26 09:08 gezelter |
503 |
chrisfen |
3038 |
|
504 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
505 |
|
|
BondOrderParameter.hpp: Cleaned up the code for BondOrderParameter |
506 |
|
|
and added a bunch of comments. Fixed a memory leak or ten. |
507 |
|
|
|
508 |
chrisfen |
3131 |
2006-09-26 07:33 gezelter |
509 |
chrisfen |
3038 |
|
510 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
511 |
|
|
BondOrderParameter.hpp: Some efficiency fixes (now computes Wigner |
512 |
|
|
3-j coefficients only once in the constructor). |
513 |
|
|
|
514 |
chrisfen |
3131 |
2006-09-25 18:30 gezelter |
515 |
chrisfen |
3038 |
|
516 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
517 |
|
|
BondOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
518 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: Mostly done with |
519 |
|
|
BondOrderParameter. Only a few performance tweaks remain |
520 |
|
|
|
521 |
chrisfen |
3131 |
2006-09-25 15:08 gezelter |
522 |
chrisfen |
3038 |
|
523 |
|
|
* src/: applications/staticProps/BondOrderParameter.cpp, |
524 |
|
|
applications/staticProps/BondOrderParameter.hpp, |
525 |
|
|
applications/staticProps/StaticProps.cpp, brains/SimCreator.cpp, |
526 |
|
|
math/SphericalHarmonic.cpp: fixing bond order parameter code |
527 |
|
|
|
528 |
chrisfen |
3131 |
2006-09-22 15:19 chrisfen |
529 |
chrisfen |
3038 |
|
530 |
|
|
* src/: UseTheForce/DarkSide/simulation.F90, brains/SimInfo.cpp, |
531 |
|
|
brains/fSimulation.h, io/ForceFieldOptions.cpp, |
532 |
|
|
io/ForceFieldOptions.hpp, io/Globals.cpp, io/Globals.hpp: refined |
533 |
|
|
the reaction field dielectric passing |
534 |
|
|
|
535 |
chrisfen |
3131 |
2006-09-21 18:41 gezelter |
536 |
chrisfen |
3038 |
|
537 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
538 |
|
|
BondOrderParameter.hpp: bug fixes (still broken, however) |
539 |
|
|
|
540 |
chrisfen |
3131 |
2006-09-21 18:36 gezelter |
541 |
chrisfen |
3038 |
|
542 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
543 |
|
|
BondOrderParameter.hpp: Following Rein ten Wolde article |
544 |
|
|
|
545 |
chrisfen |
3131 |
2006-09-21 14:47 gezelter |
546 |
chrisfen |
3038 |
|
547 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
548 |
|
|
BondOrderParameter.hpp: more bug fixes |
549 |
|
|
|
550 |
chrisfen |
3131 |
2006-09-21 13:43 gezelter |
551 |
chrisfen |
3038 |
|
552 |
|
|
* src/applications/staticProps/BondOrderParameter.cpp: more changes |
553 |
|
|
to BOP and SH |
554 |
|
|
|
555 |
chrisfen |
3131 |
2006-09-21 11:25 chrisfen |
556 |
chrisfen |
3038 |
|
557 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
558 |
|
|
io/Globals.cpp: fixed the half self term for wolf electrostatics |
559 |
|
|
and OOPSE now chooses a cutoff radius dependent alpha for damped |
560 |
|
|
electrostatics |
561 |
|
|
|
562 |
chrisfen |
3131 |
2006-09-21 11:04 gezelter |
563 |
chrisfen |
3038 |
|
564 |
|
|
* src/applications/staticProps/BondOrderParameter.cpp: Fixed a bug |
565 |
|
|
in Wl code in BondOrderParameter |
566 |
|
|
|
567 |
chrisfen |
3131 |
2006-09-21 07:45 gezelter |
568 |
chrisfen |
3038 |
|
569 |
|
|
* src/: applications/staticProps/BondOrderParameter.cpp, |
570 |
|
|
math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: Bugfixes in |
571 |
|
|
BondOrderParameter and SphericalHarmonic |
572 |
|
|
|
573 |
chrisfen |
3131 |
2006-09-20 15:16 gezelter |
574 |
chrisfen |
3038 |
|
575 |
|
|
* src/: applications/staticProps/BondOrderParameter.cpp, |
576 |
|
|
math/Makefile, math/SphericalHarmonic.cpp, |
577 |
|
|
math/SphericalHarmonic.hpp: added SphericalHarmonics, fixed a few |
578 |
|
|
problems with BondOrderParameter |
579 |
|
|
|
580 |
chrisfen |
3131 |
2006-09-20 13:13 gezelter |
581 |
chrisfen |
3038 |
|
582 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
583 |
|
|
BondOrderParameter.hpp, GofAngle2.cpp, StaticProps.cpp, |
584 |
|
|
StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed bugs |
585 |
|
|
(mostly in BondOrderParameter) |
586 |
|
|
|
587 |
chrisfen |
3131 |
2006-09-19 14:20 gezelter |
588 |
chrisfen |
3038 |
|
589 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
590 |
|
|
BondOrderParameter.hpp: Adding BondOrderParameter to StaticProps |
591 |
|
|
|
592 |
chrisfen |
3131 |
2006-09-19 14:14 gezelter |
593 |
chrisfen |
3038 |
|
594 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
595 |
|
|
BondOrderParameter.hpp, Makefile, StaticProps.cpp, StaticProps.ggo, |
596 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: Working on BondOrderParameter |
597 |
|
|
|
598 |
chrisfen |
3131 |
2006-09-18 14:31 chuckv |
599 |
chrisfen |
3038 |
|
600 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
601 |
|
|
BondOrderParameter.hpp: Latest Version |
602 |
|
|
|
603 |
chrisfen |
3131 |
2006-09-08 09:13 gezelter |
604 |
chrisfen |
3038 |
|
605 |
|
|
* src/: brains/BlockSnapshotManager.cpp, io/DumpReader.cpp, |
606 |
|
|
utils/residentMem.c: fixed a DumpReader bug, took out extra |
607 |
|
|
printing statements in residentMem and BlockSnapshotManager |
608 |
|
|
|
609 |
chrisfen |
3131 |
2006-09-04 06:37 gezelter |
610 |
chrisfen |
3038 |
|
611 |
|
|
* configure, ac-tools/configure.in, |
612 |
|
|
src/applications/utilities/Makefile: changing configure script to |
613 |
|
|
process the new utilities |
614 |
|
|
|
615 |
chrisfen |
3131 |
2006-09-01 15:58 chrisfen |
616 |
chrisfen |
3038 |
|
617 |
|
|
* src/applications/utilities/waterBoxer.in: added some features to |
618 |
|
|
waterBoxer |
619 |
|
|
|
620 |
chrisfen |
3131 |
2006-09-01 14:08 chrisfen |
621 |
chrisfen |
3038 |
|
622 |
|
|
* src/applications/utilities/: Makefile, affineScale.in, |
623 |
|
|
waterBoxer.in: added the waterBoxer script |
624 |
|
|
|
625 |
chrisfen |
3131 |
2006-09-01 12:22 chrisfen |
626 |
chrisfen |
3038 |
|
627 |
|
|
* src/applications/utilities/affineScale.in: added comment info |
628 |
|
|
|
629 |
chrisfen |
3131 |
2006-09-01 12:16 gezelter |
630 |
chrisfen |
3038 |
|
631 |
|
|
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
632 |
|
|
brains/Register.cpp, integrators/Makefile, integrators/NgammaT.cpp, |
633 |
|
|
integrators/NgammaT.hpp, io/Globals.cpp: adding NgammaT integrator |
634 |
|
|
|
635 |
chrisfen |
3131 |
2006-09-01 11:29 chrisfen |
636 |
chrisfen |
3038 |
|
637 |
|
|
* src/applications/utilities/affineScale.in: modified affineScale |
638 |
|
|
to work with the new OOPSE files |
639 |
|
|
|
640 |
chrisfen |
3131 |
2006-09-01 07:15 chrisfen |
641 |
chrisfen |
3038 |
|
642 |
|
|
* src/io/: RestReader.cpp, RestWriter.cpp: fixed TI MPI bug |
643 |
|
|
|
644 |
chrisfen |
3131 |
2006-08-31 15:34 chrisfen |
645 |
chrisfen |
3038 |
|
646 |
|
|
* src/: integrators/VelocityVerletIntegrator.cpp, |
647 |
|
|
restraints/ThermoIntegrationForceManager.cpp: fixes to zang writing |
648 |
|
|
|
649 |
chrisfen |
3131 |
2006-08-31 13:12 chrisfen |
650 |
chrisfen |
3038 |
|
651 |
|
|
* samples/alkane/butane.in, samples/alkane/butane.md, |
652 |
|
|
samples/argon/500.in, samples/argon/500.md, samples/argon/ar864.in, |
653 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
654 |
|
|
samples/argon/argonNVT.md, samples/cutoff/GB-Ar-max.md, |
655 |
|
|
samples/cutoff/GB-Ar-mix.md, samples/cutoff/GB-Ar-traditional.md, |
656 |
|
|
samples/cutoff/cutoff_test.in, samples/cutoff/cutoff_test.md, |
657 |
|
|
samples/cutoff/gb-ar.in, samples/cutoff/max.md, |
658 |
|
|
samples/cutoff/mix.md, samples/cutoff/traditional.md, |
659 |
|
|
samples/dipole/splitInWater.in, samples/dipole/splitInWater.md, |
660 |
|
|
samples/dipole/split_SSD.in, samples/dipole/split_SSD.md, |
661 |
|
|
samples/dipole/twoSplitDipole.in, samples/dipole/twoSplitDipole.md, |
662 |
|
|
samples/gbljtest/2gb.in, samples/gbljtest/2gb.md, |
663 |
|
|
samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
664 |
|
|
samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
665 |
|
|
samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
666 |
|
|
samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
667 |
|
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
668 |
|
|
samples/metals/EAM/Au_bulk.in, samples/metals/EAM/Au_bulk_FBD.md, |
669 |
|
|
samples/metals/EAM/Au_bulk_voter.md, |
670 |
|
|
samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.in, |
671 |
|
|
samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.md, |
672 |
|
|
samples/metals/EAM/nanoparticle/Au_nanoparticle.in, |
673 |
|
|
samples/metals/EAM/nanoparticle/Au_nanoparticle.md, |
674 |
|
|
samples/metals/EAM/nanorod/Au_nanoparticle.in, |
675 |
|
|
samples/metals/EAM/nanorod/Au_nanoparticle_FCC.md, |
676 |
|
|
samples/metals/Sutton-Chen/Au_bulk.in, |
677 |
|
|
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
678 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
679 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
680 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.md, |
681 |
|
|
samples/thermoIntegration/liquid/ssde.in, |
682 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
683 |
|
|
samples/thermoIntegration/solid/ssde.in, |
684 |
|
|
samples/thermoIntegration/solid/ssde.md, samples/water/dimer/cl.in, |
685 |
|
|
samples/water/dimer/cl.md, samples/water/dimer/mix.in, |
686 |
|
|
samples/water/dimer/mix.md, samples/water/dimer/mix2.in, |
687 |
|
|
samples/water/dimer/mix2.md, samples/water/dimer/ssd.in, |
688 |
|
|
samples/water/dimer/ssd.md, samples/water/dimer/tap.in, |
689 |
|
|
samples/water/dimer/tap.md, samples/water/dimer/two.in, |
690 |
|
|
samples/water/dimer/two.md, samples/water/spce/spce.in, |
691 |
|
|
samples/water/spce/spce.md, samples/water/ssd/ssd.in, |
692 |
|
|
samples/water/ssd/ssd.md, samples/water/ssd-ion/ssd-ion.md, |
693 |
|
|
samples/water/ssd-ion/ssdCl.in, samples/water/ssd-ion/ssdCl.md, |
694 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
695 |
|
|
samples/water/ssdrf/ssdrf.in, samples/water/ssdrf/ssdrf.md, |
696 |
|
|
samples/water/tap/tap.in, samples/water/tap/tap.md, |
697 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
698 |
|
|
samples/water/tip4p/tp4.in, samples/water/tip4p/tp4.md, |
699 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
700 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
701 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: converted samples |
702 |
|
|
over to the OOPSE-4 file format |
703 |
|
|
|
704 |
|
|
Fixed an MPI bug in thermodynamic integration |
705 |
|
|
|
706 |
chrisfen |
3131 |
2006-08-30 14:13 gezelter |
707 |
chrisfen |
3038 |
|
708 |
|
|
* src/applications/hydrodynamics/Hydro.cpp: removed extra file in |
709 |
|
|
Hydro.cpp |
710 |
|
|
|
711 |
chrisfen |
3131 |
2006-08-30 14:04 gezelter |
712 |
chrisfen |
3038 |
|
713 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
714 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
715 |
|
|
applications/staticProps/StaticProps.cpp, |
716 |
|
|
applications/utilities/dumpConverter, openbabel/oopseformat.cpp: |
717 |
|
|
Changing utility programs to use the new file format |
718 |
|
|
|
719 |
chrisfen |
3131 |
2006-08-30 13:33 gezelter |
720 |
chrisfen |
3038 |
|
721 |
|
|
* src/: brains/SimCreator.cpp, io/DumpReader.cpp, |
722 |
|
|
io/DumpWriter.cpp: fixed some bugs in DumpWriter, eliminated some |
723 |
|
|
extra printing of debugging information |
724 |
|
|
|
725 |
chrisfen |
3131 |
2006-08-30 11:42 tim |
726 |
chrisfen |
3038 |
|
727 |
|
|
* configure, ac-tools/OOPSE.m4, forceFields/Au.u3.funcfl, |
728 |
|
|
forceFields/Ni.u3.funcfl, samples/argon/lj.md, |
729 |
|
|
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
730 |
|
|
src/brains/SimCreator.hpp, src/brains/SimInfo.cpp, |
731 |
|
|
src/brains/SimInfo.hpp, src/io/DumpReader.cpp, |
732 |
|
|
src/io/DumpReader.hpp, src/io/DumpWriter.cpp, |
733 |
|
|
src/io/DumpWriter.hpp, src/io/Globals.cpp, src/io/Globals.hpp, |
734 |
|
|
src/mdParser/SimplePreprocessor.hpp, src/openbabel/Makefile, |
735 |
|
|
src/openbabel/oopseformat.cpp, src/primitives/StuntDouble.cpp, |
736 |
|
|
src/primitives/StuntDouble.hpp, src/utils/StringUtils.cpp, |
737 |
|
|
src/utils/StringUtils.hpp: Massive changes preparing for release of |
738 |
|
|
OOPSE-4: The main difference is that the new MD file format (.md, |
739 |
|
|
.dump, .eor) now contains meta-data information along with the |
740 |
|
|
configuration information. |
741 |
|
|
|
742 |
chrisfen |
3131 |
2006-08-24 10:42 xsun |
743 |
chrisfen |
3038 |
|
744 |
|
|
* src/io/Globals.cpp: change the globals.cpp to make sure we can |
745 |
|
|
set targetPressure and surfaceTension to be negative. |
746 |
|
|
|
747 |
chrisfen |
3131 |
2006-08-14 13:32 chrisfen |
748 |
chrisfen |
3038 |
|
749 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed an ordering |
750 |
|
|
issue in quadrupole-charge interactions |
751 |
|
|
|
752 |
chrisfen |
3131 |
2006-08-02 12:40 gezelter |
753 |
chrisfen |
3038 |
|
754 |
|
|
* make/Makefile.in, samples/water/ssde/ssde.md, src/config.h.in, |
755 |
|
|
src/antlr/Makefile, src/applications/atom2md/atom2md.cpp, |
756 |
|
|
src/brains/Snapshot.cpp, src/brains/Snapshot.hpp, |
757 |
|
|
src/openbabel/Makefile, src/openbabel/oopseformat.cpp, |
758 |
|
|
src/openbabel/oopseformat.hpp: starting change of file formats |
759 |
|
|
|
760 |
chrisfen |
3131 |
2006-08-02 11:06 gezelter |
761 |
chrisfen |
3038 |
|
762 |
|
|
* src/applications/: atom2md/Makefile, atom2md/atom2md.cpp, |
763 |
|
|
atom2mdin/Makefile, atom2mdin/atom2mdin.cpp: Changing atom2mdin |
764 |
|
|
into atom2md to reflect new unified file format |
765 |
|
|
|
766 |
chrisfen |
3131 |
2006-07-27 14:02 chrisfen |
767 |
chrisfen |
3038 |
|
768 |
|
|
* src/applications/utilities/dumpConverter: fixed a pvf bug |
769 |
|
|
|
770 |
chrisfen |
3131 |
2006-07-27 13:36 tim |
771 |
chrisfen |
3038 |
|
772 |
|
|
* src/applications/utilities/dumpConverter: fixed dumpConverter |
773 |
|
|
problems |
774 |
|
|
|
775 |
chrisfen |
3131 |
2006-07-27 12:05 gezelter |
776 |
chrisfen |
3038 |
|
777 |
|
|
* src/applications/utilities/dumpConverter: added dumpConverter |
778 |
|
|
|
779 |
chrisfen |
3131 |
2006-07-26 14:45 gezelter |
780 |
chrisfen |
3038 |
|
781 |
|
|
* make/Makefile.in: removed shapes sample |
782 |
|
|
|
783 |
chrisfen |
3131 |
2006-07-26 14:45 gezelter |
784 |
chrisfen |
3038 |
|
785 |
|
|
* src/applications/utilities/affineScale.in: fixed a spelling bug |
786 |
|
|
|
787 |
chrisfen |
3131 |
2006-07-26 14:01 gezelter |
788 |
chrisfen |
3038 |
|
789 |
|
|
* configure: added perl interpreter to affineScale script |
790 |
|
|
|
791 |
chrisfen |
3131 |
2006-07-26 14:01 gezelter |
792 |
chrisfen |
3038 |
|
793 |
|
|
* ac-tools/configure.in: added perl substitution for affineScale |
794 |
|
|
script |
795 |
|
|
|
796 |
chrisfen |
3131 |
2006-07-26 14:00 gezelter |
797 |
chrisfen |
3038 |
|
798 |
|
|
* make/Makefile.in: added install target for scripts |
799 |
|
|
|
800 |
chrisfen |
3131 |
2006-07-26 14:00 gezelter |
801 |
chrisfen |
3038 |
|
802 |
|
|
* src/applications/utilities/: Makefile, affineScale.in: Adding a |
803 |
|
|
directory for scripts Adding affineScale script |
804 |
|
|
|
805 |
chrisfen |
3131 |
2006-07-24 07:51 xsun |
806 |
chrisfen |
3038 |
|
807 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed a getSigma bug |
808 |
|
|
|
809 |
chrisfen |
3131 |
2006-07-19 05:46 chrisfen |
810 |
chrisfen |
3038 |
|
811 |
|
|
* samples/: thermoIntegration/liquid/water.md, |
812 |
|
|
thermoIntegration/solid/water.md, water/dimer/water.md, |
813 |
|
|
water/spce/water.md, water/ssd/water.md, water/ssd-ion/water.md, |
814 |
|
|
water/ssde/water.md, water/ssdrf/water.md, water/tap/water.md, |
815 |
|
|
water/tip3p_ice/water.md, water/tip4p/water.md: Added tred to |
816 |
|
|
sample water.md files |
817 |
|
|
|
818 |
chrisfen |
3131 |
2006-07-19 05:35 chrisfen |
819 |
chrisfen |
3038 |
|
820 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp, |
821 |
|
|
RigidBodyVisitor.cpp, RigidBodyVisitor.hpp: Added TRED water |
822 |
|
|
visitor for Dump2XYZ visualization |
823 |
|
|
|
824 |
chrisfen |
3131 |
2006-07-19 05:33 chrisfen |
825 |
chrisfen |
3038 |
|
826 |
|
|
* forceFields/DUFF2.frc: Added TRED parameters to forcefield |
827 |
|
|
|
828 |
chrisfen |
3131 |
2006-07-17 11:13 xsun |
829 |
chrisfen |
3038 |
|
830 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed d / sigma0 confusion |
831 |
|
|
|
832 |
chrisfen |
3131 |
2006-07-15 19:48 gezelter |
833 |
chrisfen |
3038 |
|
834 |
|
|
* src/io/ForceFieldOptions.cpp: testing commit logger |
835 |
|
|
|
836 |
chrisfen |
3131 |
2006-07-15 19:46 gezelter |
837 |
chrisfen |
3038 |
|
838 |
|
|
* src/io/ForceFieldOptions.cpp: removed printing of GBN and GBM |
839 |
|
|
from previous debugging |
840 |
|
|
|
841 |
chrisfen |
3131 |
2006-07-14 07:47 xsun |
842 |
chrisfen |
3038 |
|
843 |
|
|
* configure, ac-tools/OOPSE.m4: Fixed a bug in the fftw part of the |
844 |
|
|
configure script. |
845 |
|
|
|
846 |
chrisfen |
3131 |
2006-07-07 12:44 gezelter |
847 |
chrisfen |
3038 |
|
848 |
|
|
* configure, ac-tools/configure.in, samples/gbljtest/2gb.md, |
849 |
|
|
src/UseTheForce/DarkSide/gb.F90: removed icc from C++ search lines, |
850 |
|
|
did some formatting work on GB module, mucked around with a GB |
851 |
|
|
example |
852 |
|
|
|
853 |
chrisfen |
3131 |
2006-07-07 07:18 chuckv |
854 |
chrisfen |
3038 |
|
855 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
856 |
|
|
BondOrderParameter.hpp: Adding more changes to orientational bond |
857 |
|
|
order parameter. |
858 |
|
|
|
859 |
chrisfen |
3131 |
2006-07-03 12:40 chuckv |
860 |
chrisfen |
3038 |
|
861 |
|
|
* src/math/Wigner3jm.F90: Added utility function to winger3jm from |
862 |
|
|
slatac. |
863 |
|
|
|
864 |
chrisfen |
3131 |
2006-07-03 07:06 chrisfen |
865 |
chrisfen |
3038 |
|
866 |
|
|
* src/UseTheForce/DarkSide/mpole.F90: Added the multipole |
867 |
|
|
interaction routine. It doesn't work yet, so it's not included in |
868 |
|
|
the build. |
869 |
|
|
|
870 |
chrisfen |
3131 |
2006-07-03 06:18 chrisfen |
871 |
chrisfen |
3038 |
|
872 |
|
|
* src/: UseTheForce/doForces.F90, |
873 |
|
|
UseTheForce/doForces_interface.F90, |
874 |
|
|
UseTheForce/doForces_interface.h, |
875 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
876 |
|
|
UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp, |
877 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
878 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
879 |
|
|
brains/fSimulation.h, integrators/VelocityVerletIntegrator.cpp, |
880 |
|
|
io/Globals.cpp, io/Globals.hpp, |
881 |
|
|
restraints/ThermoIntegrationForceManager.cpp: Added simulation box |
882 |
|
|
dipole moment accumulation for the purposes of calculating |
883 |
|
|
dielectric constants |
884 |
|
|
|
885 |
chrisfen |
3131 |
2006-07-01 15:27 kdaily |
886 |
chrisfen |
3038 |
|
887 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed forces and torques for GB |
888 |
|
|
|
889 |
chrisfen |
3131 |
2006-06-28 07:35 chrisfen |
890 |
chrisfen |
3038 |
|
891 |
|
|
* src/io/: DumpReader.cpp, RestReader.cpp, RestReader.hpp: more |
892 |
|
|
efficient file reading for thermodynamic integration, and fixed |
893 |
|
|
some formatting |
894 |
|
|
|
895 |
chrisfen |
3131 |
2006-06-27 09:36 chuckv |
896 |
chrisfen |
3038 |
|
897 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
898 |
|
|
BondOrderParameter.hpp: Beginnings of a order parameter. |
899 |
|
|
|
900 |
chrisfen |
3131 |
2006-06-27 09:19 chuckv |
901 |
chrisfen |
3038 |
|
902 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
903 |
|
|
BondOrderParameter.hpp: Adding code for bond orientational |
904 |
|
|
parameters. |
905 |
|
|
|
906 |
chrisfen |
3131 |
2006-06-22 08:21 chrisfen |
907 |
chrisfen |
3038 |
|
908 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
909 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/RestWriter.cpp, |
910 |
|
|
io/RestWriter.hpp, restraints/ThermoIntegrationForceManager.cpp: |
911 |
|
|
MPI thermodynamic integration works now. |
912 |
|
|
|
913 |
chrisfen |
3131 |
2006-06-21 11:28 chrisfen |
914 |
chrisfen |
3038 |
|
915 |
|
|
* src/visitors/AtomVisitor.cpp: fixed a build problem... |
916 |
|
|
GB_12b_ratio no longer exists (replaced with BG_l). |
917 |
|
|
|
918 |
chrisfen |
3131 |
2006-06-19 10:55 chuckv |
919 |
chrisfen |
3038 |
|
920 |
|
|
* src/math/: Makefile, Wigner3jm.F90, Wigner3jm_interface.h: Added |
921 |
|
|
support for Winger3jm coefficients. |
922 |
|
|
|
923 |
chrisfen |
3131 |
2006-06-18 18:36 chrisfen |
924 |
chrisfen |
3038 |
|
925 |
|
|
* src/: io/RestReader.cpp, io/RestWriter.cpp, |
926 |
|
|
restraints/ThermoIntegrationForceManager.cpp: fixes for mpi |
927 |
|
|
thermodynamic integration, close to fully working... |
928 |
|
|
|
929 |
chrisfen |
3131 |
2006-06-17 10:02 tim |
930 |
chrisfen |
3038 |
|
931 |
|
|
* src/visitors/AtomVisitor.cpp: output the principle axis of GB |
932 |
|
|
|
933 |
chrisfen |
3131 |
2006-06-15 11:38 gezelter |
934 |
chrisfen |
3038 |
|
935 |
|
|
* configure, ac-tools/OOPSE.m4, ac-tools/configure.in, |
936 |
|
|
samples/water/tip4p/tp4.md: added mpi compilers, demoted pg |
937 |
|
|
compilers after pathscale |
938 |
|
|
|
939 |
chrisfen |
3131 |
2006-06-09 11:26 chrisfen |
940 |
chrisfen |
3038 |
|
941 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: reformulated some of |
942 |
|
|
the electrostatics |
943 |
|
|
|
944 |
chrisfen |
3131 |
2006-06-07 15:49 chrisfen |
945 |
chrisfen |
3038 |
|
946 |
|
|
* samples/water/ssd/ssd.md, |
947 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: damping now works for |
948 |
|
|
charge-quadrupole and dipole-dipole |
949 |
|
|
|
950 |
chrisfen |
3131 |
2006-06-07 11:05 chrisfen |
951 |
chrisfen |
3038 |
|
952 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, io/RestReader.cpp: |
953 |
|
|
Fixed a spelling error and a bug in MPI Thermodynamic Integration |
954 |
|
|
on file read-in |
955 |
|
|
|
956 |
chrisfen |
3131 |
2006-06-06 11:26 chrisfen |
957 |
chrisfen |
3038 |
|
958 |
|
|
* src/io/: DumpReader.cpp, MultipoleAtomTypesSectionParser.cpp: |
959 |
|
|
fixed some typos |
960 |
|
|
|
961 |
chrisfen |
3131 |
2006-06-06 10:43 gezelter |
962 |
chrisfen |
3038 |
|
963 |
|
|
* forceFields/DUFF2.frc, samples/gbljtest/2gb.in, |
964 |
|
|
samples/gbljtest/2gb.md, samples/gbljtest/gb.md, |
965 |
|
|
samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
966 |
|
|
samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
967 |
|
|
samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
968 |
|
|
samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
969 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
970 |
|
|
src/integrators/LDForceManager.cpp, |
971 |
|
|
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
972 |
|
|
src/utils/interpolation.F90, src/visitors/AtomVisitor.hpp: testing |
973 |
|
|
GB, removing CM drift in Langevin Dynamics, fixing a memory leak, |
974 |
|
|
adding a visitor |
975 |
|
|
|
976 |
chrisfen |
3131 |
2006-06-05 11:44 gezelter |
977 |
chrisfen |
3038 |
|
978 |
|
|
* src/UseTheForce/DarkSide/: fForceOptions.F90, gb.F90: Added |
979 |
|
|
methods to access GB_mu and GB_nu from the force field options |
980 |
|
|
|
981 |
chrisfen |
3131 |
2006-06-05 11:24 gezelter |
982 |
chrisfen |
3038 |
|
983 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
984 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/fForceOptions.h, |
985 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
986 |
|
|
src/UseTheForce/DarkSide/gb_interface.F90, |
987 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
988 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
989 |
|
|
src/applications/hydrodynamics/ApproximationModel.cpp, |
990 |
|
|
src/applications/hydrodynamics/ApproximationModel.hpp, |
991 |
|
|
src/applications/hydrodynamics/CompositeShape.cpp, |
992 |
|
|
src/applications/hydrodynamics/CompositeShape.hpp, |
993 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
994 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
995 |
|
|
src/applications/hydrodynamics/ShapeBuilder.cpp, |
996 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
997 |
|
|
src/hydrodynamics/HydroProp.cpp, src/hydrodynamics/HydroProp.hpp, |
998 |
|
|
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
999 |
|
|
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
1000 |
|
|
src/integrators/LDForceManager.cpp, |
1001 |
|
|
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
1002 |
|
|
src/io/ForceFieldOptions.hpp, |
1003 |
|
|
src/io/GayBerneAtomTypesSectionParser.cpp, |
1004 |
|
|
src/io/GayBerneAtomTypesSectionParser.hpp, |
1005 |
|
|
src/types/DirectionalAtomType.cpp, |
1006 |
|
|
src/types/DirectionalAtomType.hpp, src/utils/HydroProps.hpp: |
1007 |
|
|
Massive changes for GB code with multiple ellipsoid types (a la |
1008 |
|
|
Cleaver's paper). |
1009 |
|
|
|
1010 |
|
|
Also, changes in hydrodynamics code to make HydroProp a somewhat |
1011 |
|
|
smarter class (rather than just a struct). |
1012 |
|
|
|
1013 |
chrisfen |
3131 |
2006-06-01 11:06 xsun |
1014 |
chrisfen |
3038 |
|
1015 |
|
|
* src/applications/staticProps/: Makefile, RippleOP.cpp, |
1016 |
|
|
RippleOP.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
1017 |
|
|
StaticPropsCmd.h: Add the RippleOP to calculate the orderparameter |
1018 |
|
|
of the ripples. |
1019 |
|
|
|
1020 |
chrisfen |
3131 |
2006-05-25 14:40 chrisfen |
1021 |
chrisfen |
3038 |
|
1022 |
|
|
* forceFields/DUFF2.frc, samples/thermoIntegration/liquid/water.md, |
1023 |
|
|
samples/thermoIntegration/solid/water.md, |
1024 |
|
|
samples/water/dimer/water.md, samples/water/spce/water.md, |
1025 |
|
|
samples/water/ssd/water.md, samples/water/ssd-ion/water.md, |
1026 |
|
|
samples/water/ssde/water.md, samples/water/ssdrf/water.md, |
1027 |
|
|
samples/water/tap/water.md, samples/water/tip3p_ice/water.md, |
1028 |
|
|
samples/water/tip4p/water.md, src/io/Globals.cpp: Added TIP5P-E and |
1029 |
|
|
fixed a bug for Thermodynamic integration (you can now have a |
1030 |
|
|
lambda of 0) |
1031 |
|
|
|
1032 |
chrisfen |
3131 |
2006-05-25 10:02 tim |
1033 |
chrisfen |
3038 |
|
1034 |
|
|
* src/applications/hydrodynamics/ApproximationModel.cpp: Fix a type |
1035 |
|
|
promotion problem |
1036 |
|
|
|
1037 |
chrisfen |
3131 |
2006-05-25 09:27 tim |
1038 |
chrisfen |
3038 |
|
1039 |
|
|
* src/applications/hydrodynamics/: AnalyticalModel.hpp, |
1040 |
|
|
ApproximationModel.cpp, Hydro.cpp, HydrodynamicsModel.hpp: replace |
1041 |
|
|
double with RealType |
1042 |
|
|
|
1043 |
chrisfen |
3131 |
2006-05-25 08:27 gezelter |
1044 |
chrisfen |
3038 |
|
1045 |
|
|
* configure: What? |
1046 |
|
|
|
1047 |
chrisfen |
3131 |
2006-05-25 08:24 gezelter |
1048 |
chrisfen |
3038 |
|
1049 |
|
|
* ac-tools/OOPSE.m4: more changes |
1050 |
|
|
|
1051 |
chrisfen |
3131 |
2006-05-25 08:19 gezelter |
1052 |
chrisfen |
3038 |
|
1053 |
|
|
* configure, ac-tools/OOPSE.m4: more changes for MPICH with |
1054 |
|
|
profiling libraries required |
1055 |
|
|
|
1056 |
chrisfen |
3131 |
2006-05-25 07:54 gezelter |
1057 |
chrisfen |
3038 |
|
1058 |
|
|
* configure, ac-tools/OOPSE.m4: MPI stuff |
1059 |
|
|
|
1060 |
chrisfen |
3131 |
2006-05-24 11:31 gezelter |
1061 |
chrisfen |
3038 |
|
1062 |
|
|
* configure, ac-tools/OOPSE.m4, src/config.h.in, |
1063 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
1064 |
|
|
src/applications/hydrodynamics/AnalyticalModel.hpp, |
1065 |
|
|
src/applications/hydrodynamics/ApproximationModel.cpp, |
1066 |
|
|
src/applications/hydrodynamics/ApproximationModel.hpp, |
1067 |
|
|
src/applications/hydrodynamics/CompositeShape.cpp, |
1068 |
|
|
src/applications/hydrodynamics/CompositeShape.hpp, |
1069 |
|
|
src/applications/hydrodynamics/Ellipsoid.cpp, |
1070 |
|
|
src/applications/hydrodynamics/Ellipsoid.hpp, |
1071 |
|
|
src/applications/hydrodynamics/Hydro.cpp, |
1072 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
1073 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
1074 |
|
|
src/applications/hydrodynamics/RoughShell.cpp, |
1075 |
|
|
src/applications/hydrodynamics/RoughShell.hpp, |
1076 |
|
|
src/applications/hydrodynamics/Shape.hpp, |
1077 |
|
|
src/applications/hydrodynamics/ShapeBuilder.cpp, |
1078 |
|
|
src/applications/hydrodynamics/ShapeBuilder.hpp, |
1079 |
|
|
src/applications/hydrodynamics/Spheric.cpp, |
1080 |
|
|
src/applications/hydrodynamics/Spheric.hpp: fixes for Hydrodynamics |
1081 |
|
|
|
1082 |
chrisfen |
3131 |
2006-05-24 09:18 tim |
1083 |
chrisfen |
3038 |
|
1084 |
|
|
* src/integrators/LDForceManager.cpp: fix a bug in parsing |
1085 |
|
|
HydroProp file |
1086 |
|
|
|
1087 |
chrisfen |
3131 |
2006-05-24 08:24 gezelter |
1088 |
chrisfen |
3038 |
|
1089 |
|
|
* src/integrators/LDForceManager.cpp: Fixed a bug when spherical |
1090 |
|
|
boundary conditions were off. |
1091 |
|
|
|
1092 |
chrisfen |
3131 |
2006-05-23 14:12 xsun |
1093 |
chrisfen |
3038 |
|
1094 |
|
|
* src/applications/staticProps/Hxy.cpp: fixed an initialization bug |
1095 |
|
|
of Hxy.cpp. |
1096 |
|
|
|
1097 |
chrisfen |
3131 |
2006-05-23 11:46 tim |
1098 |
chrisfen |
3038 |
|
1099 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: wrapping back to PBC by |
1100 |
|
|
molecule instead of by individual atom |
1101 |
|
|
|
1102 |
chrisfen |
3131 |
2006-05-22 08:30 xsun |
1103 |
chrisfen |
3038 |
|
1104 |
|
|
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, StaticProps.ggo, |
1105 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: fixed the bugs of Hxy.cpp. |
1106 |
|
|
|
1107 |
chrisfen |
3131 |
2006-05-19 14:26 chrisfen |
1108 |
chrisfen |
3038 |
|
1109 |
|
|
* ChangeLog, src/io/DumpWriter.cpp: Last bug showed up in 2 places, |
1110 |
|
|
fixed the other one. |
1111 |
|
|
|
1112 |
chrisfen |
3131 |
2006-05-19 13:45 tim |
1113 |
chrisfen |
2727 |
|
1114 |
chrisfen |
2762 |
* src/io/DumpWriter.cpp: Fix a bug of printing empty line in |
1115 |
|
|
DumpWriter |
1116 |
|
|
|
1117 |
chrisfen |
3131 |
2006-05-19 08:11 tim |
1118 |
chrisfen |
2762 |
|
1119 |
|
|
* make/Makefile.in: change the order of include path and library |
1120 |
|
|
path |
1121 |
|
|
|
1122 |
chrisfen |
3131 |
2006-05-17 14:51 tim |
1123 |
chrisfen |
2762 |
|
1124 |
|
|
* ChangeLog, samples/water/ssd/ssd.md, src/config.h.in, |
1125 |
|
|
src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp, |
1126 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
1127 |
|
|
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
1128 |
|
|
src/UseTheForce/doForces_interface.h, |
1129 |
|
|
src/UseTheForce/fForceOptions.h, |
1130 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
1131 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
1132 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
1133 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
1134 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
1135 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
1136 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
1137 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.h, |
1138 |
|
|
src/applications/dynamicProps/CrossTimeCorrFunc.cpp, |
1139 |
|
|
src/applications/dynamicProps/CrossTimeCorrFunc.hpp, |
1140 |
|
|
src/applications/dynamicProps/DipoleCorrFunc.cpp, |
1141 |
|
|
src/applications/dynamicProps/DipoleCorrFunc.hpp, |
1142 |
|
|
src/applications/dynamicProps/LegendreCorrFunc.cpp, |
1143 |
|
|
src/applications/dynamicProps/LegendreCorrFunc.hpp, |
1144 |
|
|
src/applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
1145 |
|
|
src/applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
1146 |
|
|
src/applications/dynamicProps/RCorrFunc.cpp, |
1147 |
|
|
src/applications/dynamicProps/RCorrFunc.hpp, |
1148 |
|
|
src/applications/dynamicProps/TimeCorrFunc.hpp, |
1149 |
|
|
src/applications/dynamicProps/VCorrFunc.cpp, |
1150 |
|
|
src/applications/dynamicProps/VCorrFunc.hpp, |
1151 |
|
|
src/applications/hydrodynamics/Makefile, |
1152 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
1153 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
1154 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
1155 |
|
|
src/applications/randomBuilder/randomBuilder.cpp, |
1156 |
|
|
src/applications/simpleBuilder/randomBuilder.cpp, |
1157 |
|
|
src/applications/staticProps/DensityPlot.cpp, |
1158 |
|
|
src/applications/staticProps/DensityPlot.hpp, |
1159 |
|
|
src/applications/staticProps/GofAngle2.cpp, |
1160 |
|
|
src/applications/staticProps/GofAngle2.hpp, |
1161 |
|
|
src/applications/staticProps/GofR.cpp, |
1162 |
|
|
src/applications/staticProps/GofR.hpp, |
1163 |
|
|
src/applications/staticProps/GofRAngle.cpp, |
1164 |
|
|
src/applications/staticProps/GofRAngle.hpp, |
1165 |
|
|
src/applications/staticProps/GofXyz.cpp, |
1166 |
|
|
src/applications/staticProps/GofXyz.hpp, |
1167 |
|
|
src/applications/staticProps/Hxy.cpp, |
1168 |
|
|
src/applications/staticProps/Hxy.hpp, |
1169 |
|
|
src/applications/staticProps/P2OrderParameter.cpp, |
1170 |
|
|
src/applications/staticProps/P2OrderParameter.hpp, |
1171 |
|
|
src/applications/staticProps/RhoZ.cpp, |
1172 |
|
|
src/applications/staticProps/RhoZ.hpp, |
1173 |
|
|
src/applications/staticProps/SCDOrderParameter.cpp, |
1174 |
|
|
src/applications/staticProps/SCDOrderParameter.hpp, |
1175 |
|
|
src/applications/staticProps/StaticProps.cpp, |
1176 |
|
|
src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp, |
1177 |
|
|
src/brains/DataStorage.hpp, src/brains/ForceManager.cpp, |
1178 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
1179 |
|
|
src/brains/SimInfo.hpp, src/brains/Snapshot.cpp, |
1180 |
|
|
src/brains/Snapshot.hpp, src/brains/Stats.hpp, |
1181 |
|
|
src/brains/Thermo.cpp, src/brains/Thermo.hpp, |
1182 |
|
|
src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp, |
1183 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp, |
1184 |
|
|
src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp, |
1185 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
1186 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
1187 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
1188 |
|
|
src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp, |
1189 |
|
|
src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp, |
1190 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.hpp, |
1191 |
|
|
src/integrators/LDForceManager.cpp, |
1192 |
|
|
src/integrators/LDForceManager.hpp, |
1193 |
|
|
src/integrators/LangevinDynamics.cpp, |
1194 |
|
|
src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp, |
1195 |
|
|
src/integrators/NPAT.hpp, src/integrators/NPT.cpp, |
1196 |
|
|
src/integrators/NPT.hpp, src/integrators/NPTf.cpp, |
1197 |
|
|
src/integrators/NPTf.hpp, src/integrators/NPTi.cpp, |
1198 |
|
|
src/integrators/NPTi.hpp, src/integrators/NPTxyz.cpp, |
1199 |
|
|
src/integrators/NPTxyz.hpp, src/integrators/NPrT.cpp, |
1200 |
|
|
src/integrators/NPrT.hpp, src/integrators/NVE.cpp, |
1201 |
|
|
src/integrators/NVE.hpp, src/integrators/NVT.cpp, |
1202 |
|
|
src/integrators/NVT.hpp, src/integrators/RotationAlgorithm.hpp, |
1203 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
1204 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
1205 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
1206 |
|
|
src/io/AtomTypesSectionParser.cpp, |
1207 |
|
|
src/io/BendTypesSectionParser.cpp, |
1208 |
|
|
src/io/BondTypesSectionParser.cpp, |
1209 |
|
|
src/io/ChargeAtomTypesSectionParser.cpp, |
1210 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
1211 |
|
|
src/io/DumpReader.cpp, src/io/DumpWriter.cpp, |
1212 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
1213 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp, |
1214 |
|
|
src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp, |
1215 |
|
|
src/io/RestReader.cpp, src/io/RestReader.hpp, |
1216 |
|
|
src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp, |
1217 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1218 |
|
|
src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp, |
1219 |
|
|
src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp, |
1220 |
|
|
src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp, |
1221 |
|
|
src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp, |
1222 |
|
|
src/math/CholeskyDecomposition.hpp, |
1223 |
|
|
src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp, |
1224 |
|
|
src/math/MatVec3.c, src/math/MatVec3.h, |
1225 |
|
|
src/math/MersenneTwister.hpp, src/math/Polynomial.hpp, |
1226 |
|
|
src/math/Quaternion.hpp, src/math/RandNumGen.hpp, |
1227 |
|
|
src/math/RealSphericalHarmonic.cpp, |
1228 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp, |
1229 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
1230 |
|
|
src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp, |
1231 |
|
|
src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp, |
1232 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
1233 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp, |
1234 |
|
|
src/minimizers/Minimizer.hpp, |
1235 |
|
|
src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp, |
1236 |
|
|
src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp, |
1237 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1238 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
1239 |
|
|
src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp, |
1240 |
|
|
src/primitives/DirectionalAtom.cpp, |
1241 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1242 |
|
|
src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp, |
1243 |
|
|
src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp, |
1244 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1245 |
|
|
src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp, |
1246 |
|
|
src/primitives/Torsion.cpp, src/primitives/Torsion.hpp, |
1247 |
|
|
src/primitives/UreyBradleyBend.cpp, |
1248 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
1249 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
1250 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp, |
1251 |
|
|
src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp, |
1252 |
|
|
src/selection/SelectionEvaluator.cpp, |
1253 |
|
|
src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp, |
1254 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
1255 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
1256 |
|
|
src/types/BendType.hpp, src/types/BondType.hpp, |
1257 |
|
|
src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp, |
1258 |
|
|
src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp, |
1259 |
|
|
src/types/DirectionalAtomType.cpp, |
1260 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
1261 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
1262 |
|
|
src/types/MorseBondType.hpp, src/types/OplsTorsionType.hpp, |
1263 |
|
|
src/types/PolynomialBendType.hpp, src/types/PolynomialBondType.hpp, |
1264 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
1265 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
1266 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
1267 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
1268 |
|
|
src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp, |
1269 |
|
|
src/utils/GenericData.hpp, src/utils/MoLocator.cpp, |
1270 |
|
|
src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp, |
1271 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp, |
1272 |
|
|
src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp, |
1273 |
|
|
src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h, |
1274 |
|
|
src/utils/residentMem.c, src/utils/residentMem.h, |
1275 |
|
|
src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp: |
1276 |
|
|
Adding single precision capabilities to c++ side |
1277 |
|
|
|
1278 |
chrisfen |
3131 |
2006-05-17 12:54 gezelter |
1279 |
chrisfen |
2762 |
|
1280 |
tim |
2759 |
* configure, ac-tools/configure.in, make/Makefile.in, |
1281 |
|
|
src/UseTheForce/doForces.F90, |
1282 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
1283 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
1284 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
1285 |
|
|
src/UseTheForce/DarkSide/simulation_interface.F90, |
1286 |
|
|
src/utils/definitions.F90: Adding single precision capabilities to |
1287 |
|
|
the fortran side |
1288 |
|
|
|
1289 |
chrisfen |
3131 |
2006-05-17 09:10 gezelter |
1290 |
tim |
2759 |
|
1291 |
|
|
* configure, ac-tools/configure.in, src/config.h.in: adding |
1292 |
|
|
--enable-single to configure script |
1293 |
|
|
|
1294 |
chrisfen |
3131 |
2006-05-17 08:37 gezelter |
1295 |
tim |
2759 |
|
1296 |
|
|
* ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, |
1297 |
|
|
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
1298 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1299 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
1300 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
1301 |
|
|
src/UseTheForce/DarkSide/lj_interface.F90, |
1302 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
1303 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
1304 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
1305 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.F90, |
1306 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, src/math/derfc.F90, |
1307 |
|
|
src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran |
1308 |
|
|
side prepped for single precision... |
1309 |
|
|
|
1310 |
chrisfen |
3131 |
2006-05-17 07:03 chrisfen |
1311 |
tim |
2759 |
|
1312 |
|
|
* samples/water/ssd-ion/ssdCl.md, |
1313 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: electrostatic |
1314 |
|
|
refinement |
1315 |
|
|
|
1316 |
chrisfen |
3131 |
2006-05-16 20:03 gezelter |
1317 |
tim |
2759 |
|
1318 |
|
|
* configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes |
1319 |
|
|
|
1320 |
chrisfen |
3131 |
2006-05-16 13:38 gezelter |
1321 |
tim |
2759 |
|
1322 |
|
|
* configure, ac-tools/OOPSE.m4, ac-tools/config.guess, |
1323 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, |
1324 |
|
|
ac-tools/missing, ac-tools/mkinstalldirs, make/Makefile.in, |
1325 |
|
|
src/config.h.in, src/applications/staticProps/Hxy.cpp, |
1326 |
|
|
src/applications/staticProps/Hxy.hpp, |
1327 |
|
|
src/applications/staticProps/StaticProps.cpp: Autoconf fixes for |
1328 |
|
|
FFTW. Multiple FFTW version support. |
1329 |
|
|
|
1330 |
chrisfen |
3131 |
2006-05-15 19:06 gezelter |
1331 |
tim |
2759 |
|
1332 |
|
|
* README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1333 |
|
|
make/Makefile.in, src/config.h.in, |
1334 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
1335 |
|
|
src/applications/hydrodynamics/AnalyticalModel.hpp, |
1336 |
|
|
src/applications/staticProps/Hxy.cpp, |
1337 |
|
|
src/applications/staticProps/Hxy.hpp, |
1338 |
|
|
src/applications/staticProps/StaticProps.cpp, |
1339 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
1340 |
|
|
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
1341 |
|
|
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
1342 |
|
|
src/integrators/LDForceManager.cpp, |
1343 |
|
|
src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, |
1344 |
|
|
src/utils/HydroProps.hpp: [no log message] |
1345 |
|
|
|
1346 |
chrisfen |
3131 |
2006-05-12 14:34 xsun |
1347 |
tim |
2759 |
|
1348 |
|
|
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, |
1349 |
|
|
StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to |
1350 |
|
|
calculate undulation spectrum |
1351 |
|
|
|
1352 |
chrisfen |
3131 |
2006-05-09 18:44 tim |
1353 |
tim |
2759 |
|
1354 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1355 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
1356 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
1357 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
1358 |
|
|
applications/hydrodynamics/ApproximationModel.cpp, |
1359 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a |
1360 |
|
|
gay-berne switch to Dump2XYZ |
1361 |
|
|
|
1362 |
chrisfen |
3131 |
2006-05-05 10:58 gezelter |
1363 |
tim |
2759 |
|
1364 |
|
|
* src/UseTheForce/DarkSide/qpole.F90: Adding qpole |
1365 |
|
|
|
1366 |
chrisfen |
3131 |
2006-05-05 07:34 tim |
1367 |
tim |
2759 |
|
1368 |
|
|
* ac-tools/aclocal.m4: finding ifort arguments that won't die under |
1369 |
|
|
two different versions of the intel fortran compiler |
1370 |
|
|
|
1371 |
chrisfen |
3131 |
2006-05-03 06:15 chrisfen |
1372 |
tim |
2759 |
|
1373 |
|
|
* src/applications/randomBuilder/Makefile: missing makefile was |
1374 |
|
|
hanging up 'make clean' |
1375 |
|
|
|
1376 |
chrisfen |
3131 |
2006-04-25 15:59 chuckv |
1377 |
tim |
2759 |
|
1378 |
|
|
* src/applications/randomBuilder/: randomBuilder.cpp, |
1379 |
|
|
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added |
1380 |
|
|
random builder to cvs. |
1381 |
|
|
|
1382 |
chrisfen |
3131 |
2006-04-25 15:54 chuckv |
1383 |
tim |
2759 |
|
1384 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
1385 |
|
|
Change in siminfo used in nanoparticleBuilder. |
1386 |
|
|
|
1387 |
chrisfen |
3131 |
2006-04-25 15:30 chuckv |
1388 |
tim |
2759 |
|
1389 |
|
|
* make/Makefile.in: Added random builder |
1390 |
|
|
|
1391 |
chrisfen |
3131 |
2006-04-25 15:29 chuckv |
1392 |
tim |
2759 |
|
1393 |
|
|
* src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, |
1394 |
|
|
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a |
1395 |
|
|
random builder to oopse. |
1396 |
|
|
|
1397 |
chrisfen |
3131 |
2006-04-25 06:35 gezelter |
1398 |
tim |
2759 |
|
1399 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
1400 |
|
|
ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table |
1401 |
|
|
to pick vdw radii for hydrodynamics if the LJ sigma can't be found. |
1402 |
|
|
|
1403 |
chrisfen |
3131 |
2006-04-24 19:09 gezelter |
1404 |
tim |
2759 |
|
1405 |
|
|
* configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, |
1406 |
|
|
src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, |
1407 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
1408 |
|
|
src/brains/SimInfo.hpp, src/brains/Thermo.cpp, |
1409 |
|
|
src/brains/Thermo.hpp, src/integrators/LDForceManager.cpp, |
1410 |
|
|
src/integrators/LDForceManager.hpp, |
1411 |
|
|
src/integrators/LangevinDynamics.cpp, src/io/Globals.cpp, |
1412 |
|
|
src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding |
1413 |
|
|
spherical boundary conditions to LD integrator |
1414 |
|
|
|
1415 |
chrisfen |
3131 |
2006-04-24 19:06 gezelter |
1416 |
tim |
2759 |
|
1417 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: |
1418 |
|
|
Added EAM atom types to Hydro models |
1419 |
|
|
|
1420 |
chrisfen |
3131 |
2006-04-21 13:02 chrisfen |
1421 |
tim |
2759 |
|
1422 |
|
|
* src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the |
1423 |
|
|
EAM module |
1424 |
|
|
|
1425 |
chrisfen |
3131 |
2006-04-21 12:32 chrisfen |
1426 |
tim |
2759 |
|
1427 |
|
|
* ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, |
1428 |
|
|
samples/shape/C60.shape, samples/shape/C70.shape, |
1429 |
|
|
samples/shape/Makefile, samples/shape/Shapes.frc, |
1430 |
|
|
samples/shape/cholesterol.shape, samples/shape/ethylBenzene.shape, |
1431 |
|
|
samples/shape/linear.in, samples/shape/linear.md, |
1432 |
|
|
samples/shape/linear.shape, samples/shape/toluene.shape, |
1433 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
1434 |
|
|
samples/thermoIntegration/solid/ssde.md, |
1435 |
|
|
samples/water/spce/spce.md, samples/water/ssd/ssd.md, |
1436 |
|
|
samples/water/ssd-ion/ssdCl.md, samples/water/ssde/ssde.md, |
1437 |
|
|
samples/water/ssdrf/ssdrf.md, samples/water/tip3p_ice/tp3.md, |
1438 |
|
|
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90, |
1439 |
|
|
src/UseTheForce/DarkSide/LJ.F90: Removed sqrt splines and shape |
1440 |
|
|
stuff (doesn't work, so why was it in there?). Changed some of the |
1441 |
|
|
water samples to use shifted_force. Probably should set the |
1442 |
|
|
defaults to use the damped version now that we sped it up. |
1443 |
|
|
|
1444 |
chrisfen |
3131 |
2006-04-20 20:19 chrisfen |
1445 |
tim |
2759 |
|
1446 |
chrisfen |
2727 |
* samples/water/spce/spce.md, |
1447 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
1448 |
|
|
|
1449 |
chrisfen |
3131 |
2006-04-20 14:02 chrisfen |
1450 |
chrisfen |
2727 |
|
1451 |
|
|
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
1452 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
1453 |
|
|
|
1454 |
chrisfen |
3131 |
2006-04-20 11:24 gezelter |
1455 |
chrisfen |
2727 |
|
1456 |
|
|
* samples/metals/EAM/Au_bulk_voter.md, |
1457 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1458 |
|
|
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
1459 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
1460 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
1461 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1462 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
1463 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
1464 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
1465 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.h, |
1466 |
|
|
src/utils/interpolation.F90: Complete rewrite of spline code and |
1467 |
|
|
everything that uses it. |
1468 |
|
|
|
1469 |
chrisfen |
3131 |
2006-04-17 14:49 gezelter |
1470 |
chrisfen |
2727 |
|
1471 |
|
|
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
1472 |
|
|
samples/metals/EAM/Au_bulk_voter.md, |
1473 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1474 |
|
|
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
1475 |
|
|
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
1476 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1477 |
|
|
src/UseTheForce/DarkSide/interpolation.F90, |
1478 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
1479 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
1480 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
1481 |
|
|
src/applications/hydrodynamics/Hydro.ggo, |
1482 |
|
|
src/applications/hydrodynamics/HydroCmd.c, |
1483 |
|
|
src/applications/hydrodynamics/HydroCmd.h, |
1484 |
|
|
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
1485 |
|
|
src/utils/interpolation.F90: Many performance improvements |
1486 |
|
|
|
1487 |
chrisfen |
3131 |
2006-04-15 19:51 chrisfen |
1488 |
chrisfen |
2727 |
|
1489 |
|
|
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
1490 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
1491 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
1492 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
1493 |
|
|
switcheroo |
1494 |
|
|
|
1495 |
chrisfen |
3131 |
2006-04-15 14:58 chrisfen |
1496 |
chrisfen |
2727 |
|
1497 |
|
|
* src/utils/Makefile.in: Since status.F90 is used by |
1498 |
|
|
interpolation.F90, the former needs to be listed above the later in |
1499 |
|
|
the Makefile. |
1500 |
|
|
|
1501 |
chrisfen |
3131 |
2006-04-14 14:59 gezelter |
1502 |
chrisfen |
2727 |
|
1503 |
|
|
* src/utils/interpolation.F90: changed the interface a bit |
1504 |
|
|
|
1505 |
chrisfen |
3131 |
2006-04-14 14:49 gezelter |
1506 |
chrisfen |
2727 |
|
1507 |
|
|
* src/utils/interpolation.F90: added some logical flags |
1508 |
|
|
|
1509 |
chrisfen |
3131 |
2006-04-14 14:06 chrisfen |
1510 |
chrisfen |
2727 |
|
1511 |
|
|
* src/utils/interpolation.F90: Wiped the spline with derivatives |
1512 |
|
|
and corrected a boundary comparision error by eliminating the |
1513 |
|
|
check. This algorithm REQUIRES known first derivatives at the |
1514 |
|
|
endpoints. |
1515 |
|
|
|
1516 |
chrisfen |
3131 |
2006-04-14 13:04 gezelter |
1517 |
chrisfen |
2727 |
|
1518 |
|
|
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
1519 |
|
|
interpolation module |
1520 |
|
|
|
1521 |
chrisfen |
3131 |
2006-04-14 12:57 gezelter |
1522 |
chrisfen |
2727 |
|
1523 |
|
|
* src/utils/interpolation.F90: Heavily modified interpolation |
1524 |
|
|
module, also moved to "utils" |
1525 |
|
|
|
1526 |
chrisfen |
3131 |
2006-04-12 14:15 chuckv |
1527 |
chrisfen |
2727 |
|
1528 |
|
|
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
1529 |
|
|
module. |
1530 |
|
|
|
1531 |
chrisfen |
3131 |
2006-04-11 08:33 gezelter |
1532 |
chrisfen |
2727 |
|
1533 |
|
|
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
1534 |
|
|
StaticPropsCmd.h: [no log message] |
1535 |
|
|
|
1536 |
chrisfen |
3131 |
2006-04-03 08:37 chuckv |
1537 |
chrisfen |
2727 |
|
1538 |
|
|
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
1539 |
|
|
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
1540 |
|
|
simParallel for error reporting. |
1541 |
|
|
|
1542 |
chrisfen |
3131 |
2006-03-31 10:09 tim |
1543 |
chrisfen |
2727 |
|
1544 |
|
|
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
1545 |
|
|
|
1546 |
chrisfen |
3131 |
2006-03-30 13:08 chuckv |
1547 |
chrisfen |
2727 |
|
1548 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
1549 |
|
|
where SCList capacity was not reset to zero on destruction. |
1550 |
|
|
|
1551 |
chrisfen |
3131 |
2006-03-30 11:37 chuckv |
1552 |
chrisfen |
2727 |
|
1553 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
1554 |
|
|
More testing of nanoparticleBuilder. |
1555 |
|
|
|
1556 |
chrisfen |
3131 |
2006-03-29 14:24 chuckv |
1557 |
chrisfen |
2727 |
|
1558 |
|
|
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
1559 |
|
|
file exists. |
1560 |
|
|
|
1561 |
chrisfen |
3131 |
2006-03-29 11:17 chuckv |
1562 |
chrisfen |
2727 |
|
1563 |
|
|
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
1564 |
|
|
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
1565 |
|
|
latticeOrt in shapedlatice and latticebuilder. |
1566 |
|
|
|
1567 |
chrisfen |
3131 |
2006-03-29 10:11 tim |
1568 |
chrisfen |
2727 |
|
1569 |
|
|
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
1570 |
|
|
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
1571 |
|
|
in calculating correlation functions |
1572 |
|
|
|
1573 |
chrisfen |
3131 |
2006-03-29 10:09 tim |
1574 |
chrisfen |
2727 |
|
1575 |
|
|
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
1576 |
|
|
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
1577 |
|
|
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
1578 |
|
|
RoughShell Model is working; (20)Adding a new option into Hydro |
1579 |
|
|
which allows user to generate the beads only |
1580 |
|
|
|
1581 |
chrisfen |
3131 |
2006-03-27 08:21 chuckv |
1582 |
chrisfen |
2727 |
|
1583 |
|
|
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
1584 |
|
|
nanoparticle builder. |
1585 |
|
|
|
1586 |
chrisfen |
3131 |
2006-03-27 08:03 chuckv |
1587 |
chrisfen |
2727 |
|
1588 |
|
|
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
1589 |
|
|
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
1590 |
|
|
makefile |
1591 |
|
|
|
1592 |
chrisfen |
3131 |
2006-03-24 12:46 chuckv |
1593 |
chrisfen |
2727 |
|
1594 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
1595 |
|
|
Debugging changes to nanoparticle builder. |
1596 |
|
|
|
1597 |
chrisfen |
3131 |
2006-03-24 09:29 tim |
1598 |
chrisfen |
2727 |
|
1599 |
|
|
* src/applications/dynamicProps/: DynamicProps.cpp, |
1600 |
|
|
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
1601 |
|
|
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
1602 |
|
|
|
1603 |
chrisfen |
3131 |
2006-03-24 08:49 tim |
1604 |
chrisfen |
2727 |
|
1605 |
|
|
* src/applications/dynamicProps/: DynamicProps.cpp, |
1606 |
|
|
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
1607 |
|
|
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
1608 |
|
|
function. The command line option for DynamicProps is now changed. |
1609 |
|
|
--rcorr is for position correlation and --rmsd is for mean square |
1610 |
|
|
displacement. |
1611 |
|
|
|
1612 |
chrisfen |
3131 |
2006-03-23 07:03 tim |
1613 |
chrisfen |
2727 |
|
1614 |
|
|
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
1615 |
|
|
AnalyticalModel.hpp, ApproximationModel.cpp, |
1616 |
|
|
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
1617 |
|
|
method |
1618 |
|
|
|
1619 |
chrisfen |
3131 |
2006-03-23 07:02 tim |
1620 |
chrisfen |
2727 |
|
1621 |
|
|
* src/io/Globals.hpp: remove a unknown method |
1622 |
|
|
|
1623 |
chrisfen |
3131 |
2006-03-23 07:00 tim |
1624 |
chrisfen |
2727 |
|
1625 |
|
|
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
1626 |
|
|
|
1627 |
chrisfen |
3131 |
2006-03-23 06:59 tim |
1628 |
chrisfen |
2727 |
|
1629 |
|
|
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
1630 |
|
|
can not be opened for preprocessing |
1631 |
|
|
|
1632 |
chrisfen |
3131 |
2006-03-22 12:57 chuckv |
1633 |
chrisfen |
2727 |
|
1634 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
1635 |
|
|
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
1636 |
|
|
shaped lattice. |
1637 |
|
|
|
1638 |
chrisfen |
3131 |
2006-03-21 07:33 tim |
1639 |
chrisfen |
2727 |
|
1640 |
|
|
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
1641 |
|
|
in calculating hydrodynamics tensor when the radius of beads are |
1642 |
|
|
not the same |
1643 |
|
|
|
1644 |
chrisfen |
3131 |
2006-03-20 16:26 tim |
1645 |
chrisfen |
2727 |
|
1646 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1647 |
|
|
applications/hydrodynamics/BeadModel.cpp, |
1648 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
1649 |
|
|
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
1650 |
|
|
for ellipsoid |
1651 |
|
|
|
1652 |
chrisfen |
3131 |
2006-03-20 11:12 tim |
1653 |
chrisfen |
2727 |
|
1654 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1655 |
|
|
applications/hydrodynamics/Ellipsoid.cpp, |
1656 |
|
|
applications/hydrodynamics/Ellipsoid.hpp, |
1657 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
1658 |
|
|
integrators/LDForceManager.cpp: Verify the correctness of |
1659 |
|
|
Ellipsoid's hydrodynamics properties |
1660 |
|
|
|
1661 |
chrisfen |
3131 |
2006-03-17 15:51 tim |
1662 |
chrisfen |
2727 |
|
1663 |
|
|
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
1664 |
|
|
version of Hydro is working now. |
1665 |
|
|
|
1666 |
chrisfen |
3131 |
2006-03-17 15:20 tim |
1667 |
chrisfen |
2727 |
|
1668 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1669 |
|
|
applications/hydrodynamics/AnalyticalModel.hpp, |
1670 |
|
|
applications/hydrodynamics/ApproximationModel.cpp, |
1671 |
|
|
applications/hydrodynamics/ApproximationModel.hpp, |
1672 |
|
|
applications/hydrodynamics/BeadModel.hpp, |
1673 |
|
|
applications/hydrodynamics/CompositeShape.cpp, |
1674 |
|
|
applications/hydrodynamics/CompositeShape.hpp, |
1675 |
|
|
applications/hydrodynamics/Ellipsoid.cpp, |
1676 |
|
|
applications/hydrodynamics/Ellipsoid.hpp, |
1677 |
|
|
applications/hydrodynamics/Hydro.cpp, |
1678 |
|
|
applications/hydrodynamics/Hydro.ggo, |
1679 |
|
|
applications/hydrodynamics/HydroCmd.c, |
1680 |
|
|
applications/hydrodynamics/HydroCmd.h, |
1681 |
|
|
applications/hydrodynamics/HydrodynamicsModel.cpp, |
1682 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1683 |
|
|
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
1684 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
1685 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
1686 |
|
|
applications/hydrodynamics/Makefile, |
1687 |
|
|
applications/hydrodynamics/RoughShell.cpp, |
1688 |
|
|
applications/hydrodynamics/RoughShell.hpp, |
1689 |
|
|
applications/hydrodynamics/Shape.hpp, |
1690 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
1691 |
|
|
applications/hydrodynamics/ShapeBuilder.hpp, |
1692 |
|
|
applications/hydrodynamics/Spheric.cpp, |
1693 |
|
|
applications/hydrodynamics/Spheric.hpp, |
1694 |
|
|
applications/hydrodynamics/StuntDoubleShape.cpp, |
1695 |
|
|
applications/hydrodynamics/StuntDoubleShape.hpp, |
1696 |
|
|
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
1697 |
|
|
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
1698 |
|
|
utils/HydroProps.hpp: refactor Hydrodynamics module. |
1699 |
|
|
|
1700 |
chrisfen |
3131 |
2006-03-17 08:10 chuckv |
1701 |
chrisfen |
2727 |
|
1702 |
|
|
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
1703 |
|
|
Generic Shaped Lattice for oopse. Can overload to get spherical or |
1704 |
|
|
nanorod. |
1705 |
|
|
|
1706 |
chrisfen |
3131 |
2006-03-16 14:50 tim |
1707 |
chrisfen |
2727 |
|
1708 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1709 |
|
|
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
1710 |
|
|
LagevinDynamics is working? |
1711 |
|
|
|
1712 |
chrisfen |
3131 |
2006-03-16 13:52 gezelter |
1713 |
chrisfen |
2727 |
|
1714 |
|
|
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
1715 |
|
|
problem |
1716 |
|
|
|
1717 |
chrisfen |
3131 |
2006-03-15 14:08 tim |
1718 |
chrisfen |
2727 |
|
1719 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
1720 |
|
|
conversion for diffusion tensor is wrong |
1721 |
|
|
|
1722 |
chrisfen |
3131 |
2006-03-15 13:28 tim |
1723 |
chrisfen |
2727 |
|
1724 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1725 |
|
|
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
1726 |
|
|
|
1727 |
chrisfen |
3131 |
2006-03-15 12:58 tim |
1728 |
chrisfen |
2727 |
|
1729 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
1730 |
|
|
the unit in HydrodynamicsModel |
1731 |
|
|
|
1732 |
chrisfen |
3131 |
2006-03-15 09:35 tim |
1733 |
chrisfen |
2727 |
|
1734 |
|
|
* src/primitives/RigidBody.cpp: using setFrc in |
1735 |
|
|
RigidBody::calcForcesAndTorques will discard if there are force and |
1736 |
|
|
torque applied in rigid body itself. use addFrc instead. |
1737 |
|
|
|
1738 |
chrisfen |
3131 |
2006-03-15 07:51 tim |
1739 |
chrisfen |
2727 |
|
1740 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
1741 |
|
|
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
1742 |
|
|
|
1743 |
chrisfen |
3131 |
2006-03-15 07:50 tim |
1744 |
chrisfen |
2727 |
|
1745 |
|
|
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
1746 |
|
|
hydrodynamics module into build system |
1747 |
|
|
|
1748 |
chrisfen |
3131 |
2006-03-14 15:46 tim |
1749 |
chrisfen |
2727 |
|
1750 |
|
|
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
1751 |
|
|
|
1752 |
chrisfen |
3131 |
2006-03-13 14:42 tim |
1753 |
chrisfen |
2727 |
|
1754 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1755 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1756 |
|
|
applications/hydrodynamics/StuntDoubleShape.cpp, |
1757 |
|
|
applications/hydrodynamics/StuntDoubleShape.hpp, |
1758 |
|
|
brains/Register.cpp, integrators/LDForceManager.cpp, |
1759 |
|
|
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
1760 |
|
|
integrators/LangevinDynamics.hpp, integrators/Makefile, |
1761 |
|
|
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
1762 |
|
|
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
1763 |
|
|
progress |
1764 |
|
|
|
1765 |
chrisfen |
3131 |
2006-03-07 08:43 gezelter |
1766 |
chrisfen |
2727 |
|
1767 |
|
|
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
1768 |
|
|
double/int bug. Surprised no one ever noticed before... |
1769 |
|
|
|
1770 |
chrisfen |
3131 |
2006-02-24 13:17 tim |
1771 |
chrisfen |
2727 |
|
1772 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
1773 |
|
|
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
1774 |
|
|
product of Rij |
1775 |
|
|
|
1776 |
chrisfen |
3131 |
2006-02-23 15:16 tim |
1777 |
chrisfen |
2727 |
|
1778 |
|
|
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
1779 |
|
|
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
1780 |
|
|
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
1781 |
|
|
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
1782 |
|
|
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
1783 |
|
|
StuntDoubleShape.hpp: Bead Model is working |
1784 |
|
|
|
1785 |
chrisfen |
3131 |
2006-02-22 12:35 tim |
1786 |
chrisfen |
2727 |
|
1787 |
|
|
* src/: applications/hydrodynamics/Hydro.cpp, |
1788 |
|
|
applications/hydrodynamics/Hydro.ggo, |
1789 |
|
|
applications/hydrodynamics/HydroCmd.c, |
1790 |
|
|
applications/hydrodynamics/HydroCmd.h, |
1791 |
|
|
applications/hydrodynamics/HydrodynamicsModel.cpp, |
1792 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1793 |
|
|
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
1794 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
1795 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
1796 |
|
|
applications/hydrodynamics/MoleculeShape.cpp, |
1797 |
|
|
applications/hydrodynamics/MoleculeShape.hpp, |
1798 |
|
|
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
1799 |
|
|
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
1800 |
|
|
Module |
1801 |
|
|
|
1802 |
chrisfen |
3131 |
2006-02-16 14:05 gezelter |
1803 |
chrisfen |
2727 |
|
1804 |
|
|
* src/brains/Snapshot.cpp: fixed a spelling error |
1805 |
|
|
|
1806 |
chrisfen |
3131 |
2006-02-16 13:40 gezelter |
1807 |
chrisfen |
2727 |
|
1808 |
|
|
* src/: UseTheForce/doForces.F90, |
1809 |
|
|
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
1810 |
|
|
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
1811 |
|
|
larger than 1/2 the length of the shortest box dimension. added a |
1812 |
|
|
few fortran utility routines |
1813 |
|
|
|
1814 |
chrisfen |
3131 |
2006-02-15 12:46 chuckv |
1815 |
chrisfen |
2727 |
|
1816 |
|
|
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
1817 |
|
|
sphericalNanoparticle.hpp: Changed Names of class files. |
1818 |
|
|
|
1819 |
chrisfen |
3131 |
2006-02-10 07:45 kdaily |
1820 |
chrisfen |
2727 |
|
1821 |
|
|
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
1822 |
|
|
message] |
1823 |
|
|
|
1824 |
chrisfen |
3131 |
2006-02-10 07:12 tim |
1825 |
chrisfen |
2727 |
|
1826 |
|
|
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
1827 |
|
|
converting integer to double |
1828 |
|
|
|
1829 |
chrisfen |
3131 |
2006-02-08 10:21 chrisfen |
1830 |
chrisfen |
2727 |
|
1831 |
|
|
* forceFields/DUFF2.frc: added DPD molecule type parameters |
1832 |
|
|
|
1833 |
chrisfen |
3131 |
2006-02-07 08:39 tim |
1834 |
chrisfen |
2727 |
|
1835 |
|
|
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
1836 |
|
|
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
1837 |
|
|
trajectory file during analysis |
1838 |
|
|
|
1839 |
chrisfen |
3131 |
2006-02-02 09:14 tim |
1840 |
chrisfen |
2727 |
|
1841 |
|
|
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
1842 |
|
|
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
1843 |
|
|
in AtomStamp where orientation is not set correctly. |
1844 |
|
|
|
1845 |
chrisfen |
3131 |
2006-02-02 08:49 gezelter |
1846 |
chrisfen |
2727 |
|
1847 |
|
|
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
1848 |
|
|
contain directional atoms |
1849 |
|
|
|
1850 |
chrisfen |
3131 |
2006-02-02 07:49 xsun |
1851 |
chrisfen |
2727 |
|
1852 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1853 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
1854 |
|
|
for GBlipid atom type |
1855 |
|
|
|
1856 |
chrisfen |
3131 |
2006-02-01 18:57 gezelter |
1857 |
chrisfen |
2727 |
|
1858 |
|
|
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
1859 |
|
|
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
1860 |
|
|
|
1861 |
chrisfen |
3131 |
2006-02-01 13:06 chrisfen |
1862 |
chrisfen |
2727 |
|
1863 |
|
|
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
1864 |
|
|
to build |
1865 |
|
|
|
1866 |
chrisfen |
3131 |
2006-02-01 12:54 chrisfen |
1867 |
chrisfen |
2727 |
|
1868 |
|
|
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
1869 |
|
|
cutoff radius setting to a more logical procedure - still may |
1870 |
|
|
change... |
1871 |
|
|
|
1872 |
chrisfen |
3131 |
2006-02-01 09:26 gezelter |
1873 |
chrisfen |
2727 |
|
1874 |
|
|
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
1875 |
|
|
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
1876 |
|
|
|
1877 |
chrisfen |
3131 |
2006-01-30 14:25 tim |
1878 |
chrisfen |
2727 |
|
1879 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
1880 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
1881 |
|
|
applications/dynamicProps/DynamicProps.ggo, |
1882 |
|
|
applications/dynamicProps/DynamicPropsCmd.c, |
1883 |
|
|
applications/dynamicProps/DynamicPropsCmd.h, |
1884 |
|
|
applications/dynamicProps/LegendreCorrFunc.cpp, |
1885 |
|
|
applications/dynamicProps/LegendreCorrFunc.hpp, |
1886 |
|
|
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
1887 |
|
|
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
1888 |
|
|
Adding :LegendrePolynomial |
1889 |
|
|
|
1890 |
chrisfen |
3131 |
2006-01-19 14:54 chuckv |
1891 |
chrisfen |
2727 |
|
1892 |
|
|
* src/applications/nanoparticleBuilder/: Makefile, |
1893 |
|
|
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
1894 |
|
|
nanoparticle builder |
1895 |
|
|
|
1896 |
chrisfen |
3131 |
2006-01-18 13:08 chuckv |
1897 |
chrisfen |
2727 |
|
1898 |
|
|
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
1899 |
|
|
nanoparticle builder. |
1900 |
|
|
|
1901 |
chrisfen |
3131 |
2006-01-17 08:16 gezelter |
1902 |
chrisfen |
2727 |
|
1903 |
|
|
* AUTHORS, README: Cleaning up for 3.0.1 release |
1904 |
|
|
|
1905 |
chrisfen |
3131 |
2006-01-17 07:50 gezelter |
1906 |
chrisfen |
2727 |
|
1907 |
|
|
* ChangeLog: Prepping 3.0.1 release |
1908 |
|
|
|
1909 |
chrisfen |
3131 |
2006-01-17 07:32 gezelter |
1910 |
gezelter |
2571 |
|
1911 |
|
|
* src/config.h.in: new version number |
1912 |
|
|
|
1913 |
chrisfen |
3131 |
2006-01-17 07:32 gezelter |
1914 |
gezelter |
2571 |
|
1915 |
|
|
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
1916 |
|
|
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
1917 |
|
|
oopseManual.pdf: Updated Documentation |
1918 |
|
|
|
1919 |
chrisfen |
3131 |
2006-01-16 15:10 gezelter |
1920 |
gezelter |
2571 |
|
1921 |
|
|
* ChangeLog, README: Getting ready for release! |
1922 |
|
|
|
1923 |
chrisfen |
3131 |
2006-01-16 07:26 gezelter |
1924 |
gezelter |
2568 |
|
1925 |
|
|
* configure: Testing commit |
1926 |
|
|
|
1927 |
chrisfen |
3131 |
2006-01-13 13:57 chuckv |
1928 |
gezelter |
2568 |
|
1929 |
|
|
* src/: UseTheForce/SC_FF.cpp, |
1930 |
|
|
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
1931 |
|
|
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
1932 |
|
|
Handled by forceField now. |
1933 |
|
|
|
1934 |
chrisfen |
3131 |
2006-01-13 11:17 chuckv |
1935 |
gezelter |
2568 |
|
1936 |
|
|
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
1937 |
|
|
|
1938 |
chrisfen |
3131 |
2006-01-13 08:33 gezelter |
1939 |
gezelter |
2568 |
|
1940 |
|
|
* Makefile: [no log message] |
1941 |
|
|
|
1942 |
chrisfen |
3131 |
2006-01-13 08:26 gezelter |
1943 |
gezelter |
2568 |
|
1944 |
|
|
* Makefile: testing to make sure GNU make is the make that was used |
1945 |
|
|
to build OOPSE |
1946 |
|
|
|
1947 |
chrisfen |
3131 |
2006-01-13 07:48 gezelter |
1948 |
gezelter |
2568 |
|
1949 |
|
|
* configure, ac-tools/configure.in: changed compiler search order |
1950 |
|
|
|
1951 |
chrisfen |
3131 |
2006-01-12 16:09 chuckv |
1952 |
gezelter |
2568 |
|
1953 |
|
|
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
1954 |
|
|
samples/metals/Sutton-Chen/Au_bulk.in, |
1955 |
|
|
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
1956 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
1957 |
|
|
units |
1958 |
|
|
|
1959 |
chrisfen |
3131 |
2006-01-12 13:16 gezelter |
1960 |
gezelter |
2568 |
|
1961 |
|
|
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
1962 |
|
|
version info and the copyright date |
1963 |
|
|
|
1964 |
chrisfen |
3131 |
2006-01-12 12:52 gezelter |
1965 |
gezelter |
2568 |
|
1966 |
|
|
* src/config.h.in: added some missing checks for header files |
1967 |
|
|
(particularly zlib.h), used autoheader to help generate config.h.in |
1968 |
|
|
|
1969 |
chrisfen |
3131 |
2006-01-12 12:51 gezelter |
1970 |
gezelter |
2568 |
|
1971 |
|
|
* configure, ac-tools/configure.in: added some missing checks for |
1972 |
|
|
header files (particularly zlib.h) |
1973 |
|
|
|
1974 |
chrisfen |
3131 |
2006-01-12 12:19 gezelter |
1975 |
gezelter |
2568 |
|
1976 |
|
|
* make/Makefile.in: fixed a dependency problem for the Executable |
1977 |
|
|
builds |
1978 |
|
|
|
1979 |
chrisfen |
3131 |
2006-01-12 12:02 gezelter |
1980 |
gezelter |
2568 |
|
1981 |
|
|
* samples/gbljtest/Makefile: Missing Makefile in this sample |
1982 |
|
|
directory |
1983 |
|
|
|
1984 |
chrisfen |
3131 |
2006-01-12 12:01 gezelter |
1985 |
gezelter |
2568 |
|
1986 |
|
|
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
1987 |
|
|
Old makefile.in no longer required |
1988 |
|
|
|
1989 |
chrisfen |
3131 |
2006-01-12 12:01 gezelter |
1990 |
gezelter |
2568 |
|
1991 |
|
|
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
1992 |
|
|
needs to be installed |
1993 |
|
|
|
1994 |
chrisfen |
3131 |
2006-01-12 11:56 chuckv |
1995 |
gezelter |
2568 |
|
1996 |
|
|
* src/io/DumpWriter.cpp: Changed formating. |
1997 |
|
|
|
1998 |
chrisfen |
3131 |
2006-01-12 08:47 chrisfen |
1999 |
gezelter |
2568 |
|
2000 |
|
|
* samples/water/tip4p/tp4.md, |
2001 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
2002 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
2003 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
2004 |
|
|
src/brains/SimInfo.cpp: unifying function name in electrostatics |
2005 |
|
|
|
2006 |
chrisfen |
3131 |
2006-01-12 08:04 tim |
2007 |
gezelter |
2568 |
|
2008 |
|
|
* samples/metals/: EAM/nanoparticle/Makefile, |
2009 |
|
|
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
2010 |
|
|
Sutton-Chen/Makefile: fix make install problem for metals samples |
2011 |
|
|
|
2012 |
chrisfen |
3131 |
2006-01-12 07:22 tim |
2013 |
gezelter |
2568 |
|
2014 |
|
|
* make/Makefile.in: remove samples/metals from install list. |
2015 |
|
|
|
2016 |
chrisfen |
3131 |
2006-01-12 06:31 tim |
2017 |
gezelter |
2568 |
|
2018 |
|
|
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
2019 |
|
|
handle multiple line macro, just convert multiple line macro into |
2020 |
|
|
single line macro. |
2021 |
|
|
|
2022 |
chrisfen |
3131 |
2006-01-11 20:13 chrisfen |
2023 |
gezelter |
2568 |
|
2024 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
2025 |
|
|
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
2026 |
|
|
changes to electrostatics for shifted-potential and shifted-force |
2027 |
|
|
with mono and multipoles |
2028 |
|
|
|
2029 |
chrisfen |
3131 |
2006-01-11 15:04 gezelter |
2030 |
gezelter |
2568 |
|
2031 |
|
|
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
2032 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
2033 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
2034 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
2035 |
|
|
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
2036 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
2037 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
2038 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
2039 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
2040 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
2041 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
2042 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.h, |
2043 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.h, |
2044 |
|
|
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
2045 |
|
|
src/utils/fError.c, configure, make/Makefile.in: autoconf |
2046 |
|
|
modernization and cruft removal |
2047 |
|
|
|
2048 |
chrisfen |
3131 |
2006-01-11 15:04 gezelter |
2049 |
gezelter |
2568 |
|
2050 |
|
|
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
2051 |
|
|
modernization and cruft-removal |
2052 |
|
|
|
2053 |
chrisfen |
3131 |
2006-01-11 14:50 tim |
2054 |
gezelter |
2568 |
|
2055 |
|
|
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
2056 |
|
|
some error messages |
2057 |
|
|
|
2058 |
chrisfen |
3131 |
2006-01-11 11:01 tim |
2059 |
gezelter |
2568 |
|
2060 |
|
|
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
2061 |
|
|
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
2062 |
|
|
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
2063 |
|
|
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
2064 |
|
|
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
2065 |
|
|
an exception when error is found. |
2066 |
|
|
|
2067 |
chrisfen |
3131 |
2006-01-11 10:41 gezelter |
2068 |
gezelter |
2568 |
|
2069 |
|
|
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
2070 |
|
|
error |
2071 |
|
|
|
2072 |
chrisfen |
3131 |
2006-01-10 14:55 chuckv |
2073 |
gezelter |
2568 |
|
2074 |
|
|
* forceFields/SuttonChen.frc: Changed conversion factor. |
2075 |
|
|
|
2076 |
chrisfen |
3131 |
2006-01-10 13:14 chuckv |
2077 |
gezelter |
2568 |
|
2078 |
|
|
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
2079 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
2080 |
|
|
working now. |
2081 |
|
|
|
2082 |
chrisfen |
3131 |
2006-01-09 14:22 chuckv |
2083 |
gezelter |
2568 |
|
2084 |
|
|
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
2085 |
|
|
|
2086 |
chrisfen |
3131 |
2006-01-09 14:14 tim |
2087 |
gezelter |
2568 |
|
2088 |
|
|
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
2089 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
2090 |
|
|
StaticPropsCmd.h: fixing RhoZ |
2091 |
|
|
|
2092 |
chrisfen |
3131 |
2006-01-09 11:26 chuckv |
2093 |
gezelter |
2568 |
|
2094 |
|
|
* forceFields/SuttonChen.frc, |
2095 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
2096 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
2097 |
|
|
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
2098 |
|
|
section parsers. |
2099 |
|
|
|
2100 |
chrisfen |
3131 |
2006-01-09 11:11 tim |
2101 |
gezelter |
2568 |
|
2102 |
|
|
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
2103 |
|
|
utils/StringUtils.hpp: replace isType<int> with isInteger |
2104 |
|
|
|
2105 |
chrisfen |
3131 |
2006-01-06 13:15 tim |
2106 |
gezelter |
2568 |
|
2107 |
|
|
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
2108 |
|
|
forceFieldOptions from SC_FF |
2109 |
|
|
|
2110 |
chrisfen |
3131 |
2006-01-06 12:27 chuckv |
2111 |
gezelter |
2568 |
|
2112 |
|
|
* forceFields/SuttonChen.frc: Add force file. |
2113 |
|
|
|
2114 |
chrisfen |
3131 |
2005-12-31 14:42 chuckv |
2115 |
gezelter |
2568 |
|
2116 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
2117 |
|
|
segfaults or produces 0 potential, but rather produces Inf for the |
2118 |
|
|
potential. Progress.... |
2119 |
|
|
|
2120 |
chrisfen |
3131 |
2005-12-30 15:15 chuckv |
2121 |
gezelter |
2568 |
|
2122 |
|
|
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
2123 |
|
|
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
2124 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
2125 |
|
|
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
2126 |
|
|
Sutton-Chen bug fixes. |
2127 |
|
|
|
2128 |
chrisfen |
3131 |
2005-12-30 13:25 tim |
2129 |
gezelter |
2568 |
|
2130 |
|
|
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
2131 |
|
|
potential return from fortran is already accumulated, it should not |
2132 |
|
|
be accumulated again; nGroupTypesCol is not initialized; |
2133 |
|
|
GroupMaxCutoffCol is not allocated; |
2134 |
|
|
|
2135 |
chrisfen |
3131 |
2005-12-30 07:32 tim |
2136 |
gezelter |
2568 |
|
2137 |
|
|
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
2138 |
|
|
MPI version, we need to cast const char* to void* for |
2139 |
|
|
stringstream.str(); Previous Makefile use bjects of single version |
2140 |
|
|
to make the MPI library; |
2141 |
|
|
|
2142 |
chrisfen |
3131 |
2005-12-29 16:18 chuckv |
2143 |
gezelter |
2568 |
|
2144 |
|
|
* make/Makefile.in, samples/metals/Makefile, |
2145 |
|
|
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
2146 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
2147 |
|
|
Almost there... |
2148 |
|
|
|
2149 |
chrisfen |
3131 |
2005-12-29 12:19 chuckv |
2150 |
gezelter |
2568 |
|
2151 |
|
|
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
2152 |
|
|
forcefield. |
2153 |
|
|
|
2154 |
chrisfen |
3131 |
2005-12-29 12:07 chuckv |
2155 |
gezelter |
2568 |
|
2156 |
|
|
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
2157 |
|
|
metals.md: added files for sutton-chen |
2158 |
|
|
|
2159 |
chrisfen |
3131 |
2005-12-29 08:37 chuckv |
2160 |
gezelter |
2568 |
|
2161 |
|
|
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
2162 |
|
|
metals.md: More cvs changing. |
2163 |
|
|
|
2164 |
chrisfen |
3131 |
2005-12-29 08:34 chuckv |
2165 |
gezelter |
2568 |
|
2166 |
|
|
* samples/metals/Au_nanoparticle.in: More moving... |
2167 |
|
|
|
2168 |
chrisfen |
3131 |
2005-12-29 08:33 chuckv |
2169 |
gezelter |
2568 |
|
2170 |
|
|
* samples/metals/EAM/nanoparticle/: |
2171 |
|
|
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
2172 |
|
|
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
2173 |
|
|
changes to directory structure. |
2174 |
|
|
|
2175 |
chrisfen |
3131 |
2005-12-29 08:21 chuckv |
2176 |
gezelter |
2568 |
|
2177 |
|
|
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
2178 |
|
|
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
2179 |
|
|
|
2180 |
chrisfen |
3131 |
2005-12-29 08:17 chuckv |
2181 |
gezelter |
2568 |
|
2182 |
|
|
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
2183 |
|
|
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
2184 |
|
|
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
2185 |
|
|
directory structure |
2186 |
|
|
|
2187 |
chrisfen |
3131 |
2005-12-29 08:03 chuckv |
2188 |
gezelter |
2568 |
|
2189 |
|
|
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
2190 |
|
|
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
2191 |
|
|
call to set force options in SimCreator. |
2192 |
|
|
|
2193 |
chrisfen |
3131 |
2005-12-28 13:44 chuckv |
2194 |
gezelter |
2568 |
|
2195 |
|
|
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
2196 |
|
|
changes to forcefield options. |
2197 |
|
|
|
2198 |
chrisfen |
3131 |
2005-12-28 13:42 chuckv |
2199 |
gezelter |
2568 |
|
2200 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
2201 |
|
|
passed to fortran. |
2202 |
|
|
|
2203 |
chrisfen |
3131 |
2005-12-23 15:04 chuckv |
2204 |
gezelter |
2568 |
|
2205 |
|
|
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
2206 |
|
|
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
2207 |
|
|
changes. |
2208 |
|
|
|
2209 |
chrisfen |
3131 |
2005-12-16 13:52 tim |
2210 |
gezelter |
2568 |
|
2211 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
2212 |
|
|
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
2213 |
|
|
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
2214 |
|
|
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
2215 |
|
|
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
2216 |
|
|
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
2217 |
|
|
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
2218 |
|
|
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
2219 |
|
|
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
2220 |
|
|
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
2221 |
|
|
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
2222 |
|
|
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
2223 |
|
|
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
2224 |
|
|
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
2225 |
|
|
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
2226 |
|
|
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
2227 |
|
|
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
2228 |
|
|
__FUNCTION__ to __func__ to match C99 standard, and then added an |
2229 |
|
|
autoconf test to check for __func__ usability. Changed some |
2230 |
|
|
default compile flags for the Sun architecture |
2231 |
|
|
|
2232 |
chrisfen |
3131 |
2005-12-16 11:01 gezelter |
2233 |
gezelter |
2568 |
|
2234 |
|
|
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
2235 |
|
|
|
2236 |
chrisfen |
3131 |
2005-12-16 10:55 tim |
2237 |
gezelter |
2568 |
|
2238 |
|
|
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
2239 |
|
|
change to build oopse under solaris |
2240 |
|
|
|
2241 |
chrisfen |
3131 |
2005-12-16 10:26 tim |
2242 |
gezelter |
2568 |
|
2243 |
|
|
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
2244 |
|
|
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
2245 |
|
|
came with SUN compiler does not have a conforming std::use_facet, |
2246 |
|
|
define a macro to handle it. Adding exception handling to |
2247 |
|
|
SimCreator. |
2248 |
|
|
|
2249 |
chrisfen |
3131 |
2005-12-16 07:53 gezelter |
2250 |
gezelter |
2568 |
|
2251 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
2252 |
|
|
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
2253 |
|
|
which was living inside the GB particle. No alien-like ripping out |
2254 |
|
|
of the stomach was required. |
2255 |
|
|
|
2256 |
chrisfen |
3131 |
2005-12-15 18:57 tim |
2257 |
gezelter |
2568 |
|
2258 |
|
|
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
2259 |
|
|
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
2260 |
|
|
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
2261 |
|
|
replace grammar for numerical parsing |
2262 |
|
|
|
2263 |
chrisfen |
3131 |
2005-12-15 13:43 gezelter |
2264 |
gezelter |
2568 |
|
2265 |
|
|
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
2266 |
|
|
|
2267 |
chrisfen |
3131 |
2005-12-15 06:48 gezelter |
2268 |
gezelter |
2568 |
|
2269 |
|
|
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
2270 |
|
|
dependencies and replacing them with real autoconf checks |
2271 |
|
|
|
2272 |
chrisfen |
3131 |
2005-12-15 06:47 gezelter |
2273 |
gezelter |
2568 |
|
2274 |
|
|
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
2275 |
|
|
ac-tools/configure.in, src/config.h.in: Adding checks for various |
2276 |
|
|
features used by ANTLR |
2277 |
|
|
|
2278 |
chrisfen |
3131 |
2005-12-14 10:02 tim |
2279 |
gezelter |
2568 |
|
2280 |
|
|
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
2281 |
|
|
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
2282 |
|
|
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
2283 |
|
|
nasty negative integer parsing problem by refining the grammar |
2284 |
|
|
|
2285 |
chrisfen |
3131 |
2005-12-12 11:32 gezelter |
2286 |
gezelter |
2568 |
|
2287 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
2288 |
|
|
UseTheForce/doForces_interface.h, |
2289 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
2290 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
2291 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
2292 |
|
|
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
2293 |
|
|
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
2294 |
|
|
some minor changes to allow compilation with the portland group |
2295 |
|
|
compilers |
2296 |
|
|
|
2297 |
chrisfen |
3131 |
2005-12-10 08:54 tim |
2298 |
gezelter |
2568 |
|
2299 |
|
|
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
2300 |
|
|
problem for icc7 |
2301 |
|
|
|
2302 |
chrisfen |
3131 |
2005-12-09 13:18 gezelter |
2303 |
gezelter |
2568 |
|
2304 |
|
|
* src/utils/CaseConversion.hpp: added missing include |
2305 |
|
|
|
2306 |
chrisfen |
3131 |
2005-12-09 09:11 gezelter |
2307 |
gezelter |
2568 |
|
2308 |
|
|
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
2309 |
|
|
compiler |
2310 |
|
|
|
2311 |
chrisfen |
3131 |
2005-12-08 14:05 gezelter |
2312 |
gezelter |
2568 |
|
2313 |
|
|
* src/io/ForceFieldOptions.cpp: added copyright |
2314 |
|
|
|
2315 |
chrisfen |
3131 |
2005-12-08 14:04 gezelter |
2316 |
gezelter |
2568 |
|
2317 |
|
|
* src/UseTheForce/doForces.F90: added info printout |
2318 |
|
|
|
2319 |
chrisfen |
3131 |
2005-12-08 14:04 gezelter |
2320 |
gezelter |
2568 |
|
2321 |
|
|
* configure, ac-tools/configure.in: added pathscale |
2322 |
|
|
|
2323 |
chrisfen |
3131 |
2005-12-08 07:38 chuckv |
2324 |
gezelter |
2568 |
|
2325 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
2326 |
|
|
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
2327 |
|
|
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
2328 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2329 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
2330 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
2331 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
2332 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
2333 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
2334 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
2335 |
|
|
io/GayBerneAtomTypesSectionParser.hpp, |
2336 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
2337 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
2338 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
2339 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
2340 |
|
|
io/ShapeAtomTypesSectionParser.hpp, |
2341 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
2342 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
2343 |
|
|
io/StickyPowerAtomTypesSectionParser.cpp, |
2344 |
|
|
io/StickyPowerAtomTypesSectionParser.hpp, |
2345 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
2346 |
|
|
Wow thats alot o' files. Now passing forceFieldOptions to all of |
2347 |
|
|
the parsers. |
2348 |
|
|
|
2349 |
chrisfen |
3131 |
2005-12-07 15:10 chuckv |
2350 |
gezelter |
2568 |
|
2351 |
|
|
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
2352 |
|
|
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
2353 |
|
|
Started adding support for ForceOptions to section parsers. |
2354 |
|
|
|
2355 |
chrisfen |
3131 |
2005-12-07 15:01 gezelter |
2356 |
gezelter |
2568 |
|
2357 |
|
|
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
2358 |
|
|
|
2359 |
chrisfen |
3131 |
2005-12-07 15:00 chuckv |
2360 |
gezelter |
2568 |
|
2361 |
|
|
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
2362 |
|
|
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
2363 |
|
|
section parser |
2364 |
|
|
|
2365 |
chrisfen |
3131 |
2005-12-07 11:58 chuckv |
2366 |
gezelter |
2568 |
|
2367 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
2368 |
|
|
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
2369 |
|
|
suttonchen_interface.h: Removed geometric distance mixing from |
2370 |
|
|
individual modules and now use force options to detemine what the |
2371 |
|
|
deal is. |
2372 |
|
|
|
2373 |
chrisfen |
3131 |
2005-12-07 11:46 chuckv |
2374 |
gezelter |
2568 |
|
2375 |
|
|
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
2376 |
|
|
Further fixes for compiler issues. |
2377 |
|
|
|
2378 |
chrisfen |
3131 |
2005-12-07 11:44 chuckv |
2379 |
gezelter |
2568 |
|
2380 |
|
|
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
2381 |
|
|
|
2382 |
chrisfen |
3131 |
2005-12-07 11:38 chuckv |
2383 |
gezelter |
2568 |
|
2384 |
|
|
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
2385 |
|
|
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
2386 |
|
|
support for fortran force options. |
2387 |
|
|
|
2388 |
chrisfen |
3131 |
2005-12-06 13:01 tim |
2389 |
gezelter |
2568 |
|
2390 |
|
|
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
2391 |
|
|
|
2392 |
chrisfen |
3131 |
2005-12-06 11:26 chuckv |
2393 |
gezelter |
2568 |
|
2394 |
|
|
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
2395 |
|
|
|
2396 |
chrisfen |
3131 |
2005-12-06 09:53 chuckv |
2397 |
gezelter |
2568 |
|
2398 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
2399 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
2400 |
|
|
crystal |
2401 |
|
|
|
2402 |
chrisfen |
3131 |
2005-12-06 09:52 chuckv |
2403 |
gezelter |
2568 |
|
2404 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
2405 |
|
|
dumpwriter. |
2406 |
|
|
|
2407 |
chrisfen |
3131 |
2005-12-06 08:49 tim |
2408 |
gezelter |
2568 |
|
2409 |
|
|
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
2410 |
|
|
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
2411 |
|
|
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
2412 |
|
|
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
2413 |
|
|
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
2414 |
|
|
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
2415 |
|
|
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
2416 |
|
|
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
2417 |
|
|
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
2418 |
|
|
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
2419 |
|
|
minimizer/water.md, shape/linear.md, |
2420 |
|
|
thermoIntegration/liquid/ssde.md, |
2421 |
|
|
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
2422 |
|
|
thermoIntegration/solid/water.md, water/dimer/cl.md, |
2423 |
|
|
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
2424 |
|
|
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
2425 |
|
|
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
2426 |
|
|
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
2427 |
|
|
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
2428 |
|
|
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
2429 |
|
|
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
2430 |
|
|
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
2431 |
|
|
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
2432 |
|
|
keywords from samples |
2433 |
|
|
|
2434 |
chrisfen |
3131 |
2005-12-05 15:37 tim |
2435 |
gezelter |
2568 |
|
2436 |
|
|
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
2437 |
|
|
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
2438 |
|
|
|
2439 |
chrisfen |
3131 |
2005-12-05 14:23 gezelter |
2440 |
gezelter |
2568 |
|
2441 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
2442 |
|
|
UseTheForce/Makefile, brains/Register.cpp, |
2443 |
|
|
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
2444 |
|
|
handler for CLAY force field |
2445 |
|
|
|
2446 |
chrisfen |
3131 |
2005-12-05 13:45 chuckv |
2447 |
gezelter |
2568 |
|
2448 |
|
|
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
2449 |
|
|
in openbabel. |
2450 |
|
|
|
2451 |
chrisfen |
3131 |
2005-12-05 11:10 tim |
2452 |
gezelter |
2568 |
|
2453 |
|
|
* src/types/MoleculeStamp.cpp: reformat error message |
2454 |
|
|
|
2455 |
chrisfen |
3131 |
2005-12-05 11:07 gezelter |
2456 |
gezelter |
2568 |
|
2457 |
|
|
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
2458 |
|
|
|
2459 |
chrisfen |
3131 |
2005-12-05 10:23 tim |
2460 |
gezelter |
2568 |
|
2461 |
|
|
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
2462 |
|
|
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
2463 |
|
|
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
2464 |
|
|
adding more checking for topology |
2465 |
|
|
|
2466 |
chrisfen |
3131 |
2005-12-02 14:37 gezelter |
2467 |
gezelter |
2568 |
|
2468 |
|
|
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
2469 |
|
|
removal |
2470 |
|
|
|
2471 |
chrisfen |
3131 |
2005-12-02 14:37 gezelter |
2472 |
gezelter |
2568 |
|
2473 |
|
|
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
2474 |
|
|
|
2475 |
chrisfen |
3131 |
2005-12-02 14:37 gezelter |
2476 |
gezelter |
2568 |
|
2477 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
2478 |
|
|
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
2479 |
|
|
traditional.md: removing deprecated nAtoms and nComponents lines |
2480 |
|
|
|
2481 |
chrisfen |
3131 |
2005-12-02 12:34 tim |
2482 |
gezelter |
2568 |
|
2483 |
|
|
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
2484 |
|
|
|
2485 |
chrisfen |
3131 |
2005-12-02 12:18 tim |
2486 |
gezelter |
2568 |
|
2487 |
|
|
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
2488 |
|
|
FragmentStamp |
2489 |
|
|
|
2490 |
chrisfen |
3131 |
2005-12-02 12:11 gezelter |
2491 |
gezelter |
2568 |
|
2492 |
|
|
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
2493 |
|
|
longer thrown with consts (fixes compilation bug on the Mac). |
2494 |
|
|
|
2495 |
chrisfen |
3131 |
2005-12-02 12:10 gezelter |
2496 |
gezelter |
2568 |
|
2497 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
2498 |
|
|
printing out of timestep |
2499 |
|
|
|
2500 |
chrisfen |
3131 |
2005-12-02 12:10 gezelter |
2501 |
gezelter |
2568 |
|
2502 |
|
|
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
2503 |
|
|
junk |
2504 |
|
|
|
2505 |
chrisfen |
3131 |
2005-12-02 12:10 gezelter |
2506 |
gezelter |
2568 |
|
2507 |
|
|
* make/Makefile.in: Change build process for libOOPSE.a so that the |
2508 |
|
|
libraries aren't unpacked. libOOPSE.a is now made directly from |
2509 |
|
|
the object files |
2510 |
|
|
|
2511 |
chrisfen |
3131 |
2005-12-02 12:09 gezelter |
2512 |
gezelter |
2568 |
|
2513 |
|
|
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
2514 |
|
|
needed for new build of libOOPSE.a |
2515 |
|
|
|
2516 |
chrisfen |
3131 |
2005-12-02 10:43 tim |
2517 |
gezelter |
2568 |
|
2518 |
|
|
* src/types/DataHolder.hpp: adding DataHolder |
2519 |
|
|
|
2520 |
chrisfen |
3131 |
2005-12-02 09:01 gezelter |
2521 |
gezelter |
2568 |
|
2522 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
2523 |
|
|
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
2524 |
|
|
case for the cutoff policies |
2525 |
|
|
|
2526 |
chrisfen |
3131 |
2005-12-02 07:38 tim |
2527 |
gezelter |
2568 |
|
2528 |
|
|
* make/Makefile.in: update Makefile |
2529 |
|
|
|
2530 |
chrisfen |
3131 |
2005-12-02 07:38 tim |
2531 |
gezelter |
2568 |
|
2532 |
|
|
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
2533 |
|
|
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
2534 |
|
|
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
2535 |
|
|
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
2536 |
|
|
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
2537 |
|
|
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
2538 |
|
|
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
2539 |
|
|
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
2540 |
|
|
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
2541 |
|
|
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
2542 |
|
|
antlr/CommonASTWithHiddenTokens.cpp, |
2543 |
|
|
antlr/CommonASTWithHiddenTokens.hpp, |
2544 |
|
|
antlr/CommonHiddenStreamToken.cpp, |
2545 |
|
|
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
2546 |
|
|
antlr/CommonToken.hpp, antlr/IOException.hpp, |
2547 |
|
|
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
2548 |
|
|
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
2549 |
|
|
antlr/Makefile, antlr/MismatchedCharException.cpp, |
2550 |
|
|
antlr/MismatchedCharException.hpp, |
2551 |
|
|
antlr/MismatchedTokenException.cpp, |
2552 |
|
|
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
2553 |
|
|
antlr/NoViableAltException.hpp, |
2554 |
|
|
antlr/NoViableAltForCharException.cpp, |
2555 |
|
|
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
2556 |
|
|
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
2557 |
|
|
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
2558 |
|
|
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
2559 |
|
|
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
2560 |
|
|
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
2561 |
|
|
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
2562 |
|
|
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
2563 |
|
|
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
2564 |
|
|
antlr/TokenStreamHiddenTokenFilter.cpp, |
2565 |
|
|
antlr/TokenStreamHiddenTokenFilter.hpp, |
2566 |
|
|
antlr/TokenStreamIOException.hpp, |
2567 |
|
|
antlr/TokenStreamRecognitionException.hpp, |
2568 |
|
|
antlr/TokenStreamRetryException.hpp, |
2569 |
|
|
antlr/TokenStreamRewriteEngine.cpp, |
2570 |
|
|
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
2571 |
|
|
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
2572 |
|
|
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
2573 |
|
|
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
2574 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
2575 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
2576 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2577 |
|
|
constraints/ZconstraintForceManager.cpp, |
2578 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
2579 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
2580 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
2581 |
|
|
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
2582 |
|
|
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
2583 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
2584 |
|
|
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
2585 |
|
|
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
2586 |
|
|
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
2587 |
|
|
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
2588 |
|
|
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
2589 |
|
|
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
2590 |
|
|
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
2591 |
|
|
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
2592 |
|
|
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
2593 |
|
|
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
2594 |
|
|
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
2595 |
|
|
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
2596 |
|
|
selection/Makefile, selection/NameFinder.cpp, |
2597 |
|
|
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
2598 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
2599 |
|
|
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
2600 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
2601 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
2602 |
|
|
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
2603 |
|
|
types/Component.cpp, types/Component.hpp, |
2604 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
2605 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
2606 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2607 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
2608 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
2609 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
2610 |
|
|
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
2611 |
|
|
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
2612 |
|
|
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
2613 |
|
|
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
2614 |
|
|
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
2615 |
|
|
with antlr parser |
2616 |
|
|
|
2617 |
chrisfen |
3131 |
2005-11-30 13:00 chuckv |
2618 |
gezelter |
2568 |
|
2619 |
|
|
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
2620 |
|
|
calculate rho(Z) to calculate density profiles for water slabs. |
2621 |
|
|
|
2622 |
chrisfen |
3131 |
2005-11-29 14:54 chuckv |
2623 |
gezelter |
2568 |
|
2624 |
|
|
* configure, ac-tools/configure.in: added checks for some functions |
2625 |
|
|
to configure script |
2626 |
|
|
|
2627 |
chrisfen |
3131 |
2005-11-22 17:05 chuckv |
2628 |
gezelter |
2568 |
|
2629 |
|
|
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
2630 |
|
|
obbond.cpp: Changed file names that conflict w/ oopse file name |
2631 |
|
|
object files. |
2632 |
|
|
|
2633 |
chrisfen |
3131 |
2005-11-21 14:59 gezelter |
2634 |
gezelter |
2568 |
|
2635 |
|
|
* src/utils/residentMem.c: compilation bug |
2636 |
|
|
|
2637 |
chrisfen |
3131 |
2005-11-21 14:59 gezelter |
2638 |
gezelter |
2568 |
|
2639 |
|
|
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
2640 |
|
|
|
2641 |
chrisfen |
3131 |
2005-11-21 14:59 gezelter |
2642 |
gezelter |
2568 |
|
2643 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
2644 |
|
|
|
2645 |
chrisfen |
3131 |
2005-11-21 14:59 gezelter |
2646 |
gezelter |
2568 |
|
2647 |
|
|
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
2648 |
|
|
issue |
2649 |
|
|
|
2650 |
chrisfen |
3131 |
2005-11-21 14:58 gezelter |
2651 |
gezelter |
2568 |
|
2652 |
|
|
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
2653 |
|
|
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
2654 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
2655 |
|
|
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
2656 |
|
|
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
2657 |
|
|
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
2658 |
|
|
|
2659 |
chrisfen |
3131 |
2005-11-21 08:22 tim |
2660 |
gezelter |
2568 |
|
2661 |
|
|
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
2662 |
|
|
|
2663 |
chrisfen |
3131 |
2005-11-21 06:59 tim |
2664 |
gezelter |
2568 |
|
2665 |
|
|
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
2666 |
|
|
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
2667 |
|
|
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
2668 |
|
|
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
2669 |
|
|
|
2670 |
chrisfen |
3131 |
2005-11-18 12:17 tim |
2671 |
gezelter |
2568 |
|
2672 |
|
|
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
2673 |
|
|
adding support for soft linking |
2674 |
|
|
|
2675 |
chrisfen |
3131 |
2005-11-18 12:17 tim |
2676 |
gezelter |
2568 |
|
2677 |
|
|
* make/Makefile.in: Adding support for soft linking |
2678 |
|
|
|
2679 |
chrisfen |
3131 |
2005-11-18 09:50 gezelter |
2680 |
gezelter |
2568 |
|
2681 |
|
|
* make/Makefile.in: Adding linking stuff |
2682 |
|
|
|
2683 |
chrisfen |
3131 |
2005-11-18 08:38 tim |
2684 |
gezelter |
2568 |
|
2685 |
|
|
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
2686 |
|
|
src/applications/atom2mdin/atom2mdin.cpp, |
2687 |
chrisfen |
2762 |
src/applications/mdinConverter/Makefile, |
2688 |
|
|
src/applications/mdinConverter/mdinConverter.cpp, |
2689 |
gezelter |
2568 |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
2690 |
|
|
rename mdinConverter to atom2mdin |
2691 |
|
|
|
2692 |
chrisfen |
3131 |
2005-11-17 12:44 gezelter |
2693 |
gezelter |
2568 |
|
2694 |
|
|
* src/openbabel/obconversion.cpp: fixed a bug |
2695 |
|
|
|
2696 |
chrisfen |
3131 |
2005-11-17 12:39 gezelter |
2697 |
gezelter |
2568 |
|
2698 |
|
|
* configure: Adding some config checks for OpenBabel codes we are |
2699 |
|
|
using |
2700 |
|
|
|
2701 |
chrisfen |
3131 |
2005-11-17 12:39 gezelter |
2702 |
gezelter |
2568 |
|
2703 |
|
|
* ac-tools/configure.in: Adding some checks for OpenBabel code |
2704 |
|
|
|
2705 |
chrisfen |
3131 |
2005-11-17 12:39 gezelter |
2706 |
gezelter |
2568 |
|
2707 |
|
|
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
2708 |
|
|
|
2709 |
chrisfen |
3131 |
2005-11-17 12:38 gezelter |
2710 |
gezelter |
2568 |
|
2711 |
|
|
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
2712 |
|
|
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
2713 |
|
|
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
2714 |
|
|
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
2715 |
|
|
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
2716 |
|
|
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
2717 |
|
|
Unifying config.h stuff and making sure the OpenBabel codes can |
2718 |
|
|
find our default (and environment variable) Force Field |
2719 |
|
|
directories. |
2720 |
|
|
|
2721 |
chrisfen |
3131 |
2005-11-17 10:35 tim |
2722 |
gezelter |
2568 |
|
2723 |
|
|
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
2724 |
|
|
|
2725 |
chrisfen |
3131 |
2005-11-16 15:10 tim |
2726 |
gezelter |
2568 |
|
2727 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
2728 |
|
|
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
2729 |
|
|
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
2730 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
2731 |
|
|
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
2732 |
|
|
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
2733 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
2734 |
|
|
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
2735 |
|
|
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
2736 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
2737 |
|
|
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
2738 |
|
|
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
2739 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
2740 |
|
|
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
2741 |
|
|
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
2742 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
2743 |
|
|
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
2744 |
|
|
get compiled |
2745 |
|
|
|
2746 |
chrisfen |
3131 |
2005-11-16 13:37 chuckv |
2747 |
gezelter |
2568 |
|
2748 |
|
|
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
2749 |
|
|
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
2750 |
|
|
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
2751 |
|
|
optional parameters.... |
2752 |
|
|
|
2753 |
chrisfen |
3131 |
2005-11-16 13:24 tim |
2754 |
chrisfen |
2762 |
|
2755 |
|
|
* src/applications/mdinConverter/: Makefile, mdinConverter.cpp: |
2756 |
|
|
adding mdinConverter |
2757 |
|
|
|
2758 |
chrisfen |
3131 |
2005-11-16 13:22 tim |
2759 |
gezelter |
2568 |
|
2760 |
|
|
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
2761 |
|
|
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
2762 |
|
|
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
2763 |
|
|
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
2764 |
|
|
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
2765 |
|
|
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
2766 |
|
|
adding more readers/writers |
2767 |
|
|
|
2768 |
chrisfen |
3131 |
2005-11-16 13:20 tim |
2769 |
gezelter |
2568 |
|
2770 |
|
|
* make/Makefile.in: adding openbabel |
2771 |
|
|
|
2772 |
chrisfen |
3131 |
2005-11-16 13:20 tim |
2773 |
gezelter |
2568 |
|
2774 |
|
|
* src/brains/: Register.cpp, Register.hpp: register openbabel |
2775 |
|
|
readers/writers |
2776 |
|
|
|
2777 |
chrisfen |
3131 |
2005-11-16 11:57 chrisfen |
2778 |
gezelter |
2568 |
|
2779 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
2780 |
|
|
potential self term |
2781 |
|
|
|
2782 |
chrisfen |
3131 |
2005-11-16 11:57 chrisfen |
2783 |
gezelter |
2568 |
|
2784 |
|
|
* samples/water/spce/spce.md: just some parameters |
2785 |
|
|
|
2786 |
chrisfen |
3131 |
2005-11-16 11:42 tim |
2787 |
gezelter |
2568 |
|
2788 |
|
|
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
2789 |
|
|
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
2790 |
|
|
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
2791 |
|
|
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
2792 |
|
|
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
2793 |
|
|
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
2794 |
|
|
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
2795 |
|
|
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
2796 |
|
|
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
2797 |
|
|
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
2798 |
|
|
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
2799 |
|
|
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
2800 |
|
|
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
2801 |
|
|
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
2802 |
|
|
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
2803 |
|
|
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
2804 |
|
|
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
2805 |
|
|
zipstreamimpl.hpp: adding openbabel |
2806 |
|
|
|
2807 |
chrisfen |
3131 |
2005-11-15 11:42 chrisfen |
2808 |
gezelter |
2568 |
|
2809 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
2810 |
|
|
commented code |
2811 |
|
|
|
2812 |
chrisfen |
3131 |
2005-11-15 11:04 chrisfen |
2813 |
gezelter |
2568 |
|
2814 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
2815 |
|
|
charge-charge interactions a bit... |
2816 |
|
|
|
2817 |
chrisfen |
3131 |
2005-11-15 11:03 chrisfen |
2818 |
gezelter |
2568 |
|
2819 |
|
|
* samples/water/spce/: spce.md, water.md: just playing |
2820 |
|
|
|
2821 |
chrisfen |
3131 |
2005-11-15 08:38 chrisfen |
2822 |
gezelter |
2568 |
|
2823 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
2824 |
|
|
shifted_potential case |
2825 |
|
|
|
2826 |
chrisfen |
3131 |
2005-11-15 08:37 chrisfen |
2827 |
gezelter |
2568 |
|
2828 |
|
|
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
2829 |
|
|
just playing around - we need to refresh all the samples sometime |
2830 |
|
|
soon... |
2831 |
|
|
|
2832 |
chrisfen |
3131 |
2005-11-15 08:18 chuckv |
2833 |
gezelter |
2568 |
|
2834 |
|
|
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
2835 |
|
|
preforce calc public in suttonchen. |
2836 |
|
|
|
2837 |
chrisfen |
3131 |
2005-11-15 08:05 chuckv |
2838 |
gezelter |
2568 |
|
2839 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
2840 |
|
|
SimInfo |
2841 |
|
|
|
2842 |
chrisfen |
3131 |
2005-11-15 08:01 chuckv |
2843 |
gezelter |
2568 |
|
2844 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
2845 |
|
|
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
2846 |
|
|
|
2847 |
chrisfen |
3131 |
2005-11-15 07:34 chuckv |
2848 |
gezelter |
2568 |
|
2849 |
|
|
* forceFields/Makefile: Added sutton-chen to makefile. |
2850 |
|
|
|
2851 |
chrisfen |
3131 |
2005-11-14 14:20 chuckv |
2852 |
gezelter |
2568 |
|
2853 |
|
|
* src/UseTheForce/DarkSide/: suttonchen.F90, |
2854 |
|
|
suttonchen_interface.h: Build Fixes for sutton-chen. |
2855 |
|
|
|
2856 |
chrisfen |
3131 |
2005-11-14 14:03 chuckv |
2857 |
gezelter |
2568 |
|
2858 |
|
|
* src/io/Makefile: Missed makefile for sutton-chen. |
2859 |
|
|
|
2860 |
chrisfen |
3131 |
2005-11-14 14:03 chuckv |
2861 |
gezelter |
2568 |
|
2862 |
|
|
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
2863 |
|
|
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
2864 |
|
|
|
2865 |
chrisfen |
3131 |
2005-11-14 13:29 chuckv |
2866 |
gezelter |
2568 |
|
2867 |
|
|
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
2868 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
2869 |
|
|
UseTheForce/DarkSide/suttonchen.F90, |
2870 |
|
|
UseTheForce/DarkSide/suttonchen_interface.F90, |
2871 |
|
|
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
2872 |
|
|
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
2873 |
|
|
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
2874 |
|
|
fix do_forces to use Sutton-Chen. |
2875 |
|
|
|
2876 |
chrisfen |
3131 |
2005-11-11 09:21 chrisfen |
2877 |
gezelter |
2568 |
|
2878 |
|
|
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
2879 |
|
|
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
2880 |
|
|
some files |
2881 |
|
|
|
2882 |
chrisfen |
3131 |
2005-11-11 07:22 chrisfen |
2883 |
gezelter |
2568 |
|
2884 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
2885 |
|
|
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
2886 |
|
|
switching function option |
2887 |
|
|
|
2888 |
chrisfen |
3131 |
2005-11-11 07:21 chrisfen |
2889 |
gezelter |
2568 |
|
2890 |
|
|
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
2891 |
|
|
5th order polynomial switching function |
2892 |
|
|
|
2893 |
chrisfen |
3131 |
2005-11-11 07:21 chrisfen |
2894 |
gezelter |
2568 |
|
2895 |
|
|
* samples/water/ssd/ssd.md: playing with switching functions again |
2896 |
|
|
|
2897 |
chrisfen |
3131 |
2005-11-11 07:21 chrisfen |
2898 |
gezelter |
2568 |
|
2899 |
|
|
* samples/argon/500.md: playing with switching functions |
2900 |
|
|
|
2901 |
chrisfen |
3131 |
2005-11-08 16:11 chuckv |
2902 |
gezelter |
2568 |
|
2903 |
|
|
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
2904 |
|
|
files for Sutton-Chen and Quantum Sutton-Chen |
2905 |
|
|
|
2906 |
chrisfen |
3131 |
2005-11-08 05:32 chrisfen |
2907 |
gezelter |
2568 |
|
2908 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
2909 |
|
|
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
2910 |
|
|
ability to output forces and torques |
2911 |
|
|
|
2912 |
chrisfen |
3131 |
2005-11-08 05:32 chrisfen |
2913 |
gezelter |
2568 |
|
2914 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
2915 |
|
|
output of forces and torques |
2916 |
|
|
|
2917 |
chrisfen |
3131 |
2005-11-08 05:31 chrisfen |
2918 |
gezelter |
2568 |
|
2919 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
2920 |
|
|
Working on shifted_force... |
2921 |
|
|
|
2922 |
chrisfen |
3131 |
2005-11-08 05:31 chrisfen |
2923 |
gezelter |
2568 |
|
2924 |
|
|
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
2925 |
|
|
|
2926 |
chrisfen |
3131 |
2005-11-03 15:22 chrisfen |
2927 |
gezelter |
2568 |
|
2928 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
2929 |
|
|
commented section |
2930 |
|
|
|
2931 |
chrisfen |
3131 |
2005-11-03 15:12 chrisfen |
2932 |
gezelter |
2568 |
|
2933 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
2934 |
|
|
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
2935 |
|
|
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
2936 |
|
|
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
2937 |
|
|
|
2938 |
chrisfen |
3131 |
2005-11-03 15:11 chrisfen |
2939 |
gezelter |
2568 |
|
2940 |
|
|
* samples/water/spce/spce.md: mmm... damped shifted force... |
2941 |
|
|
|
2942 |
chrisfen |
3131 |
2005-11-03 15:06 chuckv |
2943 |
gezelter |
2568 |
|
2944 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
2945 |
|
|
|
2946 |
chrisfen |
3131 |
2005-11-02 15:50 chuckv |
2947 |
gezelter |
2568 |
|
2948 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
2949 |
|
|
|
2950 |
chrisfen |
3131 |
2005-11-02 13:01 chrisfen |
2951 |
gezelter |
2568 |
|
2952 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
2953 |
|
|
removed some test code |
2954 |
|
|
|
2955 |
chrisfen |
3131 |
2005-11-02 12:45 chrisfen |
2956 |
gezelter |
2568 |
|
2957 |
|
|
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
2958 |
|
|
screening method header |
2959 |
|
|
|
2960 |
chrisfen |
3131 |
2005-11-02 12:36 chrisfen |
2961 |
gezelter |
2568 |
|
2962 |
|
|
* src/brains/SimInfo.cpp: again, changing how we deal with |
2963 |
|
|
summation and screening methods |
2964 |
|
|
|
2965 |
chrisfen |
3131 |
2005-11-02 12:36 chrisfen |
2966 |
gezelter |
2568 |
|
2967 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
2968 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
2969 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
2970 |
|
|
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
2971 |
|
|
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
2972 |
|
|
and screening methods |
2973 |
|
|
|
2974 |
chrisfen |
3131 |
2005-11-02 12:35 chrisfen |
2975 |
gezelter |
2568 |
|
2976 |
|
|
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
2977 |
|
|
|
2978 |
chrisfen |
3131 |
2005-11-01 15:32 chuckv |
2979 |
gezelter |
2568 |
|
2980 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
2981 |
|
|
UseTheForce/DarkSide/atype_interface.F90, |
2982 |
|
|
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
2983 |
|
|
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
2984 |
|
|
sutton-chen |
2985 |
|
|
|
2986 |
chrisfen |
3131 |
2005-11-01 11:24 chrisfen |
2987 |
gezelter |
2568 |
|
2988 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
2989 |
|
|
removed some testing code... |
2990 |
|
|
|
2991 |
chrisfen |
3131 |
2005-11-01 11:14 chrisfen |
2992 |
gezelter |
2568 |
|
2993 |
|
|
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
2994 |
|
|
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
2995 |
|
|
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
2996 |
|
|
initialization |
2997 |
|
|
|
2998 |
chrisfen |
3131 |
2005-11-01 11:13 chrisfen |
2999 |
gezelter |
2568 |
|
3000 |
|
|
* src/applications/oopse/oopse.cpp: nothing |
3001 |
|
|
|
3002 |
chrisfen |
3131 |
2005-11-01 11:09 chrisfen |
3003 |
gezelter |
2568 |
|
3004 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
3005 |
|
|
DarkSide/simulation.F90: still fixing up wolf... |
3006 |
|
|
|
3007 |
chrisfen |
3131 |
2005-11-01 10:29 chuckv |
3008 |
gezelter |
2568 |
|
3009 |
|
|
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
3010 |
|
|
process of adding sutton-chen forcefield. |
3011 |
|
|
|
3012 |
chrisfen |
3131 |
2005-10-26 16:32 chrisfen |
3013 |
gezelter |
2568 |
|
3014 |
|
|
* src/brains/SimInfo.cpp: changed the default switching radius to |
3015 |
|
|
85% of rcut |
3016 |
|
|
|
3017 |
chrisfen |
3131 |
2005-10-26 16:31 chrisfen |
3018 |
gezelter |
2568 |
|
3019 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
3020 |
|
|
to be working now - for charges and dipoles alike |
3021 |
|
|
|
3022 |
chrisfen |
3131 |
2005-10-26 16:31 chrisfen |
3023 |
gezelter |
2568 |
|
3024 |
|
|
* src/UseTheForce/doForces.F90: reaction field looks to be working |
3025 |
|
|
now |
3026 |
|
|
|
3027 |
chrisfen |
3131 |
2005-10-26 16:30 chrisfen |
3028 |
gezelter |
2568 |
|
3029 |
|
|
* samples/water/ssdrf/water.md: added a test molecule |
3030 |
|
|
|
3031 |
chrisfen |
3131 |
2005-10-26 16:30 chrisfen |
3032 |
gezelter |
2568 |
|
3033 |
|
|
* forceFields/DUFF2.frc: added a test atom type |
3034 |
|
|
|
3035 |
chrisfen |
3131 |
2005-10-24 07:06 chrisfen |
3036 |
gezelter |
2568 |
|
3037 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
3038 |
|
|
reaction field - don't know if it works... |
3039 |
|
|
|
3040 |
chrisfen |
3131 |
2005-10-23 14:08 chrisfen |
3041 |
gezelter |
2568 |
|
3042 |
|
|
* src/: UseTheForce/doForces.F90, |
3043 |
|
|
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
3044 |
|
|
streamlined reaction field for dipoles (now a good bit faster) and |
3045 |
|
|
added reaction field for charges - still need to do charge-dipole |
3046 |
|
|
RF |
3047 |
|
|
|
3048 |
chrisfen |
3131 |
2005-10-23 14:07 chrisfen |
3049 |
gezelter |
2568 |
|
3050 |
|
|
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
3051 |
|
|
field |
3052 |
|
|
|
3053 |
chrisfen |
3131 |
2005-10-23 14:06 chrisfen |
3054 |
gezelter |
2568 |
|
3055 |
|
|
* samples/water/spce/spce.md: reaction field now works for charges |
3056 |
|
|
|
3057 |
chrisfen |
3131 |
2005-10-20 13:27 tim |
3058 |
gezelter |
2568 |
|
3059 |
|
|
* src/primitives/Torsion.cpp: Fix the other branch of force |
3060 |
|
|
calculation in Torision.cpp |
3061 |
|
|
|
3062 |
chrisfen |
3131 |
2005-10-19 12:24 chrisfen |
3063 |
gezelter |
2568 |
|
3064 |
|
|
* src/: UseTheForce/doForces.F90, |
3065 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
3066 |
|
|
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
3067 |
|
|
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
3068 |
|
|
toUpper problems - these changes should fix those... |
3069 |
|
|
|
3070 |
chrisfen |
3131 |
2005-10-19 12:23 chrisfen |
3071 |
gezelter |
2568 |
|
3072 |
|
|
* samples/water/ssdrf/ssdrf.md: nothing |
3073 |
|
|
|
3074 |
chrisfen |
3131 |
2005-10-19 10:03 gezelter |
3075 |
gezelter |
2568 |
|
3076 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
3077 |
|
|
GayBerne |
3078 |
|
|
|
3079 |
chrisfen |
3131 |
2005-10-19 09:49 tim |
3080 |
gezelter |
2568 |
|
3081 |
|
|
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
3082 |
|
|
brains/ForceManager.cpp: fix an index mismathcing between c and |
3083 |
|
|
fortran |
3084 |
|
|
|
3085 |
chrisfen |
3131 |
2005-10-18 16:03 gezelter |
3086 |
gezelter |
2568 |
|
3087 |
|
|
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
3088 |
|
|
samples for the cutoff methods that Yang Zheng has been working on |
3089 |
|
|
|
3090 |
chrisfen |
3131 |
2005-10-18 14:13 gezelter |
3091 |
gezelter |
2568 |
|
3092 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
3093 |
|
|
and a rotation matrix bug |
3094 |
|
|
|
3095 |
chrisfen |
3131 |
2005-10-18 14:13 gezelter |
3096 |
gezelter |
2568 |
|
3097 |
|
|
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
3098 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
3099 |
|
|
added a few GB test cases |
3100 |
|
|
|
3101 |
chrisfen |
3131 |
2005-10-18 14:13 gezelter |
3102 |
gezelter |
2568 |
|
3103 |
|
|
* forceFields/DUFF2.frc: Fixing GB parameters |
3104 |
|
|
|
3105 |
chrisfen |
3131 |
2005-10-18 11:36 kdaily |
3106 |
gezelter |
2568 |
|
3107 |
|
|
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
3108 |
|
|
type |
3109 |
|
|
|
3110 |
chrisfen |
3131 |
2005-10-18 08:01 chrisfen |
3111 |
gezelter |
2568 |
|
3112 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
3113 |
|
|
UseTheForce/DarkSide/Makefile, |
3114 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
3115 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
3116 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
3117 |
|
|
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
3118 |
|
|
reaction field with electrostatics.F90 |
3119 |
|
|
|
3120 |
chrisfen |
3131 |
2005-10-17 16:13 tim |
3121 |
gezelter |
2568 |
|
3122 |
|
|
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
3123 |
|
|
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
3124 |
|
|
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
3125 |
|
|
io/StatWriter.hpp: Customized StatWriter is working |
3126 |
|
|
|
3127 |
chrisfen |
3131 |
2005-10-17 15:42 kdaily |
3128 |
gezelter |
2568 |
|
3129 |
|
|
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
3130 |
|
|
paper |
3131 |
|
|
|
3132 |
chrisfen |
3131 |
2005-10-17 14:47 gezelter |
3133 |
gezelter |
2568 |
|
3134 |
|
|
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
3135 |
|
|
|
3136 |
chrisfen |
3131 |
2005-10-17 12:24 tim |
3137 |
gezelter |
2568 |
|
3138 |
|
|
* src/io/ParamConstraint.hpp: Another bug fix |
3139 |
|
|
|
3140 |
chrisfen |
3131 |
2005-10-17 12:22 tim |
3141 |
gezelter |
2568 |
|
3142 |
|
|
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
3143 |
|
|
issues in Globals |
3144 |
|
|
|
3145 |
chrisfen |
3131 |
2005-10-17 12:12 gezelter |
3146 |
gezelter |
2568 |
|
3147 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
3148 |
|
|
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
3149 |
|
|
UseTheForce/DarkSide/gb_interface.F90, |
3150 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
3151 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
3152 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
3153 |
|
|
changing GB architecture |
3154 |
|
|
|
3155 |
chrisfen |
3131 |
2005-10-17 12:12 gezelter |
3156 |
gezelter |
2568 |
|
3157 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
3158 |
|
|
gbRotRoundZ.in: Adding samples for gb tests |
3159 |
|
|
|
3160 |
chrisfen |
3131 |
2005-10-16 20:06 tim |
3161 |
gezelter |
2568 |
|
3162 |
|
|
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
3163 |
|
|
a string to event's err_msg, there are still tons of memory |
3164 |
|
|
leaking problem in Globals |
3165 |
|
|
|
3166 |
chrisfen |
3131 |
2005-10-16 17:51 tim |
3167 |
gezelter |
2568 |
|
3168 |
|
|
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
3169 |
|
|
error message in Globals |
3170 |
|
|
|
3171 |
chrisfen |
3131 |
2005-10-14 14:43 tim |
3172 |
gezelter |
2568 |
|
3173 |
|
|
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
3174 |
|
|
parameters are working now |
3175 |
|
|
|
3176 |
chrisfen |
3131 |
2005-10-14 09:43 gezelter |
3177 |
gezelter |
2568 |
|
3178 |
|
|
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
3179 |
|
|
|
3180 |
chrisfen |
3131 |
2005-10-14 09:05 gezelter |
3181 |
gezelter |
2568 |
|
3182 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
3183 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
3184 |
|
|
Adding some Gay Berne tests |
3185 |
|
|
|
3186 |
chrisfen |
3131 |
2005-10-14 09:05 gezelter |
3187 |
gezelter |
2568 |
|
3188 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
3189 |
|
|
cutoff tests |
3190 |
|
|
|
3191 |
chrisfen |
3131 |
2005-10-14 08:44 kdaily |
3192 |
gezelter |
2568 |
|
3193 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
3194 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
3195 |
|
|
src/UseTheForce/DarkSide/gb_interface.F90, |
3196 |
|
|
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
3197 |
|
|
LJ |
3198 |
|
|
|
3199 |
chrisfen |
3131 |
2005-10-14 07:48 tim |
3200 |
gezelter |
2568 |
|
3201 |
|
|
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
3202 |
|
|
|
3203 |
chrisfen |
3131 |
2005-10-14 07:18 chrisfen |
3204 |
gezelter |
2568 |
|
3205 |
|
|
* samples/thermoIntegration/liquid/ssde.md, |
3206 |
|
|
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
3207 |
|
|
src/restraints/Restraints.cpp: added default restraint spring |
3208 |
|
|
constants into Globals |
3209 |
|
|
|
3210 |
chrisfen |
3131 |
2005-10-13 15:26 tim |
3211 |
gezelter |
2568 |
|
3212 |
|
|
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
3213 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
3214 |
|
|
constraints/ZconstraintForceManager.cpp, |
3215 |
|
|
integrators/Integrator.cpp, integrators/NPT.cpp, |
3216 |
|
|
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
3217 |
|
|
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
3218 |
|
|
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
3219 |
|
|
restraints/ThermoIntegrationForceManager.cpp, |
3220 |
|
|
visitors/ZconsVisitor.cpp: rewrite Globals |
3221 |
|
|
|
3222 |
chrisfen |
3131 |
2005-10-12 14:57 chuckv |
3223 |
gezelter |
2568 |
|
3224 |
|
|
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
3225 |
|
|
potential array to fortran. |
3226 |
|
|
|
3227 |
chrisfen |
3131 |
2005-10-12 14:00 gezelter |
3228 |
gezelter |
2568 |
|
3229 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
3230 |
|
|
remember what we did |
3231 |
|
|
|
3232 |
chrisfen |
3131 |
2005-10-12 14:00 gezelter |
3233 |
gezelter |
2568 |
|
3234 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
3235 |
|
|
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
3236 |
|
|
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
3237 |
|
|
DarkSide/sticky.F90: simplifying long range potential array |
3238 |
|
|
|
3239 |
chrisfen |
3131 |
2005-10-12 14:00 gezelter |
3240 |
gezelter |
2568 |
|
3241 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
3242 |
|
|
cutoff methods |
3243 |
|
|
|
3244 |
chrisfen |
3131 |
2005-10-12 14:00 gezelter |
3245 |
gezelter |
2568 |
|
3246 |
|
|
* forceFields/DUFF2.frc: Messing with 2-point water models |
3247 |
|
|
|
3248 |
chrisfen |
3131 |
2005-10-12 13:22 chuckv |
3249 |
gezelter |
2568 |
|
3250 |
|
|
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
3251 |
|
|
interface now expects an array for pot. |
3252 |
|
|
|
3253 |
chrisfen |
3131 |
2005-10-12 13:18 chuckv |
3254 |
gezelter |
2568 |
|
3255 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
3256 |
|
|
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
3257 |
|
|
calculation of potential. |
3258 |
|
|
|
3259 |
chrisfen |
3131 |
2005-10-12 12:55 chuckv |
3260 |
gezelter |
2568 |
|
3261 |
|
|
* src/UseTheForce/doForces.F90: More changes to MPI potential |
3262 |
|
|
calculations. |
3263 |
|
|
|
3264 |
chrisfen |
3131 |
2005-10-12 11:59 chuckv |
3265 |
gezelter |
2568 |
|
3266 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
3267 |
|
|
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
3268 |
|
|
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
3269 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
3270 |
|
|
Breaky: Add Support for seperating potential contributions. |
3271 |
|
|
|
3272 |
chrisfen |
3131 |
2005-10-11 15:00 chuckv |
3273 |
gezelter |
2568 |
|
3274 |
|
|
* src/UseTheForce/doForces.F90: Free some variables that weren't |
3275 |
|
|
freed before. |
3276 |
|
|
|
3277 |
chrisfen |
3131 |
2005-10-11 14:59 chuckv |
3278 |
gezelter |
2568 |
|
3279 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
3280 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
3281 |
|
|
builder --twinned. |
3282 |
|
|
|
3283 |
chrisfen |
3131 |
2005-10-11 14:57 chuckv |
3284 |
gezelter |
2568 |
|
3285 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
3286 |
|
|
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
3287 |
|
|
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
3288 |
|
|
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
3289 |
|
|
cvs. |
3290 |
|
|
|
3291 |
chrisfen |
3131 |
2005-10-10 14:34 chuckv |
3292 |
gezelter |
2568 |
|
3293 |
|
|
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
3294 |
|
|
in MPI. |
3295 |
|
|
|
3296 |
chrisfen |
3131 |
2005-10-10 14:20 chuckv |
3297 |
gezelter |
2568 |
|
3298 |
|
|
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
3299 |
|
|
indexing of groupToGtype. We now have two seperate maps |
3300 |
|
|
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
3301 |
|
|
that is set to groupToGtypeRow in the single processor version. |
3302 |
|
|
|
3303 |
chrisfen |
3131 |
2005-10-06 11:44 chrisfen |
3304 |
gezelter |
2568 |
|
3305 |
|
|
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
3306 |
|
|
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
3307 |
|
|
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
3308 |
|
|
|
3309 |
chrisfen |
3131 |
2005-10-05 14:12 tim |
3310 |
gezelter |
2568 |
|
3311 |
|
|
* src/primitives/RigidBody.cpp: There is still something wrong with |
3312 |
|
|
inertia tensor projection |
3313 |
|
|
|
3314 |
chrisfen |
3131 |
2005-10-05 12:35 tim |
3315 |
gezelter |
2568 |
|
3316 |
|
|
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
3317 |
|
|
There is still something wrong with current implementation. |
3318 |
|
|
|
3319 |
chrisfen |
3131 |
2005-10-05 12:34 tim |
3320 |
gezelter |
2568 |
|
3321 |
|
|
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
3322 |
|
|
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
3323 |
|
|
between group and center of mass array |
3324 |
|
|
|
3325 |
chrisfen |
3131 |
2005-10-05 12:12 tim |
3326 |
gezelter |
2568 |
|
3327 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
3328 |
|
|
When cutoffGroup is turned off, there is a mismatch between group |
3329 |
|
|
and center of mass array |
3330 |
|
|
|
3331 |
chrisfen |
3131 |
2005-10-04 12:34 chrisfen |
3332 |
gezelter |
2568 |
|
3333 |
|
|
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
3334 |
|
|
mass ratio bug that results in simulation failure with massless |
3335 |
|
|
particles |
3336 |
|
|
|
3337 |
chrisfen |
3131 |
2005-10-04 12:33 chrisfen |
3338 |
gezelter |
2568 |
|
3339 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
3340 |
|
|
wolf |
3341 |
|
|
|
3342 |
chrisfen |
3131 |
2005-10-04 12:32 chrisfen |
3343 |
gezelter |
2568 |
|
3344 |
|
|
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
3345 |
|
|
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
3346 |
|
|
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
3347 |
|
|
random changes when testing |
3348 |
|
|
|
3349 |
chrisfen |
3131 |
2005-10-03 08:54 tim |
3350 |
gezelter |
2568 |
|
3351 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
3352 |
|
|
projecting the inertia tensor of directional atom in rigibody into |
3353 |
|
|
rigidbody's body frame (previous commit is wrong) |
3354 |
|
|
|
3355 |
chrisfen |
3131 |
2005-10-03 07:31 tim |
3356 |
gezelter |
2568 |
|
3357 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
3358 |
|
|
tensor of directional atom in rigibody into rigidbody's body frame |
3359 |
|
|
|
3360 |
chrisfen |
3131 |
2005-09-28 11:47 chrisfen |
3361 |
gezelter |
2568 |
|
3362 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
3363 |
|
|
|
3364 |
chrisfen |
3131 |
2005-09-28 11:46 chrisfen |
3365 |
gezelter |
2568 |
|
3366 |
|
|
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
3367 |
|
|
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
3368 |
|
|
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
3369 |
|
|
tip4p/tp4.md: fixed some samples |
3370 |
|
|
|
3371 |
chrisfen |
3131 |
2005-09-28 11:46 chrisfen |
3372 |
gezelter |
2568 |
|
3373 |
|
|
* ChangeLog: updated |
3374 |
|
|
|
3375 |
chrisfen |
3131 |
2005-09-28 09:55 tim |
3376 |
chrisfen |
2337 |
|
3377 |
|
|
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
3378 |
|
|
divergence in rotation matrix to quaternion transformation |
3379 |
|
|
|
3380 |
chrisfen |
3131 |
2005-09-28 09:32 gezelter |
3381 |
chrisfen |
2337 |
|
3382 |
|
|
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
3383 |
|
|
order error |
3384 |
|
|
|
3385 |
chrisfen |
3131 |
2005-09-28 09:32 gezelter |
3386 |
chrisfen |
2337 |
|
3387 |
|
|
* src/io/DumpReader.cpp: tracking down quaternion bug |
3388 |
|
|
|
3389 |
chrisfen |
3131 |
2005-09-28 09:32 gezelter |
3390 |
chrisfen |
2337 |
|
3391 |
|
|
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
3392 |
|
|
model |
3393 |
|
|
|
3394 |
chrisfen |
3131 |
2005-09-27 13:02 tim |
3395 |
chrisfen |
2337 |
|
3396 |
|
|
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
3397 |
|
|
to quaternion |
3398 |
|
|
|
3399 |
chrisfen |
3131 |
2005-09-26 11:38 chuckv |
3400 |
chrisfen |
2337 |
|
3401 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
3402 |
|
|
7 so derfc is external. Other compilers should treat erfc as |
3403 |
|
|
intrinsic. |
3404 |
|
|
|
3405 |
chrisfen |
3131 |
2005-09-26 10:07 chuckv |
3406 |
chrisfen |
2337 |
|
3407 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
3408 |
|
|
and declared it to be external to fix issure with ifc7. Hopefully |
3409 |
|
|
this will not cause a problem with other compilers where derfc is |
3410 |
|
|
an intrinsic function. |
3411 |
|
|
|
3412 |
chrisfen |
3131 |
2005-09-26 09:42 chuckv |
3413 |
chrisfen |
2337 |
|
3414 |
|
|
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
3415 |
|
|
in simulation module. We needed a seperate receive buffer. |
3416 |
|
|
|
3417 |
chrisfen |
3131 |
2005-09-26 08:58 chuckv |
3418 |
chrisfen |
2337 |
|
3419 |
|
|
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
3420 |
|
|
support for skinThickness keyword to Globals. |
3421 |
|
|
|
3422 |
chrisfen |
3131 |
2005-09-26 08:56 tim |
3423 |
chrisfen |
2337 |
|
3424 |
|
|
* src/io/DumpReader.cpp: fix a typo in DumpReader |
3425 |
|
|
|
3426 |
chrisfen |
3131 |
2005-09-26 07:27 chrisfen |
3427 |
chrisfen |
2337 |
|
3428 |
|
|
* samples/: minimizer/tip4p_two.md, |
3429 |
|
|
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
3430 |
|
|
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
3431 |
|
|
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
3432 |
|
|
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
3433 |
|
|
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
3434 |
|
|
water/tip4p/tp4.md: fixing up some samples |
3435 |
|
|
|
3436 |
chrisfen |
3131 |
2005-09-24 10:39 chrisfen |
3437 |
chrisfen |
2337 |
|
3438 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
3439 |
|
|
roughly the same speed as the old version when using dipoles |
3440 |
|
|
|
3441 |
|
|
energies are now exactly the same between the old version of OOPSE |
3442 |
|
|
and this version |
3443 |
|
|
|
3444 |
chrisfen |
3131 |
2005-09-24 10:38 chrisfen |
3445 |
chrisfen |
2337 |
|
3446 |
|
|
* samples/water/ssdrf/ssdrf.md: turned rf on |
3447 |
|
|
|
3448 |
chrisfen |
3131 |
2005-09-23 13:31 chuckv |
3449 |
chrisfen |
2337 |
|
3450 |
|
|
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
3451 |
|
|
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
3452 |
|
|
from skin. This will get fixed to where we can manually set skin |
3453 |
|
|
thickness. |
3454 |
|
|
|
3455 |
chrisfen |
3131 |
2005-09-22 11:50 gezelter |
3456 |
chrisfen |
2337 |
|
3457 |
|
|
* src/math/derfc.F90: added error function |
3458 |
|
|
|
3459 |
chrisfen |
3131 |
2005-09-21 17:08 chuckv |
3460 |
chrisfen |
2337 |
|
3461 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statement for |
3462 |
|
|
angular momentum and inertia tensor from velocitizer. |
3463 |
|
|
|
3464 |
chrisfen |
3131 |
2005-09-21 17:04 chuckv |
3465 |
chrisfen |
2337 |
|
3466 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statements for |
3467 |
|
|
remove angular momentum. |
3468 |
|
|
|
3469 |
chrisfen |
3131 |
2005-09-21 16:45 chuckv |
3470 |
chrisfen |
2337 |
|
3471 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
3472 |
|
|
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
3473 |
|
|
map. |
3474 |
|
|
|
3475 |
chrisfen |
3131 |
2005-09-21 13:59 tim |
3476 |
chrisfen |
2337 |
|
3477 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
3478 |
|
|
DumpReader using pure c++ io |
3479 |
|
|
|
3480 |
chrisfen |
3131 |
2005-09-21 10:20 chrisfen |
3481 |
chrisfen |
2337 |
|
3482 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
3483 |
|
|
defaultCutoff bug (HEMES!) |
3484 |
|
|
|
3485 |
chrisfen |
3131 |
2005-09-20 15:13 gezelter |
3486 |
chrisfen |
2337 |
|
3487 |
|
|
* make/Makefile.in: libz additions |
3488 |
|
|
|
3489 |
chrisfen |
3131 |
2005-09-20 15:03 gezelter |
3490 |
chrisfen |
2337 |
|
3491 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
3492 |
|
|
src/config.h.in: added check for zlib in configure |
3493 |
|
|
|
3494 |
chrisfen |
3131 |
2005-09-20 14:22 tim |
3495 |
chrisfen |
2337 |
|
3496 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
3497 |
|
|
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
3498 |
|
|
|
3499 |
chrisfen |
3131 |
2005-09-20 09:22 tim |
3500 |
chrisfen |
2337 |
|
3501 |
|
|
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
3502 |
|
|
testcase for zipstream |
3503 |
|
|
|
3504 |
chrisfen |
3131 |
2005-09-20 08:41 tim |
3505 |
chrisfen |
2337 |
|
3506 |
|
|
* src/io/zipstream.hpp: adding zipstream.hpp |
3507 |
|
|
|
3508 |
chrisfen |
3131 |
2005-09-20 08:34 chrisfen |
3509 |
chrisfen |
2337 |
|
3510 |
|
|
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
3511 |
|
|
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
3512 |
|
|
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
3513 |
|
|
zcons/zconsMoving.md: fixed up some sample md files |
3514 |
|
|
|
3515 |
chrisfen |
3131 |
2005-09-19 16:21 chrisfen |
3516 |
chrisfen |
2337 |
|
3517 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
3518 |
|
|
src/UseTheForce/doForces.F90, |
3519 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
3520 |
|
|
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
3521 |
|
|
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
3522 |
|
|
appears as though it really is working... |
3523 |
|
|
|
3524 |
chrisfen |
3131 |
2005-09-18 13:45 chrisfen |
3525 |
chrisfen |
2310 |
|
3526 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
3527 |
|
|
src/UseTheForce/doForces.F90, |
3528 |
|
|
src/UseTheForce/doForces_interface.F90, |
3529 |
|
|
src/UseTheForce/doForces_interface.h, |
3530 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
3531 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
3532 |
|
|
src/brains/SimInfo.cpp: reaction field seems to work now, still |
3533 |
|
|
need to do some testing... |
3534 |
|
|
|
3535 |
chrisfen |
3131 |
2005-09-16 16:04 chuckv |
3536 |
chrisfen |
2309 |
|
3537 |
|
|
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
3538 |
|
|
dump files. |
3539 |
|
|
|
3540 |
chrisfen |
3131 |
2005-09-16 14:07 chrisfen |
3541 |
chrisfen |
2309 |
|
3542 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
3543 |
|
|
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
3544 |
|
|
bug that ifc missed... |
3545 |
|
|
|
3546 |
chrisfen |
3131 |
2005-09-16 13:36 chrisfen |
3547 |
chrisfen |
2309 |
|
3548 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
3549 |
|
|
fixing some summation method issues |
3550 |
|
|
|
3551 |
chrisfen |
3131 |
2005-09-16 12:35 chrisfen |
3552 |
chrisfen |
2309 |
|
3553 |
|
|
* src/brains/SimInfo.cpp: fixed a capitalization error |
3554 |
|
|
|
3555 |
chrisfen |
3131 |
2005-09-16 12:34 chrisfen |
3556 |
chrisfen |
2309 |
|
3557 |
|
|
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
3558 |
|
|
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
3559 |
|
|
around |
3560 |
|
|
|
3561 |
chrisfen |
3131 |
2005-09-16 12:00 chrisfen |
3562 |
chrisfen |
2309 |
|
3563 |
|
|
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
3564 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
3565 |
|
|
are known issues - particularly with reaction field... |
3566 |
|
|
|
3567 |
chrisfen |
3131 |
2005-09-16 09:07 chrisfen |
3568 |
chrisfen |
2309 |
|
3569 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
3570 |
|
|
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
3571 |
|
|
(cutting out the old way to do reaction field) |
3572 |
|
|
|
3573 |
chrisfen |
3131 |
2005-09-15 15:05 gezelter |
3574 |
chrisfen |
2309 |
|
3575 |
|
|
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
3576 |
|
|
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
3577 |
|
|
DarkSide/electrostatic_interface.F90, |
3578 |
|
|
DarkSide/electrostatic_interface.h: Working on adding WOLF |
3579 |
|
|
|
3580 |
chrisfen |
3131 |
2005-09-15 12:17 tim |
3581 |
chrisfen |
2309 |
|
3582 |
|
|
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
3583 |
|
|
is called without calling getNFrames |
3584 |
|
|
|
3585 |
chrisfen |
3131 |
2005-09-15 06:47 chrisfen |
3586 |
chrisfen |
2309 |
|
3587 |
|
|
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
3588 |
|
|
|
3589 |
chrisfen |
3131 |
2005-09-14 19:48 chuckv |
3590 |
chrisfen |
2309 |
|
3591 |
|
|
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
3592 |
|
|
not initialized after creation. When maxval(gtypeMaxCutoff) was |
3593 |
|
|
called, the largest random garbage value was returned from the |
3594 |
|
|
array. |
3595 |
|
|
|
3596 |
chrisfen |
3131 |
2005-09-14 17:14 chrisfen |
3597 |
chrisfen |
2309 |
|
3598 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
3599 |
|
|
io/Globals.hpp: changes to include the coulombicCorrection selector |
3600 |
|
|
|
3601 |
chrisfen |
3131 |
2005-09-14 17:13 chrisfen |
3602 |
chrisfen |
2309 |
|
3603 |
|
|
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
3604 |
|
|
reactionField.F90: added in the undamped wolf, in the process of |
3605 |
|
|
doing the damped wolf |
3606 |
|
|
|
3607 |
chrisfen |
3131 |
2005-09-14 17:13 chrisfen |
3608 |
chrisfen |
2309 |
|
3609 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
3610 |
|
|
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
3611 |
|
|
the coulombicCorrection selector |
3612 |
|
|
|
3613 |
chrisfen |
3131 |
2005-09-14 17:11 chrisfen |
3614 |
chrisfen |
2309 |
|
3615 |
|
|
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
3616 |
|
|
|
3617 |
chrisfen |
3131 |
2005-09-14 17:11 chrisfen |
3618 |
chrisfen |
2309 |
|
3619 |
|
|
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
3620 |
|
|
|
3621 |
chrisfen |
3131 |
2005-09-14 17:10 chrisfen |
3622 |
chrisfen |
2309 |
|
3623 |
|
|
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
3624 |
|
|
|
3625 |
chrisfen |
3131 |
2005-09-14 13:31 chuckv |
3626 |
chrisfen |
2309 |
|
3627 |
|
|
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
3628 |
|
|
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
3629 |
|
|
|
3630 |
chrisfen |
3131 |
2005-09-14 13:28 gezelter |
3631 |
chrisfen |
2309 |
|
3632 |
|
|
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
3633 |
|
|
do_prepair |
3634 |
|
|
|
3635 |
chrisfen |
3131 |
2005-09-14 12:02 gezelter |
3636 |
chrisfen |
2309 |
|
3637 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
3638 |
|
|
createMixingMap routine. It should now set doShift correctly |
3639 |
|
|
|
3640 |
chrisfen |
3131 |
2005-09-07 15:44 chuckv |
3641 |
chrisfen |
2309 |
|
3642 |
|
|
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
3643 |
|
|
|
3644 |
chrisfen |
3131 |
2005-09-07 15:23 chuckv |
3645 |
chrisfen |
2309 |
|
3646 |
|
|
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
3647 |
|
|
logical variables |
3648 |
|
|
|
3649 |
chrisfen |
3131 |
2005-09-07 15:08 gezelter |
3650 |
chrisfen |
2309 |
|
3651 |
|
|
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
3652 |
|
|
algorithm |
3653 |
|
|
|
3654 |
chrisfen |
3131 |
2005-09-07 13:46 gezelter |
3655 |
chrisfen |
2309 |
|
3656 |
|
|
* src/: UseTheForce/doForces.F90, |
3657 |
|
|
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
3658 |
|
|
UseTheForce/notifyCutoffs_interface.F90, |
3659 |
|
|
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
3660 |
|
|
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
3661 |
|
|
cutoff Policy |
3662 |
|
|
|
3663 |
chrisfen |
3131 |
2005-09-07 12:18 gezelter |
3664 |
chrisfen |
2309 |
|
3665 |
|
|
* src/UseTheForce/doForces.F90: Some bug hunting |
3666 |
|
|
|
3667 |
chrisfen |
3131 |
2005-09-07 12:18 gezelter |
3668 |
chrisfen |
2309 |
|
3669 |
|
|
* samples/argon/argonNVT.md: Just a longer test |
3670 |
|
|
|
3671 |
chrisfen |
3131 |
2005-09-06 10:32 chuckv |
3672 |
chrisfen |
2309 |
|
3673 |
|
|
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
3674 |
|
|
etc.. |
3675 |
|
|
|
3676 |
chrisfen |
3131 |
2005-09-01 15:56 gezelter |
3677 |
chrisfen |
2309 |
|
3678 |
|
|
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
3679 |
|
|
zero |
3680 |
|
|
|
3681 |
chrisfen |
3131 |
2005-09-01 13:17 gezelter |
3682 |
chrisfen |
2309 |
|
3683 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
3684 |
|
|
createGtypeCutoffMap |
3685 |
|
|
|
3686 |
chrisfen |
3131 |
2005-08-30 11:23 chrisfen |
3687 |
chrisfen |
2309 |
|
3688 |
|
|
* src/: UseTheForce/doForces.F90, |
3689 |
|
|
UseTheForce/doForces_interface.F90, |
3690 |
|
|
UseTheForce/doForces_interface.h, |
3691 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
3692 |
|
|
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
3693 |
|
|
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
3694 |
|
|
changes for implementing the wolf potential |
3695 |
|
|
|
3696 |
chrisfen |
3131 |
2005-08-26 15:39 chrisfen |
3697 |
chrisfen |
2309 |
|
3698 |
|
|
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
3699 |
|
|
|
3700 |
chrisfen |
3131 |
2005-08-26 14:30 chrisfen |
3701 |
chrisfen |
2309 |
|
3702 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
3703 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
3704 |
|
|
some probably nonfunctional get*cut routines |
3705 |
|
|
|
3706 |
chrisfen |
3131 |
2005-08-26 13:34 chuckv |
3707 |
chrisfen |
2309 |
|
3708 |
|
|
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
3709 |
|
|
|
3710 |
chrisfen |
3131 |
2005-08-26 09:36 gezelter |
3711 |
chrisfen |
2309 |
|
3712 |
|
|
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
3713 |
|
|
interactionHash and gtypeCutoff routines |
3714 |
|
|
|
3715 |
chrisfen |
3131 |
2005-08-17 08:26 gezelter |
3716 |
chrisfen |
2309 |
|
3717 |
|
|
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
3718 |
|
|
DarkSide/simulation.F90: added fCutoffPolicy.h |
3719 |
|
|
|
3720 |
chrisfen |
3131 |
2005-08-11 14:04 gezelter |
3721 |
chrisfen |
2309 |
|
3722 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
3723 |
|
|
progress |
3724 |
|
|
|
3725 |
chrisfen |
3131 |
2005-08-10 12:17 gezelter |
3726 |
chrisfen |
2309 |
|
3727 |
|
|
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
3728 |
|
|
they belong |
3729 |
|
|
|
3730 |
chrisfen |
3131 |
2005-08-09 15:33 gezelter |
3731 |
chrisfen |
2309 |
|
3732 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
3733 |
|
|
Jones module |
3734 |
|
|
|
3735 |
chrisfen |
3131 |
2005-08-09 15:33 gezelter |
3736 |
chrisfen |
2309 |
|
3737 |
|
|
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
3738 |
|
|
|
3739 |
chrisfen |
3131 |
2005-08-09 12:40 chuckv |
3740 |
chrisfen |
2309 |
|
3741 |
|
|
* src/UseTheForce/doForces.F90: In process of re-write for group |
3742 |
|
|
based cutoff.... |
3743 |
|
|
|
3744 |
chrisfen |
3131 |
2005-07-29 12:38 gezelter |
3745 |
chrisfen |
2309 |
|
3746 |
|
|
* src/UseTheForce/doForces.F90: fixes in progress |
3747 |
|
|
|
3748 |
chrisfen |
3131 |
2005-07-29 10:34 tim |
3749 |
chrisfen |
2309 |
|
3750 |
|
|
* src/UseTheForce/doForces.F90: fix a bug which does not update |
3751 |
|
|
me_i and me_j correctly |
3752 |
|
|
|
3753 |
chrisfen |
3131 |
2005-07-28 15:12 chuckv |
3754 |
chrisfen |
2309 |
|
3755 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
3756 |
|
|
cutoffs... Segfaults nicely now... |
3757 |
|
|
|
3758 |
chrisfen |
3131 |
2005-07-20 10:04 gezelter |
3759 |
chrisfen |
2309 |
|
3760 |
|
|
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
3761 |
|
|
error messages from pathscale compiler |
3762 |
|
|
|
3763 |
chrisfen |
3131 |
2005-07-13 09:48 tim |
3764 |
chrisfen |
2309 |
|
3765 |
|
|
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
3766 |
|
|
<functional> |
3767 |
|
|
|
3768 |
chrisfen |
3131 |
2005-07-13 08:54 tim |
3769 |
chrisfen |
2309 |
|
3770 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
3771 |
|
|
UseTheForce/mpiComponentPlan.h, |
3772 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
3773 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
3774 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
3775 |
|
|
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
3776 |
|
|
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
3777 |
|
|
utils/simError.c, utils/simError.h: replace c++ style comment in c |
3778 |
|
|
files |
3779 |
|
|
|
3780 |
chrisfen |
3131 |
2005-07-03 13:53 chuckv |
3781 |
chrisfen |
2309 |
|
3782 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
3783 |
|
|
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
3784 |
|
|
subroutine to set cuttoff for Interaction map and function in |
3785 |
|
|
simulation.F90 to determine if a particular atype is present in a |
3786 |
|
|
simulation. |
3787 |
|
|
|
3788 |
chrisfen |
3131 |
2005-06-28 06:58 gezelter |
3789 |
chrisfen |
2309 |
|
3790 |
|
|
* src/UseTheForce/doForces.F90: [no log message] |
3791 |
|
|
|
3792 |
chrisfen |
3131 |
2005-06-27 15:21 chuckv |
3793 |
chrisfen |
2309 |
|
3794 |
|
|
* src/UseTheForce/doForces.F90: More breaking and destruction of |
3795 |
|
|
force code. Does not build at this point... |
3796 |
|
|
|
3797 |
chrisfen |
3131 |
2005-06-27 14:01 gezelter |
3798 |
chrisfen |
2309 |
|
3799 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
3800 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, |
3801 |
|
|
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
3802 |
|
|
Breaky breaky! |
3803 |
|
|
|
3804 |
chrisfen |
3131 |
2005-06-20 09:03 gezelter |
3805 |
chrisfen |
2309 |
|
3806 |
|
|
* samples/water/ssd/ssd.md, |
3807 |
|
|
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
3808 |
|
|
simulation |
3809 |
|
|
|
3810 |
chrisfen |
3131 |
2005-06-13 11:25 tim |
3811 |
chrisfen |
2309 |
|
3812 |
|
|
* src/: applications/staticProps/DensityPlot.cpp, |
3813 |
|
|
applications/staticProps/DensityPlot.hpp, |
3814 |
|
|
applications/staticProps/SCDOrderParameter.cpp, |
3815 |
|
|
applications/staticProps/StaticProps.cpp, |
3816 |
|
|
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
3817 |
|
|
|
3818 |
chrisfen |
3131 |
2005-05-31 15:31 chuckv |
3819 |
chrisfen |
2309 |
|
3820 |
|
|
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
3821 |
|
|
remove angular momentum. |
3822 |
|
|
|
3823 |
chrisfen |
3131 |
2005-05-31 10:34 chuckv |
3824 |
chrisfen |
2309 |
|
3825 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
3826 |
|
|
typo in nanorodBuilder. |
3827 |
|
|
|
3828 |
chrisfen |
3131 |
2005-05-30 07:01 chuckv |
3829 |
chrisfen |
2309 |
|
3830 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
3831 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
3832 |
|
|
brains/Stats.hpp, integrators/Velocitizer.cpp, |
3833 |
|
|
integrators/Velocitizer.hpp: Added method to remove system angular |
3834 |
|
|
momentum to velocitizer and added method to calculate system |
3835 |
|
|
angular momentum to siminfo. |
3836 |
|
|
|
3837 |
chrisfen |
3131 |
2005-05-29 14:16 chrisfen |
3838 |
chrisfen |
2309 |
|
3839 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
3840 |
|
|
balance from the Darkside (files) |
3841 |
|
|
|
3842 |
chrisfen |
3131 |
2005-05-29 14:15 chrisfen |
3843 |
chrisfen |
2309 |
|
3844 |
|
|
* src/UseTheForce/doForces.F90: Removed balance from doForces |
3845 |
|
|
|
3846 |
chrisfen |
3131 |
2005-05-29 14:15 chrisfen |
3847 |
chrisfen |
2309 |
|
3848 |
|
|
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
3849 |
|
|
|
3850 |
chrisfen |
3131 |
2005-05-29 14:15 chrisfen |
3851 |
chrisfen |
2309 |
|
3852 |
|
|
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
3853 |
|
|
dimer for testing purposes |
3854 |
|
|
|
3855 |
chrisfen |
3131 |
2005-05-29 14:14 chrisfen |
3856 |
chrisfen |
2309 |
|
3857 |
|
|
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
3858 |
|
|
was apparently wiped earlier this month... |
3859 |
|
|
|
3860 |
chrisfen |
3131 |
2005-05-29 14:13 chrisfen |
3861 |
chrisfen |
2309 |
|
3862 |
|
|
* ChangeLog: ran make cvslog |
3863 |
|
|
|
3864 |
chrisfen |
3131 |
2005-05-28 17:16 tim |
3865 |
chrisfen |
2246 |
|
3866 |
|
|
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
3867 |
|
|
AtomNameVisitor |
3868 |
|
|
|
3869 |
chrisfen |
3131 |
2005-05-28 17:09 tim |
3870 |
chrisfen |
2246 |
|
3871 |
|
|
* src/integrators/Integrator.cpp: dding resetIntegrator |
3872 |
|
|
|
3873 |
chrisfen |
3131 |
2005-05-28 17:06 tim |
3874 |
chrisfen |
2246 |
|
3875 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
3876 |
|
|
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
3877 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
3878 |
|
|
resetIntegrator |
3879 |
|
|
|
3880 |
chrisfen |
3131 |
2005-05-27 14:11 tim |
3881 |
chrisfen |
2246 |
|
3882 |
|
|
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
3883 |
|
|
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
3884 |
|
|
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
3885 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
3886 |
|
|
StaticProps |
3887 |
|
|
|
3888 |
chrisfen |
3131 |
2005-05-26 21:41 tim |
3889 |
chrisfen |
2246 |
|
3890 |
|
|
* src/: applications/staticProps/Makefile, |
3891 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
3892 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
3893 |
|
|
applications/staticProps/StaticProps.cpp, |
3894 |
|
|
applications/staticProps/StaticProps.ggo, |
3895 |
|
|
applications/staticProps/StaticPropsCmd.c, |
3896 |
|
|
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
3897 |
|
|
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
3898 |
|
|
|
3899 |
chrisfen |
3131 |
2005-05-26 15:45 tim |
3900 |
chrisfen |
2246 |
|
3901 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3902 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
3903 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
3904 |
|
|
applications/staticProps/Makefile, |
3905 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
3906 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
3907 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
3908 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
3909 |
|
|
applications/staticProps/StaticAnalyser.hpp, |
3910 |
|
|
applications/staticProps/StaticProps.cpp, |
3911 |
|
|
applications/staticProps/StaticProps.ggo, |
3912 |
|
|
applications/staticProps/StaticPropsCmd.c, |
3913 |
|
|
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
3914 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
3915 |
|
|
AtomNameVisitor to convert atom name to its base name; |
3916 |
|
|
wrappingvisitor now wrap back to the center of the mass; adding |
3917 |
|
|
P2OrderParameter into StaticProps |
3918 |
|
|
|
3919 |
chrisfen |
3131 |
2005-05-22 14:36 chuckv |
3920 |
chrisfen |
2246 |
|
3921 |
gezelter |
2568 |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
3922 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
3923 |
|
|
applications/nanoRodBuilder/GeometryFactory.cpp, |
3924 |
|
|
applications/nanoRodBuilder/GeometryFactory.hpp, |
3925 |
|
|
applications/nanoRodBuilder/nanorodBuilder.cpp, |
3926 |
|
|
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
3927 |
chrisfen |
2246 |
tensor. |
3928 |
|
|
|
3929 |
chrisfen |
3131 |
2005-05-22 14:05 tim |
3930 |
chrisfen |
2246 |
|
3931 |
|
|
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
3932 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
3933 |
|
|
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
3934 |
|
|
printPressureTensor |
3935 |
|
|
|
3936 |
chrisfen |
3131 |
2005-05-20 12:27 tim |
3937 |
chrisfen |
2246 |
|
3938 |
|
|
* src/integrators/NPrT.cpp: NPrT in progress |
3939 |
|
|
|
3940 |
chrisfen |
3131 |
2005-05-20 09:01 tim |
3941 |
chrisfen |
2246 |
|
3942 |
|
|
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
3943 |
|
|
utils/OOPSEConstant.hpp: NPrT in progress |
3944 |
|
|
|
3945 |
chrisfen |
3131 |
2005-05-19 14:31 tim |
3946 |
chrisfen |
2246 |
|
3947 |
|
|
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
3948 |
|
|
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
3949 |
|
|
io/Globals.hpp: NPAT is working |
3950 |
|
|
|
3951 |
chrisfen |
3131 |
2005-05-19 08:49 tim |
3952 |
chrisfen |
2246 |
|
3953 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
3954 |
|
|
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
3955 |
|
|
|
3956 |
chrisfen |
3131 |
2005-05-18 21:28 tim |
3957 |
chrisfen |
2246 |
|
3958 |
|
|
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
3959 |
|
|
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
3960 |
|
|
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
3961 |
|
|
|
3962 |
chrisfen |
3131 |
2005-05-18 12:06 chrisfen |
3963 |
chrisfen |
2246 |
|
3964 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
3965 |
|
|
some tap changes |
3966 |
|
|
|
3967 |
chrisfen |
3131 |
2005-05-18 11:31 chrisfen |
3968 |
chrisfen |
2246 |
|
3969 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
3970 |
|
|
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
3971 |
|
|
in the first solvation shell for tap |
3972 |
|
|
|
3973 |
chrisfen |
3131 |
2005-05-18 05:35 chrisfen |
3974 |
chrisfen |
2246 |
|
3975 |
|
|
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
3976 |
|
|
for testing purposes |
3977 |
|
|
|
3978 |
chrisfen |
3131 |
2005-05-17 15:35 chrisfen |
3979 |
chrisfen |
2246 |
|
3980 |
|
|
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
3981 |
|
|
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
3982 |
|
|
src/UseTheForce/doForces.F90, |
3983 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
3984 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
3985 |
|
|
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
3986 |
|
|
correcting changes to the previous merge that were not caught |
3987 |
|
|
|
3988 |
chrisfen |
3131 |
2005-05-16 21:20 chuckv |
3989 |
chrisfen |
2229 |
|
3990 |
|
|
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
3991 |
|
|
Fixed merge issues between Kyle and Chris so OOPSE will actually |
3992 |
|
|
build. |
3993 |
|
|
|
3994 |
chrisfen |
3131 |
2005-05-16 20:46 kdaily |
3995 |
chrisfen |
2229 |
|
3996 |
|
|
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
3997 |
|
|
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
3998 |
|
|
|
3999 |
chrisfen |
3131 |
2005-05-16 19:08 kdaily |
4000 |
chrisfen |
2229 |
|
4001 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
4002 |
|
|
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
4003 |
|
|
src/types/DirectionalAtomType.cpp, |
4004 |
|
|
src/types/DirectionalAtomType.hpp: added gb |
4005 |
|
|
|
4006 |
chrisfen |
3131 |
2005-05-13 13:36 chrisfen |
4007 |
chrisfen |
2229 |
|
4008 |
|
|
* forceFields/DUFF2.frc: Better tap |
4009 |
|
|
|
4010 |
chrisfen |
3131 |
2005-05-12 12:43 chrisfen |
4011 |
chrisfen |
2229 |
|
4012 |
|
|
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
4013 |
|
|
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
4014 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
4015 |
|
|
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
4016 |
|
|
Need to parametrize. |
4017 |
|
|
|
4018 |
chrisfen |
3131 |
2005-05-11 16:15 chuckv |
4019 |
chrisfen |
2229 |
|
4020 |
|
|
* src/: io/ShapeAtomTypesSectionParser.cpp, |
4021 |
|
|
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
4022 |
|
|
build issues under ifc7. |
4023 |
|
|
|
4024 |
chrisfen |
3131 |
2005-05-09 15:07 chuckv |
4025 |
chrisfen |
2229 |
|
4026 |
|
|
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
4027 |
|
|
builder changes. |
4028 |
|
|
|
4029 |
chrisfen |
3131 |
2005-05-05 08:06 chrisfen |
4030 |
chrisfen |
2229 |
|
4031 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
4032 |
|
|
to TAP |
4033 |
|
|
|
4034 |
chrisfen |
3131 |
2005-05-05 07:47 chrisfen |
4035 |
chrisfen |
2229 |
|
4036 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
4037 |
|
|
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
4038 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
4039 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
4040 |
|
|
src/UseTheForce/DarkSide/atype_interface.F90, |
4041 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
4042 |
|
|
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
4043 |
|
|
src/brains/fSimulation.h, src/io/Makefile, |
4044 |
|
|
src/io/StickyAtomTypesSectionParser.cpp, |
4045 |
|
|
src/io/StickyPowerAtomTypesSectionParser.cpp, |
4046 |
|
|
src/io/StickyPowerAtomTypesSectionParser.hpp, |
4047 |
|
|
src/types/AtomType.cpp, src/types/AtomType.hpp, |
4048 |
|
|
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
4049 |
|
|
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
4050 |
|
|
not parametrized, but OOPSE will now let me run it... |
4051 |
|
|
|
4052 |
chrisfen |
3131 |
2005-05-03 15:55 chuckv |
4053 |
chrisfen |
2229 |
|
4054 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
4055 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
4056 |
|
|
Adding support for generic geometry to nanorodbuilder. |
4057 |
|
|
|
4058 |
chrisfen |
3131 |
2005-05-03 10:55 chuckv |
4059 |
chrisfen |
2229 |
|
4060 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
4061 |
|
|
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
4062 |
|
|
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
4063 |
|
|
|
4064 |
chrisfen |
3131 |
2005-04-29 12:16 gezelter |
4065 |
chrisfen |
2229 |
|
4066 |
|
|
* make/Makefile.in: [no log message] |
4067 |
|
|
|
4068 |
chrisfen |
3131 |
2005-04-29 09:26 chrisfen |
4069 |
chrisfen |
2229 |
|
4070 |
|
|
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
4071 |
|
|
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
4072 |
|
|
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
4073 |
|
|
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
4074 |
|
|
samples/water/tip4p/water.md: Added TIP4P-Ew |
4075 |
|
|
|
4076 |
chrisfen |
3131 |
2005-04-27 17:24 chuckv |
4077 |
chrisfen |
2229 |
|
4078 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
4079 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
4080 |
|
|
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
4081 |
|
|
nanoRodBuilder.... |
4082 |
|
|
|
4083 |
chrisfen |
3131 |
2005-04-27 13:13 chrisfen |
4084 |
chrisfen |
2229 |
|
4085 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
4086 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
4087 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
4088 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
4089 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
4090 |
|
|
write statements and am closer to a working shapes |
4091 |
|
|
|
4092 |
chrisfen |
3131 |
2005-04-22 14:57 chuckv |
4093 |
chrisfen |
2229 |
|
4094 |
|
|
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
4095 |
|
|
|
4096 |
chrisfen |
3131 |
2005-04-22 14:52 tim |
4097 |
chrisfen |
2229 |
|
4098 |
|
|
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
4099 |
|
|
Trim.hpp: adding CharClassificationFunctor to fix the locale |
4100 |
|
|
problem of c++ |
4101 |
|
|
|
4102 |
chrisfen |
3131 |
2005-04-21 07:12 chrisfen |
4103 |
chrisfen |
2229 |
|
4104 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.in, |
4105 |
|
|
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
4106 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
4107 |
|
|
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
4108 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
4109 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
4110 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
4111 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
4112 |
|
|
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
4113 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
4114 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
4115 |
|
|
src/io/ShapeAtomTypesSectionParser.cpp, |
4116 |
|
|
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
4117 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
4118 |
|
|
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
4119 |
|
|
bounds overwrite (I think...). At least the parser loads the |
4120 |
|
|
forcefield fine... |
4121 |
|
|
|
4122 |
chrisfen |
3131 |
2005-04-18 08:44 chrisfen |
4123 |
chrisfen |
2229 |
|
4124 |
|
|
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
4125 |
|
|
Mac (capitalization confusion of filenames) |
4126 |
|
|
|
4127 |
chrisfen |
3131 |
2005-04-17 20:50 chrisfen |
4128 |
chrisfen |
2229 |
|
4129 |
|
|
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
4130 |
|
|
UseTheForce/Shapes_FF.cpp, |
4131 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
4132 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
4133 |
|
|
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
4134 |
|
|
|
4135 |
chrisfen |
3131 |
2005-04-15 15:43 gezelter |
4136 |
chrisfen |
2229 |
|
4137 |
|
|
* README: gmake in case people forget |
4138 |
|
|
|
4139 |
chrisfen |
3131 |
2005-04-15 15:40 gezelter |
4140 |
chrisfen |
2229 |
|
4141 |
|
|
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
4142 |
|
|
banner. Vanity. |
4143 |
|
|
|
4144 |
chrisfen |
3131 |
2005-04-15 15:22 gezelter |
4145 |
chrisfen |
2229 |
|
4146 |
|
|
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
4147 |
|
|
in banner (and version numbers in config.h) |
4148 |
|
|
|
4149 |
chrisfen |
3131 |
2005-04-15 15:22 gezelter |
4150 |
chrisfen |
2229 |
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4151 |
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* ChangeLog, LICENSE, README: Documentation changes |
4152 |
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4153 |
chrisfen |
3131 |
2005-04-15 15:03 gezelter |
4154 |
gezelter |
2205 |
|
4155 |
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* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
4156 |
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UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
4157 |
|
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UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
4158 |
|
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UseTheForce/ForceFieldCreator.hpp, |
4159 |
|
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UseTheForce/ForceFieldFactory.cpp, |
4160 |
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UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
4161 |
|
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UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
4162 |
|
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UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
4163 |
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UseTheForce/notifyCutoffs.F90, |
4164 |
|
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UseTheForce/notifyCutoffs_interface.F90, |
4165 |
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UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
4166 |
|
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UseTheForce/DarkSide/atype.F90, |
4167 |
|
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UseTheForce/DarkSide/atype_interface.F90, |
4168 |
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UseTheForce/DarkSide/eam.F90, |
4169 |
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UseTheForce/DarkSide/eam_interface.F90, |
4170 |
|
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UseTheForce/DarkSide/eam_interface.h, |
4171 |
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UseTheForce/DarkSide/electrostatic.F90, |
4172 |
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UseTheForce/DarkSide/electrostatic_interface.F90, |
4173 |
|
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UseTheForce/DarkSide/electrostatic_interface.h, |
4174 |
|
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UseTheForce/DarkSide/force_globals.F90, |
4175 |
|
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UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
4176 |
|
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UseTheForce/DarkSide/lj_interface.F90, |
4177 |
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UseTheForce/DarkSide/lj_interface.h, |
4178 |
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UseTheForce/DarkSide/neighborLists.F90, |
4179 |
|
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UseTheForce/DarkSide/reactionField.F90, |
4180 |
|
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UseTheForce/DarkSide/shapes.F90, |
4181 |
|
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UseTheForce/DarkSide/shapes_interface.F90, |
4182 |
|
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UseTheForce/DarkSide/shapes_interface.h, |
4183 |
|
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UseTheForce/DarkSide/simParallel.F90, |
4184 |
|
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UseTheForce/DarkSide/simParallel_interface.F90, |
4185 |
|
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UseTheForce/DarkSide/simParallel_interface.h, |
4186 |
|
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UseTheForce/DarkSide/simulation.F90, |
4187 |
|
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UseTheForce/DarkSide/simulation_interface.F90, |
4188 |
|
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UseTheForce/DarkSide/simulation_interface.h, |
4189 |
|
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UseTheForce/DarkSide/sticky.F90, |
4190 |
|
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UseTheForce/DarkSide/sticky_interface.F90, |
4191 |
|
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UseTheForce/DarkSide/sticky_interface.h, |
4192 |
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UseTheForce/DarkSide/switcheroo.F90, |
4193 |
|
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applications/dump2Xyz/Dump2XYZ.cpp, |
4194 |
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applications/dump2Xyz/Dump2XYZCmd.c, |
4195 |
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applications/dump2Xyz/Dump2XYZCmd.h, |
4196 |
|
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applications/dynamicProps/CrossTimeCorrFunc.cpp, |
4197 |
|
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applications/dynamicProps/CrossTimeCorrFunc.hpp, |
4198 |
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applications/dynamicProps/DipoleCorrFunc.cpp, |
4199 |
|
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applications/dynamicProps/DipoleCorrFunc.hpp, |
4200 |
|
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applications/dynamicProps/DynamicProps.cpp, |
4201 |
|
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applications/dynamicProps/DynamicPropsCmd.c, |
4202 |
|
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applications/dynamicProps/DynamicPropsCmd.h, |
4203 |
|
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applications/dynamicProps/FrameTimeCorrFunc.hpp, |
4204 |
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applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
4205 |
|
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applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
4206 |
|
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applications/dynamicProps/RCorrFunc.cpp, |
4207 |
|
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applications/dynamicProps/RCorrFunc.hpp, |
4208 |
|
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applications/dynamicProps/TimeCorrFunc.cpp, |
4209 |
|
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applications/dynamicProps/TimeCorrFunc.hpp, |
4210 |
|
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applications/dynamicProps/VCorrFunc.cpp, |
4211 |
|
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applications/dynamicProps/VCorrFunc.hpp, |
4212 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
4213 |
|
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applications/nanoRodBuilder/GeometryBuilder.hpp, |
4214 |
|
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applications/nanoRodBuilder/nanorodBuilder.cpp, |
4215 |
|
|
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
4216 |
|
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applications/nanoRodBuilder/nanorodBuilderCmd.h, |
4217 |
|
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applications/oopse/oopse.cpp, |
4218 |
|
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applications/simpleBuilder/simpleBuilder.cpp, |
4219 |
|
|
applications/simpleBuilder/simpleBuilderCmd.c, |
4220 |
|
|
applications/simpleBuilder/simpleBuilderCmd.h, |
4221 |
|
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applications/staticProps/GofAngle2.cpp, |
4222 |
|
|
applications/staticProps/GofAngle2.hpp, |
4223 |
|
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applications/staticProps/GofR.cpp, |
4224 |
|
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applications/staticProps/GofR.hpp, |
4225 |
|
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applications/staticProps/GofRAngle.cpp, |
4226 |
|
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applications/staticProps/GofRAngle.hpp, |
4227 |
|
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applications/staticProps/GofXyz.cpp, |
4228 |
|
|
applications/staticProps/GofXyz.hpp, |
4229 |
|
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applications/staticProps/RadialDistrFunc.cpp, |
4230 |
|
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applications/staticProps/RadialDistrFunc.hpp, |
4231 |
|
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applications/staticProps/StaticProps.cpp, |
4232 |
|
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applications/staticProps/StaticPropsCmd.c, |
4233 |
|
|
applications/staticProps/StaticPropsCmd.h, |
4234 |
|
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brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
4235 |
|
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brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
4236 |
|
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brains/Exclude.hpp, brains/ForceManager.cpp, |
4237 |
|
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brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
4238 |
|
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brains/MoleculeCreator.hpp, brains/Register.cpp, |
4239 |
|
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brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
4240 |
|
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brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
4241 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
4242 |
|
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brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
4243 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
4244 |
|
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brains/fSimulation.h, constraints/ConstraintElem.hpp, |
4245 |
|
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constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
4246 |
|
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constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
4247 |
|
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constraints/ZconstraintForceManager.cpp, |
4248 |
|
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constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
4249 |
|
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integrators/DLM.hpp, integrators/Integrator.cpp, |
4250 |
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integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
4251 |
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integrators/IntegratorFactory.cpp, |
4252 |
|
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integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
4253 |
|
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integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
4254 |
|
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integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
4255 |
|
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integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
4256 |
|
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integrators/NVT.cpp, integrators/NVT.hpp, |
4257 |
|
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integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
4258 |
|
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integrators/Velocitizer.hpp, |
4259 |
|
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integrators/VelocityVerletIntegrator.cpp, |
4260 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
4261 |
|
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io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
4262 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
4263 |
|
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io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
4264 |
|
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io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
4265 |
|
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io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
4266 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
4267 |
|
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io/DirectionalAtomTypesSectionParser.cpp, |
4268 |
|
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io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
4269 |
|
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io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
4270 |
|
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io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
4271 |
|
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io/Globals.cpp, io/Globals.hpp, |
4272 |
|
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io/LennardJonesAtomTypesSectionParser.cpp, |
4273 |
|
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io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
4274 |
|
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io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
4275 |
|
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io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
4276 |
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io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
4277 |
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io/SectionParser.cpp, io/SectionParser.hpp, |
4278 |
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io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
4279 |
|
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io/StatWriter.cpp, io/StatWriter.hpp, |
4280 |
|
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io/StickyAtomTypesSectionParser.cpp, |
4281 |
|
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io/StickyAtomTypesSectionParser.hpp, |
4282 |
|
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io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
4283 |
|
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io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
4284 |
|
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io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
4285 |
|
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io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
4286 |
|
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io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
4287 |
|
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io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
4288 |
|
|
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
4289 |
|
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lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
4290 |
|
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lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
4291 |
|
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lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
4292 |
|
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math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
4293 |
|
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math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
4294 |
|
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math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
4295 |
|
|
math/Quaternion.hpp, math/RandNumGen.hpp, |
4296 |
|
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math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
4297 |
|
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math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
4298 |
|
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math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
4299 |
|
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math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
4300 |
|
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minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
4301 |
|
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minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
4302 |
|
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minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
4303 |
|
|
minimizers/MinimizerFactory.hpp, |
4304 |
|
|
minimizers/MinimizerParameterSet.cpp, |
4305 |
|
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minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
4306 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
4307 |
|
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minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
4308 |
|
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primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
4309 |
|
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primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
4310 |
|
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primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
4311 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
4312 |
|
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primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
4313 |
|
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primitives/Molecule.cpp, primitives/Molecule.hpp, |
4314 |
|
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primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
4315 |
|
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primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
4316 |
|
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primitives/Torsion.cpp, primitives/Torsion.hpp, |
4317 |
|
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primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
4318 |
|
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profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
4319 |
|
|
profiling/timing.F90, restraints/Restraints.cpp, |
4320 |
|
|
restraints/Restraints.hpp, |
4321 |
|
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restraints/ThermoIntegrationForceManager.cpp, |
4322 |
|
|
restraints/ThermoIntegrationForceManager.hpp, |
4323 |
|
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selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
4324 |
|
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selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
4325 |
|
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selection/NameFinder.cpp, selection/NameFinder.hpp, |
4326 |
|
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selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
4327 |
|
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selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
4328 |
|
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selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
4329 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
4330 |
|
|
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
4331 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
4332 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
4333 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
4334 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
4335 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
4336 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
4337 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
4338 |
|
|
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
4339 |
|
|
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
4340 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
4341 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
4342 |
|
|
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
4343 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
4344 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
4345 |
|
|
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
4346 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
4347 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
4348 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
4349 |
|
|
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
4350 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
4351 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
4352 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
4353 |
|
|
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
4354 |
|
|
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
4355 |
|
|
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
4356 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
4357 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
4358 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
4359 |
|
|
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
4360 |
|
|
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
4361 |
|
|
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
4362 |
|
|
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
4363 |
|
|
utils/residentMem.h, utils/simError.c, utils/simError.h, |
4364 |
|
|
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
4365 |
|
|
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
4366 |
|
|
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
4367 |
|
|
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
4368 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
4369 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
4370 |
|
|
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
4371 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
4372 |
|
|
been drafted to perform our indentation services |
4373 |
|
|
|
4374 |
chrisfen |
3131 |
2005-04-15 15:03 gezelter |
4375 |
gezelter |
2205 |
|
4376 |
|
|
* configure, ac-tools/configure.in: Jedi mind-trick warning |
4377 |
|
|
messages have been added to make users ignore CGAL. |
4378 |
|
|
|
4379 |
chrisfen |
3131 |
2005-04-15 11:41 tim |
4380 |
gezelter |
2205 |
|
4381 |
|
|
* make/Makefile.in: fix make install |
4382 |
|
|
|
4383 |
chrisfen |
3131 |
2005-04-15 11:41 tim |
4384 |
gezelter |
2205 |
|
4385 |
|
|
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
4386 |
|
|
add Makefile of samples |
4387 |
|
|
|
4388 |
chrisfen |
3131 |
2005-04-15 11:33 tim |
4389 |
gezelter |
2205 |
|
4390 |
|
|
* samples/: lipid/Makefile, water/dimer/Makefile, |
4391 |
|
|
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
4392 |
|
|
installed correctly |
4393 |
|
|
|
4394 |
chrisfen |
3131 |
2005-04-14 14:41 gezelter |
4395 |
gezelter |
2205 |
|
4396 |
|
|
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
4397 |
|
|
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
4398 |
|
|
scripts/filepp, scripts/filepp.in: configure now searches for perl |
4399 |
|
|
to use with filepp |
4400 |
|
|
|
4401 |
chrisfen |
3131 |
2005-04-14 14:20 gezelter |
4402 |
tim |
2102 |
|
4403 |
gezelter |
2199 |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
4404 |
|
|
MoLocator |
4405 |
|
|
|
4406 |
chrisfen |
3131 |
2005-04-14 12:12 gezelter |
4407 |
gezelter |
2199 |
|
4408 |
|
|
* LICENSE: [no log message] |
4409 |
|
|
|
4410 |
chrisfen |
3131 |
2005-04-14 09:10 chuckv |
4411 |
gezelter |
2199 |
|
4412 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
4413 |
|
|
nanorodbuilder now exit's when libCGAL is not present. |
4414 |
|
|
|
4415 |
chrisfen |
3131 |
2005-04-14 08:20 tim |
4416 |
gezelter |
2199 |
|
4417 |
|
|
* src/io/make_nodes.h: fix one more warning message in make_nodes |
4418 |
|
|
|
4419 |
chrisfen |
3131 |
2005-04-13 16:36 chuckv |
4420 |
gezelter |
2199 |
|
4421 |
|
|
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
4422 |
|
|
interface name for SGI Compiler |
4423 |
|
|
|
4424 |
chrisfen |
3131 |
2005-04-13 16:29 chrisfen |
4425 |
gezelter |
2199 |
|
4426 |
|
|
* samples/water/ssde/ssde.md: oops... bad sample |
4427 |
|
|
|
4428 |
chrisfen |
3131 |
2005-04-13 16:00 chuckv |
4429 |
gezelter |
2199 |
|
4430 |
|
|
* src/config.h.in: Change typo in CGAL. |
4431 |
|
|
|
4432 |
chrisfen |
3131 |
2005-04-13 15:43 tim |
4433 |
gezelter |
2199 |
|
4434 |
|
|
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
4435 |
|
|
selection/SelectionCompiler.hpp: fix some warning messages |
4436 |
|
|
|
4437 |
chrisfen |
3131 |
2005-04-13 15:30 gezelter |
4438 |
gezelter |
2199 |
|
4439 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
4440 |
|
|
make/Makefile.in, src/config.h.in, |
4441 |
|
|
src/applications/nanoRodBuilder/Makefile, |
4442 |
|
|
src/applications/nanoRodBuilder/Makefile.in, |
4443 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
4444 |
|
|
checks |
4445 |
|
|
|
4446 |
chrisfen |
3131 |
2005-04-13 13:36 chuckv |
4447 |
gezelter |
2199 |
|
4448 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
4449 |
|
|
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
4450 |
|
|
DarkSide/electrostatic_interface.F90, |
4451 |
|
|
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
4452 |
|
|
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
4453 |
|
|
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
4454 |
|
|
destroy methods for Fortran modules. |
4455 |
|
|
|
4456 |
chrisfen |
3131 |
2005-04-13 13:17 chuckv |
4457 |
gezelter |
2199 |
|
4458 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
4459 |
|
|
shapes_interface.h: Added destroy method to clean up memory |
4460 |
|
|
|
4461 |
chrisfen |
3131 |
2005-04-13 11:41 tim |
4462 |
gezelter |
2199 |
|
4463 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4464 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4465 |
|
|
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
4466 |
|
|
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
4467 |
|
|
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
4468 |
|
|
fixed |
4469 |
|
|
|
4470 |
chrisfen |
3131 |
2005-04-12 15:44 chuckv |
4471 |
gezelter |
2199 |
|
4472 |
|
|
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
4473 |
|
|
for nanoRodBuilder. |
4474 |
|
|
|
4475 |
chrisfen |
3131 |
2005-04-12 15:42 tim |
4476 |
gezelter |
2199 |
|
4477 |
|
|
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
4478 |
|
|
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
4479 |
|
|
and simpleBuilder(forget to delete lattice) |
4480 |
|
|
|
4481 |
chrisfen |
3131 |
2005-04-12 15:33 tim |
4482 |
gezelter |
2199 |
|
4483 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4484 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
4485 |
|
|
refactory lattice |
4486 |
|
|
|
4487 |
chrisfen |
3131 |
2005-04-12 15:07 tim |
4488 |
gezelter |
2199 |
|
4489 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
4490 |
|
|
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
4491 |
|
|
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
4492 |
|
|
LatticeFactory and LatticeCreator |
4493 |
|
|
|
4494 |
chrisfen |
3131 |
2005-04-12 14:58 tim |
4495 |
gezelter |
2199 |
|
4496 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4497 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
4498 |
|
|
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
4499 |
|
|
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
4500 |
|
|
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
4501 |
|
|
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
4502 |
|
|
|
4503 |
chrisfen |
3131 |
2005-04-12 14:28 gezelter |
4504 |
gezelter |
2199 |
|
4505 |
|
|
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
4506 |
|
|
vector_class.F90: cleaned up vector_class memory leak fix by |
4507 |
|
|
deallocating in reverse order of how we allocated. Also migrated |
4508 |
|
|
MoLocator into utils directory |
4509 |
|
|
|
4510 |
chrisfen |
3131 |
2005-04-12 14:27 gezelter |
4511 |
gezelter |
2199 |
|
4512 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
4513 |
|
|
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
4514 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
4515 |
|
|
directory |
4516 |
|
|
|
4517 |
chrisfen |
3131 |
2005-04-12 14:27 gezelter |
4518 |
gezelter |
2199 |
|
4519 |
|
|
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
4520 |
|
|
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
4521 |
|
|
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
4522 |
|
|
nanoRodBuilder/LatticeCreator.hpp, |
4523 |
|
|
nanoRodBuilder/LatticeFactory.cpp, |
4524 |
|
|
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
4525 |
|
|
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
4526 |
|
|
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
4527 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
4528 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
4529 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
4530 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
4531 |
|
|
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
4532 |
|
|
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
4533 |
|
|
these files are now redundant |
4534 |
|
|
|
4535 |
chrisfen |
3131 |
2005-04-12 14:27 gezelter |
4536 |
gezelter |
2199 |
|
4537 |
|
|
* src/UseTheForce/DarkSide/: atype_interface.F90, |
4538 |
|
|
atype_interface.h: cleaned up memory leak fix |
4539 |
|
|
|
4540 |
chrisfen |
3131 |
2005-04-12 14:26 gezelter |
4541 |
gezelter |
2199 |
|
4542 |
|
|
* make/Makefile.in: added lattice subdirectory |
4543 |
|
|
|
4544 |
chrisfen |
3131 |
2005-04-12 13:57 chrisfen |
4545 |
gezelter |
2199 |
|
4546 |
|
|
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
4547 |
|
|
a space by accident |
4548 |
|
|
|
4549 |
chrisfen |
3131 |
2005-04-12 13:56 chrisfen |
4550 |
gezelter |
2199 |
|
4551 |
|
|
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
4552 |
|
|
quadrupole sample |
4553 |
|
|
|
4554 |
chrisfen |
3131 |
2005-04-12 13:56 chrisfen |
4555 |
gezelter |
2199 |
|
4556 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
4557 |
|
|
samples |
4558 |
|
|
|
4559 |
chrisfen |
3131 |
2005-04-12 11:30 tim |
4560 |
gezelter |
2199 |
|
4561 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
4562 |
|
|
type in fortran side |
4563 |
|
|
|
4564 |
chrisfen |
3131 |
2005-04-12 10:45 chuckv |
4565 |
gezelter |
2199 |
|
4566 |
|
|
* src/utils/vector_class.F90: Further changes to vector_class |
4567 |
|
|
destroy function. |
4568 |
|
|
|
4569 |
chrisfen |
3131 |
2005-04-12 10:39 chuckv |
4570 |
gezelter |
2199 |
|
4571 |
|
|
* src/utils/vector_class.F90: Fixed pointer memory leak in |
4572 |
|
|
vector_class. |
4573 |
|
|
|
4574 |
chrisfen |
3131 |
2005-04-12 10:12 chuckv |
4575 |
gezelter |
2199 |
|
4576 |
|
|
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
4577 |
|
|
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
4578 |
|
|
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
4579 |
|
|
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
4580 |
|
|
|
4581 |
chrisfen |
3131 |
2005-04-12 07:24 chrisfen |
4582 |
gezelter |
2199 |
|
4583 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
4584 |
|
|
output |
4585 |
|
|
|
4586 |
chrisfen |
3131 |
2005-04-11 17:29 chuckv |
4587 |
gezelter |
2199 |
|
4588 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
4589 |
|
|
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
4590 |
|
|
|
4591 |
chrisfen |
3131 |
2005-04-11 17:28 chuckv |
4592 |
gezelter |
2199 |
|
4593 |
|
|
* src/utils/vector_class.F90: Added code to delete vector. |
4594 |
|
|
|
4595 |
chrisfen |
3131 |
2005-04-11 14:58 tim |
4596 |
gezelter |
2199 |
|
4597 |
|
|
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
4598 |
|
|
basic_ifstrstream |
4599 |
|
|
|
4600 |
chrisfen |
3131 |
2005-04-11 14:37 chuckv |
4601 |
gezelter |
2199 |
|
4602 |
|
|
* make/Makefile.in, |
4603 |
|
|
src/applications/nanoRodBuilder/BaseLattice.cpp, |
4604 |
|
|
src/applications/nanoRodBuilder/BaseLattice.hpp, |
4605 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
4606 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
4607 |
|
|
src/applications/nanoRodBuilder/Lattice.cpp, |
4608 |
|
|
src/applications/nanoRodBuilder/Lattice.hpp, |
4609 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
4610 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
4611 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
4612 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
4613 |
|
|
src/applications/nanoRodBuilder/Makefile, |
4614 |
|
|
src/applications/nanoRodBuilder/MoLocator.cpp, |
4615 |
|
|
src/applications/nanoRodBuilder/MoLocator.hpp, |
4616 |
|
|
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
4617 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
4618 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
4619 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
4620 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
4621 |
|
|
nanoRodBuilder application (may not work yet). ((Doesn't work |
4622 |
|
|
yet.)) (((May never work....))) |
4623 |
|
|
|
4624 |
chrisfen |
3131 |
2005-04-11 13:54 tim |
4625 |
gezelter |
2199 |
|
4626 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
4627 |
|
|
prepareVisitor in Dump2XYZ |
4628 |
|
|
|
4629 |
chrisfen |
3131 |
2005-04-11 13:19 chrisfen |
4630 |
gezelter |
2199 |
|
4631 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
4632 |
|
|
quadrupoles. look! it's divide by 3 like stone says! |
4633 |
|
|
|
4634 |
chrisfen |
3131 |
2005-04-11 13:18 chrisfen |
4635 |
gezelter |
2199 |
|
4636 |
|
|
* forceFields/DUFF2.frc: fixing of the quadrupoles |
4637 |
|
|
|
4638 |
chrisfen |
3131 |
2005-04-11 13:16 tim |
4639 |
gezelter |
2199 |
|
4640 |
|
|
* src/selection/Token.hpp: change the parameter name in |
4641 |
|
|
constructors |
4642 |
|
|
|
4643 |
chrisfen |
3131 |
2005-04-11 12:49 gezelter |
4644 |
gezelter |
2199 |
|
4645 |
|
|
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
4646 |
|
|
|
4647 |
chrisfen |
3131 |
2005-04-11 12:06 gezelter |
4648 |
gezelter |
2199 |
|
4649 |
|
|
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
4650 |
|
|
versions < 3.80 |
4651 |
|
|
|
4652 |
chrisfen |
3131 |
2005-04-11 09:13 gezelter |
4653 |
gezelter |
2199 |
|
4654 |
|
|
* make/Makefile.in, src/UseTheForce/Makefile, |
4655 |
|
|
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
4656 |
|
|
some stuff to clean out module files during "make clean" |
4657 |
|
|
|
4658 |
chrisfen |
3131 |
2005-04-08 15:13 chrisfen |
4659 |
gezelter |
2199 |
|
4660 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
4661 |
|
|
interactions should be working with a remaining question of |
4662 |
|
|
interaction magnitude |
4663 |
|
|
|
4664 |
chrisfen |
3131 |
2005-04-08 15:12 chrisfen |
4665 |
gezelter |
2199 |
|
4666 |
|
|
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
4667 |
|
|
samples |
4668 |
|
|
|
4669 |
chrisfen |
3131 |
2005-04-08 11:48 chrisfen |
4670 |
gezelter |
2199 |
|
4671 |
|
|
* samples/water/ssd/ssd.md: oops... messed up a sample |
4672 |
|
|
|
4673 |
chrisfen |
3131 |
2005-04-08 07:43 chrisfen |
4674 |
gezelter |
2199 |
|
4675 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
4676 |
|
|
charge-dipole interactions |
4677 |
|
|
|
4678 |
chrisfen |
3131 |
2005-04-08 07:42 chrisfen |
4679 |
gezelter |
2199 |
|
4680 |
|
|
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
4681 |
|
|
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
4682 |
|
|
|
4683 |
chrisfen |
3131 |
2005-04-08 07:41 chrisfen |
4684 |
gezelter |
2199 |
|
4685 |
|
|
* forceFields/DUFF2.frc: added Cl- and Na+ |
4686 |
|
|
|
4687 |
chrisfen |
3131 |
2005-04-06 16:59 tim |
4688 |
gezelter |
2199 |
|
4689 |
|
|
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
4690 |
|
|
|
4691 |
chrisfen |
3131 |
2005-04-05 16:09 tim |
4692 |
gezelter |
2199 |
|
4693 |
|
|
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
4694 |
|
|
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
4695 |
|
|
in atom type name;clean the code a little bit |
4696 |
|
|
|
4697 |
chrisfen |
3131 |
2005-03-29 13:00 tim |
4698 |
gezelter |
2199 |
|
4699 |
|
|
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
4700 |
|
|
in converting rotation matrix to quaternion |
4701 |
|
|
|
4702 |
chrisfen |
3131 |
2005-03-28 14:41 tim |
4703 |
gezelter |
2199 |
|
4704 |
|
|
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
4705 |
|
|
|
4706 |
chrisfen |
3131 |
2005-03-28 14:30 tim |
4707 |
gezelter |
2199 |
|
4708 |
|
|
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
4709 |
|
|
the wrapping |
4710 |
|
|
|
4711 |
chrisfen |
3131 |
2005-03-28 07:54 tim |
4712 |
gezelter |
2199 |
|
4713 |
|
|
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
4714 |
|
|
dimension of histogram |
4715 |
|
|
|
4716 |
chrisfen |
3131 |
2005-03-22 08:38 tim |
4717 |
gezelter |
2199 |
|
4718 |
|
|
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
4719 |
|
|
src/applications/dynamicProps/Makefile, |
4720 |
|
|
src/applications/oopse/Makefile, |
4721 |
|
|
src/applications/simpleBuilder/Makefile, |
4722 |
|
|
src/applications/staticProps/Makefile: avoid building parallel |
4723 |
|
|
executable for dump2XYZ, simpleBuilder, staticProps and |
4724 |
|
|
dynamicProps |
4725 |
|
|
|
4726 |
chrisfen |
3131 |
2005-03-21 14:34 chrisfen |
4727 |
gezelter |
2199 |
|
4728 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
4729 |
|
|
forcefield files |
4730 |
|
|
|
4731 |
chrisfen |
3131 |
2005-03-21 12:51 chrisfen |
4732 |
gezelter |
2199 |
|
4733 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
4734 |
|
|
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
4735 |
|
|
data for reaction_field |
4736 |
|
|
|
4737 |
chrisfen |
3131 |
2005-03-21 12:50 chrisfen |
4738 |
gezelter |
2199 |
|
4739 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
4740 |
|
|
WILL CHANGE THIS BACK, RIGHT? |
4741 |
|
|
|
4742 |
chrisfen |
3131 |
2005-03-21 11:23 gezelter |
4743 |
gezelter |
2199 |
|
4744 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
4745 |
|
|
correct value |
4746 |
|
|
|
4747 |
chrisfen |
3131 |
2005-03-21 11:22 gezelter |
4748 |
gezelter |
2199 |
|
4749 |
|
|
* make/Makefile.in: fixed an install-related bug. |
4750 |
|
|
$(InstallCommand) had been set to $(InstallData) |
4751 |
|
|
|
4752 |
chrisfen |
3131 |
2005-03-15 06:21 gezelter |
4753 |
gezelter |
2199 |
|
4754 |
|
|
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
4755 |
|
|
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
4756 |
|
|
|
4757 |
chrisfen |
3131 |
2005-03-15 06:20 gezelter |
4758 |
gezelter |
2199 |
|
4759 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
4760 |
|
|
|
4761 |
chrisfen |
3131 |
2005-03-12 23:39 gezelter |
4762 |
gezelter |
2199 |
|
4763 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
4764 |
|
|
charge-quadrupole interactions |
4765 |
|
|
|
4766 |
chrisfen |
3131 |
2005-03-12 11:12 chrisfen |
4767 |
gezelter |
2199 |
|
4768 |
|
|
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
4769 |
|
|
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
4770 |
|
|
|
4771 |
chrisfen |
3131 |
2005-03-12 11:05 chrisfen |
4772 |
gezelter |
2199 |
|
4773 |
|
|
* samples/thermoIntegration/liquid/ssde.in, |
4774 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
4775 |
|
|
samples/thermoIntegration/liquid/water.md, |
4776 |
|
|
samples/thermoIntegration/solid/idealCrystal.in, |
4777 |
|
|
samples/thermoIntegration/solid/ssde.in, |
4778 |
|
|
samples/thermoIntegration/solid/ssde.md, |
4779 |
|
|
samples/thermoIntegration/solid/ssde.zang0, |
4780 |
|
|
samples/thermoIntegration/solid/water.md, |
4781 |
|
|
samples/water/tip3p_ice/tp3.md, |
4782 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
4783 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: added some |
4784 |
|
|
samples |
4785 |
|
|
|
4786 |
chrisfen |
3131 |
2005-03-11 09:50 tim |
4787 |
gezelter |
2199 |
|
4788 |
|
|
* src/: brains/SimCreator.cpp, |
4789 |
|
|
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
4790 |
|
|
MultipoleAtomTypesSectionParser |
4791 |
|
|
|
4792 |
chrisfen |
3131 |
2005-03-11 07:55 tim |
4793 |
gezelter |
2199 |
|
4794 |
|
|
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
4795 |
|
|
excluded |
4796 |
|
|
|
4797 |
chrisfen |
3131 |
2005-03-11 07:53 gezelter |
4798 |
gezelter |
2199 |
|
4799 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
4800 |
|
|
quadrupoles |
4801 |
|
|
|
4802 |
chrisfen |
3131 |
2005-03-11 07:52 gezelter |
4803 |
gezelter |
2199 |
|
4804 |
|
|
* forceFields/DUFF2.frc: quadrupoles for SSD models |
4805 |
|
|
|
4806 |
chrisfen |
3131 |
2005-03-11 07:00 tim |
4807 |
gezelter |
2199 |
|
4808 |
|
|
* ChangeLog, doc/SelectionExpression.html, |
4809 |
|
|
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
4810 |
|
|
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
4811 |
|
|
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
4812 |
|
|
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
4813 |
|
|
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
4814 |
|
|
SelectionExpression.html |
4815 |
|
|
|
4816 |
chrisfen |
3131 |
2005-03-10 16:43 chrisfen |
4817 |
gezelter |
2199 |
|
4818 |
tim |
2116 |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
4819 |
|
|
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
4820 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
4821 |
|
|
MPI restraints |
4822 |
|
|
|
4823 |
chrisfen |
3131 |
2005-03-10 15:56 tim |
4824 |
tim |
2116 |
|
4825 |
|
|
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
4826 |
|
|
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
4827 |
|
|
and cutoff group |
4828 |
|
|
|
4829 |
chrisfen |
3131 |
2005-03-10 14:06 gezelter |
4830 |
tim |
2116 |
|
4831 |
|
|
* src/types/MorseBondType.hpp: fixed a doxygen problem |
4832 |
|
|
|
4833 |
chrisfen |
3131 |
2005-03-10 13:51 gezelter |
4834 |
tim |
2116 |
|
4835 |
|
|
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
4836 |
|
|
the split dipole test cases |
4837 |
|
|
|
4838 |
chrisfen |
3131 |
2005-03-10 13:51 gezelter |
4839 |
tim |
2116 |
|
4840 |
|
|
* doc/SelectionExpression.html: updated some documentation |
4841 |
|
|
|
4842 |
chrisfen |
3131 |
2005-03-10 12:40 gezelter |
4843 |
tim |
2116 |
|
4844 |
|
|
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
4845 |
|
|
Makefile: LinkedList removal project starts now |
4846 |
|
|
|
4847 |
chrisfen |
3131 |
2005-03-10 12:28 tim |
4848 |
tim |
2116 |
|
4849 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4850 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
4851 |
|
|
using map to replace link list |
4852 |
|
|
|
4853 |
chrisfen |
3131 |
2005-03-10 11:11 tim |
4854 |
tim |
2116 |
|
4855 |
|
|
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
4856 |
|
|
case of split dipole |
4857 |
|
|
|
4858 |
chrisfen |
3131 |
2005-03-10 11:10 chrisfen |
4859 |
tim |
2116 |
|
4860 |
|
|
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
4861 |
|
|
src/io/RestWriter.cpp, |
4862 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
4863 |
|
|
builds... |
4864 |
|
|
|
4865 |
chrisfen |
3131 |
2005-03-10 10:44 tim |
4866 |
tim |
2116 |
|
4867 |
|
|
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
4868 |
|
|
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
4869 |
|
|
adding test case for split dipole |
4870 |
|
|
|
4871 |
chrisfen |
3131 |
2005-03-10 09:54 gezelter |
4872 |
tim |
2116 |
|
4873 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
4874 |
|
|
support for split dipoles |
4875 |
|
|
|
4876 |
chrisfen |
3131 |
2005-03-10 08:27 chrisfen |
4877 |
tim |
2116 |
|
4878 |
|
|
* samples/water/tip3p_ice/tp3.md, |
4879 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
4880 |
|
|
restraints |
4881 |
|
|
|
4882 |
chrisfen |
3131 |
2005-03-10 08:15 chrisfen |
4883 |
tim |
2116 |
|
4884 |
|
|
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
4885 |
|
|
src/UseTheForce/ForceFields.hpp, |
4886 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
4887 |
|
|
|
4888 |
chrisfen |
3131 |
2005-03-10 08:14 tim |
4889 |
tim |
2116 |
|
4890 |
|
|
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
4891 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
4892 |
|
|
src/selection/SelectionEvaluator.cpp: minor change |
4893 |
|
|
|
4894 |
chrisfen |
3131 |
2005-03-10 07:10 chrisfen |
4895 |
tim |
2116 |
|
4896 |
tim |
2102 |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
4897 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
4898 |
|
|
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
4899 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
4900 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
4901 |
|
|
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
4902 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
4903 |
|
|
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
4904 |
|
|
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
4905 |
|
|
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
4906 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
4907 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp, |
4908 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
4909 |
|
|
the new restraints code |
4910 |
|
|
|
4911 |
chrisfen |
3131 |
2005-03-09 10:48 tim |
4912 |
tim |
2102 |
|
4913 |
|
|
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
4914 |
|
|
IndexFinder |
4915 |
|
|
|
4916 |
chrisfen |
3131 |
2005-03-09 10:46 tim |
4917 |
tim |
2102 |
|
4918 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
4919 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
4920 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
4921 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
4922 |
|
|
fix compilation issue |
4923 |
|
|
|
4924 |
chrisfen |
3131 |
2005-03-09 09:58 tim |
4925 |
tim |
2102 |
|
4926 |
|
|
* forceFields/DUFF2.frc, scripts/filepp, |
4927 |
|
|
src/UseTheForce/EAM_FF.cpp, |
4928 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
4929 |
|
|
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
4930 |
|
|
in SectionParser (lineNo is not updated) |
4931 |
|
|
|
4932 |
chrisfen |
3131 |
2005-03-09 09:30 tim |
4933 |
tim |
2102 |
|
4934 |
|
|
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
4935 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
4936 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
4937 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
4938 |
|
|
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
4939 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
4940 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
4941 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
4942 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
4943 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
4944 |
|
|
io/SectionParserManager.cpp, selection/Makefile, |
4945 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
4946 |
|
|
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
4947 |
|
|
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
4948 |
|
|
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
4949 |
|
|
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
4950 |
|
|
into ChargeAtomTypesSectionParser and |
4951 |
|
|
MultipoleAtomTypesSectionParser;remove print dipole option from |
4952 |
|
|
Dump2XYZ; |
4953 |
|
|
|
4954 |
chrisfen |
3131 |
2005-03-09 09:28 tim |
4955 |
tim |
2102 |
|
4956 |
|
|
* forceFields/DUFF2.frc: change the format of DUFF2 |
4957 |
|
|
|
4958 |
chrisfen |
3131 |
2005-03-09 07:44 gezelter |
4959 |
tim |
2102 |
|
4960 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, |
4961 |
|
|
electrostatic_interface.F90, electrostatic_interface.h: new |
4962 |
|
|
electrostatic module |
4963 |
|
|
|
4964 |
chrisfen |
3131 |
2005-03-09 06:26 gezelter |
4965 |
tim |
2102 |
|
4966 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
4967 |
|
|
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
4968 |
|
|
and fixed quadrupole stuff |
4969 |
|
|
|
4970 |
chrisfen |
3131 |
2005-03-09 06:25 gezelter |
4971 |
tim |
2102 |
|
4972 |
|
|
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
4973 |
|
|
for outdated charge and dipole interfaces |
4974 |
|
|
|
4975 |
chrisfen |
3131 |
2005-03-08 13:08 gezelter |
4976 |
tim |
2102 |
|
4977 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
4978 |
|
|
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
4979 |
|
|
charge-dipole test cases |
4980 |
|
|
|
4981 |
chrisfen |
3131 |
2005-03-08 13:07 gezelter |
4982 |
tim |
2102 |
|
4983 |
|
|
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
4984 |
|
|
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
4985 |
|
|
strange icc8 bug (we think). |
4986 |
|
|
|
4987 |
chrisfen |
3131 |
2005-03-08 13:07 gezelter |
4988 |
tim |
2102 |
|
4989 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
4990 |
|
|
|
4991 |
chrisfen |
3131 |
2005-03-08 13:07 gezelter |
4992 |
tim |
2102 |
|
4993 |
|
|
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
4994 |
|
|
Unification Project |
4995 |
|
|
|
4996 |
chrisfen |
3131 |
2005-03-08 13:07 gezelter |
4997 |
tim |
2102 |
|
4998 |
|
|
* src/io/Globals.cpp: Dunno |
4999 |
|
|
|
5000 |
chrisfen |
3131 |
2005-03-08 13:06 gezelter |
5001 |
tim |
2102 |
|
5002 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
5003 |
|
|
OOPSE_itoa and checking a NULL left over from the LinkedList days |
5004 |
|
|
|
5005 |
chrisfen |
3131 |
2005-03-08 13:06 gezelter |
5006 |
tim |
2102 |
|
5007 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
5008 |
|
|
atype_interface.F90, atype_interface.h, charge.F90, |
5009 |
|
|
charge_interface.F90, charge_interface.h, dipole.F90, |
5010 |
|
|
dipole_interface.F90, dipole_interface.h: electrostatic unification |
5011 |
|
|
project fixed an uninitialized variable in Lennard Jones mixing map |
5012 |
|
|
|
5013 |
chrisfen |
3131 |
2005-03-08 13:05 gezelter |
5014 |
tim |
2102 |
|
5015 |
|
|
* src/UseTheForce/doForces.F90: electrostatic unification project |
5016 |
|
|
|
5017 |
chrisfen |
3131 |
2005-03-08 13:05 gezelter |
5018 |
tim |
2102 |
|
5019 |
|
|
* samples/water/dimer/: two.md, water.md: making some cool test |
5020 |
|
|
cases |
5021 |
|
|
|
5022 |
chrisfen |
3131 |
2005-03-08 13:05 gezelter |
5023 |
tim |
2102 |
|
5024 |
|
|
* forceFields/DUFF2.frc: Added a charge for Chlorine |
5025 |
|
|
|
5026 |
chrisfen |
3131 |
2005-03-07 14:39 tim |
5027 |
tim |
2102 |
|
5028 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
5029 |
|
|
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
5030 |
|
|
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
5031 |
|
|
Fixing a bug in BitSet.cpp |
5032 |
|
|
|
5033 |
chrisfen |
3131 |
2005-03-04 07:28 gezelter |
5034 |
tim |
2102 |
|
5035 |
|
|
* src/config.h.in: Cleaning up config.h.in by adding comments |
5036 |
|
|
|
5037 |
chrisfen |
3131 |
2005-03-04 07:28 gezelter |
5038 |
tim |
2102 |
|
5039 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
5040 |
|
|
src/brains/SimCreator.cpp: SPRNG eradication project |
5041 |
|
|
|
5042 |
chrisfen |
3131 |
2005-03-03 06:40 tim |
5043 |
tim |
2102 |
|
5044 |
|
|
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
5045 |
|
|
missing atom type problem) |
5046 |
|
|
|
5047 |
chrisfen |
3131 |
2005-03-02 08:29 tim |
5048 |
tim |
2102 |
|
5049 |
|
|
* src/math/RandNumGen.hpp: adding base class of Random Number |
5050 |
|
|
generator |
5051 |
|
|
|
5052 |
chrisfen |
3131 |
2005-03-02 08:28 tim |
5053 |
tim |
2102 |
|
5054 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
5055 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
5056 |
|
|
Velocitizer is not initialized which causes a seg fault |
5057 |
|
|
|
5058 |
chrisfen |
3131 |
2005-03-02 07:36 tim |
5059 |
tim |
2102 |
|
5060 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
5061 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
5062 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
5063 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
5064 |
|
|
math/SeqRandNumGen.hpp: remove default parameter from |
5065 |
|
|
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
5066 |
|
|
random number generator |
5067 |
|
|
|
5068 |
chrisfen |
3131 |
2005-03-01 23:32 tim |
5069 |
tim |
2102 |
|
5070 |
|
|
* test/math/testRandNumGen.cpp: Adding unit test for random number |
5071 |
|
|
generator |
5072 |
|
|
|
5073 |
chrisfen |
3131 |
2005-03-01 15:17 tim |
5074 |
tim |
2102 |
|
5075 |
|
|
* src/brains/Thermo.hpp: fixed a file inclusion problem |
5076 |
|
|
|
5077 |
chrisfen |
3131 |
2005-03-01 15:17 tim |
5078 |
tim |
2102 |
|
5079 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
5080 |
|
|
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
5081 |
|
|
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
5082 |
|
|
RandNumGenTestCase.hpp: fixed compilation problem |
5083 |
|
|
|
5084 |
chrisfen |
3131 |
2005-03-01 15:02 tim |
5085 |
tim |
2102 |
|
5086 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
5087 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
5088 |
|
|
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
5089 |
|
|
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
5090 |
|
|
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
5091 |
|
|
|
5092 |
chrisfen |
3131 |
2005-03-01 15:00 tim |
5093 |
tim |
2102 |
|
5094 |
|
|
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
5095 |
|
|
ParallelandNumGenTestCase.hpp: Change the name of test case |
5096 |
|
|
|
5097 |
chrisfen |
3131 |
2005-03-01 13:00 tim |
5098 |
tim |
2102 |
|
5099 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
5100 |
|
|
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
5101 |
|
|
generator |
5102 |
|
|
|
5103 |
chrisfen |
3131 |
2005-03-01 12:10 tim |
5104 |
tim |
2102 |
|
5105 |
|
|
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
5106 |
|
|
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
5107 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
5108 |
|
|
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
5109 |
|
|
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
5110 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
5111 |
|
|
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
5112 |
|
|
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
5113 |
|
|
|
5114 |
chrisfen |
3131 |
2005-03-01 11:11 tim |
5115 |
tim |
2102 |
|
5116 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
5117 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
5118 |
|
|
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
5119 |
|
|
OOPSERandNumGen |
5120 |
|
|
|
5121 |
chrisfen |
3131 |
2005-03-01 07:44 gezelter |
5122 |
tim |
2102 |
|
5123 |
|
|
* make/Makefile.in: Fixed the damned build problem with the |
5124 |
|
|
libraries not being removed in make clean and make distclean (at |
5125 |
|
|
least we think it is fixed). |
5126 |
|
|
|
5127 |
chrisfen |
3131 |
2005-03-01 07:26 gezelter |
5128 |
tim |
2102 |
|
5129 |
|
|
* src/math/MersenneTwister.hpp: Making small modifications to allow |
5130 |
|
|
for use on MPI machines |
5131 |
|
|
|
5132 |
chrisfen |
3131 |
2005-03-01 06:45 tim |
5133 |
tim |
2102 |
|
5134 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
5135 |
|
|
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
5136 |
|
|
math/MersenneTwister.hpp: adding MersenneTwister random number |
5137 |
|
|
generator |
5138 |
|
|
|
5139 |
chrisfen |
3131 |
2005-02-28 19:55 tim |
5140 |
tim |
2102 |
|
5141 |
|
|
* src/math/MersenneTwister.hpp: Adding a modified version of |
5142 |
|
|
MersenneTwister.hpp |
5143 |
|
|
|
5144 |
chrisfen |
3131 |
2005-02-28 09:24 tim |
5145 |
tim |
2102 |
|
5146 |
|
|
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
5147 |
|
|
definition.jpg: selection expression |
5148 |
|
|
|
5149 |
chrisfen |
3131 |
2005-02-25 13:22 tim |
5150 |
tim |
2102 |
|
5151 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
5152 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
5153 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
5154 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
5155 |
|
|
types/AtomType.hpp: adding soft potential to LJ Module |
5156 |
|
|
|
5157 |
chrisfen |
3131 |
2005-02-25 08:38 tim |
5158 |
tim |
2102 |
|
5159 |
|
|
* doc/SelectionExpression.html: adding documentation for selection |
5160 |
|
|
expression |
5161 |
|
|
|
5162 |
chrisfen |
3131 |
2005-02-24 12:55 tim |
5163 |
tim |
2102 |
|
5164 |
|
|
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
5165 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
5166 |
|
|
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
5167 |
|
|
adding basic_teebuf which can operate on multiple stream |
5168 |
|
|
simutaneously. |
5169 |
|
|
|
5170 |
chrisfen |
3131 |
2005-02-22 11:26 chrisfen |
5171 |
tim |
2102 |
|
5172 |
gezelter |
2199 |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
5173 |
|
|
sample |
5174 |
|
|
|
5175 |
chrisfen |
3131 |
2005-02-22 10:56 tim |
5176 |
gezelter |
2199 |
|
5177 |
tim |
2102 |
* src/: UseTheForce/DarkSide/reactionField.F90, |
5178 |
|
|
primitives/RigidBody.cpp: reactionfield get fixed |
5179 |
|
|
|
5180 |
chrisfen |
3131 |
2005-02-21 08:57 tim |
5181 |
tim |
2102 |
|
5182 |
|
|
* src/: applications/staticProps/GofRAngle.cpp, |
5183 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
5184 |
|
|
a bug in GofRAngle |
5185 |
|
|
|
5186 |
chrisfen |
3131 |
2005-02-21 07:28 tim |
5187 |
tim |
2102 |
|
5188 |
|
|
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
5189 |
|
|
|
5190 |
chrisfen |
3131 |
2005-02-21 07:22 tim |
5191 |
tim |
2102 |
|
5192 |
|
|
* src/utils/next_combination.hpp: fix for compilation on the Sun |
5193 |
|
|
|
5194 |
chrisfen |
3131 |
2005-02-21 07:21 tim |
5195 |
tim |
2102 |
|
5196 |
|
|
* src/utils/GenericData.hpp: fix problem in sun |
5197 |
|
|
|
5198 |
chrisfen |
3131 |
2005-02-18 15:07 tim |
5199 |
tim |
2102 |
|
5200 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5201 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
5202 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
5203 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
5204 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
5205 |
|
|
applications/staticProps/GofXyz.cpp, |
5206 |
|
|
applications/staticProps/GofXyz.hpp, |
5207 |
|
|
applications/staticProps/StaticProps.cpp, |
5208 |
|
|
applications/staticProps/StaticProps.ggo, |
5209 |
|
|
applications/staticProps/StaticPropsCmd.c, |
5210 |
|
|
applications/staticProps/StaticPropsCmd.h, |
5211 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
5212 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
5213 |
|
|
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
5214 |
|
|
|
5215 |
chrisfen |
3131 |
2005-02-18 07:58 gezelter |
5216 |
tim |
2102 |
|
5217 |
|
|
* src/brains/Register.cpp: Corrected filename collision for EAM on |
5218 |
|
|
Mac OS X |
5219 |
|
|
|
5220 |
chrisfen |
3131 |
2005-02-18 07:58 gezelter |
5221 |
tim |
2102 |
|
5222 |
|
|
* src/applications/oopse/oopse.cpp: Updated copyright information |
5223 |
|
|
|
5224 |
chrisfen |
3131 |
2005-02-18 07:58 gezelter |
5225 |
tim |
2102 |
|
5226 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
5227 |
|
|
Makefile: corrected filename collision for EAM on operating systems |
5228 |
|
|
which are not case sensitive (aka Mac OS X) |
5229 |
|
|
|
5230 |
chrisfen |
3131 |
2005-02-17 12:15 tim |
5231 |
tim |
2102 |
|
5232 |
|
|
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
5233 |
|
|
|
5234 |
chrisfen |
3131 |
2005-02-17 11:50 tim |
5235 |
tim |
2102 |
|
5236 |
|
|
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
5237 |
|
|
in GofXyz |
5238 |
|
|
|
5239 |
chrisfen |
3131 |
2005-02-17 11:09 tim |
5240 |
tim |
2102 |
|
5241 |
|
|
* src/applications/staticProps/RadialDistrFunc.hpp: make |
5242 |
|
|
processHistogram non-abstrct function |
5243 |
|
|
|
5244 |
chrisfen |
3131 |
2005-02-17 10:41 tim |
5245 |
tim |
2102 |
|
5246 |
|
|
* src/applications/staticProps/GofXyz.cpp: [no log message] |
5247 |
|
|
|
5248 |
chrisfen |
3131 |
2005-02-17 10:30 tim |
5249 |
tim |
2102 |
|
5250 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
5251 |
|
|
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
5252 |
|
|
finish GofXyz |
5253 |
|
|
|
5254 |
chrisfen |
3131 |
2005-02-17 08:21 tim |
5255 |
tim |
2102 |
|
5256 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
5257 |
|
|
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
5258 |
|
|
distribution function |
5259 |
|
|
|
5260 |
chrisfen |
3131 |
2005-02-17 07:23 tim |
5261 |
tim |
2102 |
|
5262 |
|
|
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
5263 |
|
|
|
5264 |
chrisfen |
3131 |
2005-02-17 07:18 tim |
5265 |
tim |
2102 |
|
5266 |
|
|
* src/: brains/BlockSnapshotManager.cpp, |
5267 |
|
|
selection/DistanceFinder.cpp: The change of interface of BitSet |
5268 |
|
|
cause a bug in SelectionEvaluation |
5269 |
|
|
|
5270 |
chrisfen |
3131 |
2005-02-16 13:13 tim |
5271 |
tim |
2102 |
|
5272 |
|
|
* src/utils/residentMem.c: return residentMem in byte |
5273 |
|
|
|
5274 |
chrisfen |
3131 |
2005-02-16 13:00 tim |
5275 |
tim |
2102 |
|
5276 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
5277 |
|
|
a bug in writing out the value of cosang |
5278 |
|
|
|
5279 |
chrisfen |
3131 |
2005-02-16 12:43 tim |
5280 |
tim |
2102 |
|
5281 |
|
|
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
5282 |
|
|
estimate avaliable memory |
5283 |
|
|
|
5284 |
chrisfen |
3131 |
2005-02-16 12:30 tim |
5285 |
tim |
2102 |
|
5286 |
|
|
* src/: applications/staticProps/GofAngle2.cpp, |
5287 |
|
|
applications/staticProps/GofAngle2.hpp, |
5288 |
|
|
applications/staticProps/GofR.cpp, |
5289 |
|
|
applications/staticProps/GofR.hpp, |
5290 |
|
|
applications/staticProps/GofRAngle.cpp, |
5291 |
|
|
applications/staticProps/GofRAngle.hpp, |
5292 |
|
|
applications/staticProps/GofXyz.cpp, |
5293 |
|
|
applications/staticProps/GofXyz.hpp, |
5294 |
|
|
applications/staticProps/StaticProps.cpp, |
5295 |
|
|
applications/staticProps/StaticProps.ggo, |
5296 |
|
|
applications/staticProps/StaticPropsCmd.c, |
5297 |
|
|
applications/staticProps/StaticPropsCmd.h, |
5298 |
|
|
brains/BlockSnapshotManager.cpp: change the default bin number |
5299 |
|
|
|
5300 |
chrisfen |
3131 |
2005-02-16 11:36 tim |
5301 |
tim |
2102 |
|
5302 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
5303 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
5304 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
5305 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
5306 |
|
|
applications/staticProps/GofAngle2.cpp, |
5307 |
|
|
applications/staticProps/GofR.cpp, |
5308 |
|
|
applications/staticProps/GofR.hpp, |
5309 |
|
|
applications/staticProps/GofRAngle.cpp, |
5310 |
|
|
applications/staticProps/GofRAngle.hpp, |
5311 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
5312 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
5313 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
5314 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
5315 |
|
|
files;fix the problem of counting in staticProps |
5316 |
|
|
|
5317 |
chrisfen |
3131 |
2005-02-15 11:39 tim |
5318 |
tim |
2102 |
|
5319 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
5320 |
|
|
BlockSnapshotManager |
5321 |
|
|
|
5322 |
chrisfen |
3131 |
2005-02-15 11:36 tim |
5323 |
tim |
2102 |
|
5324 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
5325 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
5326 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5327 |
|
|
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
5328 |
|
|
reference counting now |
5329 |
|
|
|
5330 |
chrisfen |
3131 |
2005-02-15 09:49 tim |
5331 |
tim |
2102 |
|
5332 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
5333 |
|
|
replace std::make_pair by VariablesType::value_type to make Sun |
5334 |
|
|
Compiler happy |
5335 |
|
|
|
5336 |
chrisfen |
3131 |
2005-02-15 09:35 tim |
5337 |
tim |
2102 |
|
5338 |
|
|
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
5339 |
|
|
TokenMap, using TokenMapType::value_type instead of std::make_pair |
5340 |
|
|
to make Sun compiler happy |
5341 |
|
|
|
5342 |
chrisfen |
3131 |
2005-02-15 09:24 tim |
5343 |
tim |
2102 |
|
5344 |
|
|
* src/applications/staticProps/: GofRAngle.cpp, |
5345 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
5346 |
|
|
|
5347 |
chrisfen |
3131 |
2005-02-15 09:11 tim |
5348 |
tim |
2102 |
|
5349 |
|
|
* src/: applications/staticProps/GofR.cpp, |
5350 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
5351 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
5352 |
|
|
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
5353 |
|
|
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
5354 |
|
|
calculation problem when two selections intersect with each other |
5355 |
|
|
|
5356 |
chrisfen |
3131 |
2005-02-15 07:24 gezelter |
5357 |
tim |
2102 |
|
5358 |
|
|
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
5359 |
|
|
xlc++ |
5360 |
|
|
|
5361 |
chrisfen |
3131 |
2005-02-15 07:17 gezelter |
5362 |
tim |
2102 |
|
5363 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
5364 |
|
|
src/utils/residentMem.c: [no log message] |
5365 |
|
|
|
5366 |
chrisfen |
3131 |
2005-02-14 22:17 gezelter |
5367 |
tim |
2102 |
|
5368 |
|
|
* src/utils/residentMem.c: bug fix for null termination |
5369 |
|
|
|
5370 |
chrisfen |
3131 |
2005-02-14 22:11 gezelter |
5371 |
tim |
2102 |
|
5372 |
|
|
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
5373 |
|
|
bugfixing residentMem |
5374 |
|
|
|
5375 |
chrisfen |
3131 |
2005-02-14 21:59 gezelter |
5376 |
tim |
2102 |
|
5377 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
5378 |
|
|
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
5379 |
|
|
|
5380 |
chrisfen |
3131 |
2005-02-14 21:08 gezelter |
5381 |
tim |
2102 |
|
5382 |
|
|
* src/utils/Makefile.in: added residentMem |
5383 |
|
|
|
5384 |
chrisfen |
3131 |
2005-02-14 21:05 gezelter |
5385 |
tim |
2102 |
|
5386 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
5387 |
|
|
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
5388 |
|
|
src/utils/residentMem.h: modifications to estimate memory in use by |
5389 |
|
|
other processes autoconf fixes ps syntax checking config.h file |
5390 |
|
|
cleaning |
5391 |
|
|
|
5392 |
chrisfen |
3131 |
2005-02-14 15:26 gezelter |
5393 |
tim |
2102 |
|
5394 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
5395 |
|
|
|
5396 |
chrisfen |
3131 |
2005-02-14 15:16 gezelter |
5397 |
tim |
2102 |
|
5398 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
5399 |
|
|
strangeness |
5400 |
|
|
|
5401 |
chrisfen |
3131 |
2005-02-14 11:42 tim |
5402 |
tim |
2102 |
|
5403 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
5404 |
|
|
BlockSnapshotManager.hpp |
5405 |
|
|
|
5406 |
chrisfen |
3131 |
2005-02-14 10:51 tim |
5407 |
tim |
2102 |
|
5408 |
|
|
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
5409 |
|
|
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
5410 |
|
|
length of first frame |
5411 |
|
|
|
5412 |
chrisfen |
3131 |
2005-02-14 10:12 tim |
5413 |
tim |
2102 |
|
5414 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
5415 |
|
|
VelocityVerletIntegrator : last frame is written twice |
5416 |
|
|
|
5417 |
chrisfen |
3131 |
2005-02-14 09:57 tim |
5418 |
tim |
2102 |
|
5419 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
5420 |
|
|
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
5421 |
|
|
primitives/StuntDouble.hpp: begin bug fix |
5422 |
|
|
|
5423 |
chrisfen |
3131 |
2005-02-14 09:35 tim |
5424 |
tim |
2102 |
|
5425 |
|
|
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
5426 |
|
|
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
5427 |
|
|
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
5428 |
|
|
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
5429 |
|
|
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
5430 |
|
|
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
5431 |
|
|
VCorrFunc.hpp: refactory CorrelationFunction |
5432 |
|
|
|
5433 |
chrisfen |
3131 |
2005-02-14 07:18 gezelter |
5434 |
tim |
2102 |
|
5435 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
5436 |
|
|
and start of switch for type of correlation function |
5437 |
|
|
|
5438 |
chrisfen |
3131 |
2005-02-13 13:18 tim |
5439 |
tim |
2102 |
|
5440 |
|
|
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
5441 |
|
|
calculating bytes per stuntdouble |
5442 |
|
|
|
5443 |
chrisfen |
3131 |
2005-02-13 13:03 tim |
5444 |
tim |
2102 |
|
5445 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
5446 |
|
|
|
5447 |
chrisfen |
3131 |
2005-02-13 12:57 tim |
5448 |
tim |
2102 |
|
5449 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
5450 |
|
|
bug in CorrelationFunction |
5451 |
|
|
|
5452 |
chrisfen |
3131 |
2005-02-13 12:36 tim |
5453 |
tim |
2102 |
|
5454 |
|
|
* src/: applications/staticProps/GofR.cpp, |
5455 |
|
|
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
5456 |
|
|
bug in SimInfo::getCutoff() |
5457 |
|
|
|
5458 |
chrisfen |
3131 |
2005-02-13 12:08 tim |
5459 |
tim |
2102 |
|
5460 |
|
|
* make/Makefile.in: adding staticProps and dynamicProps into |
5461 |
|
|
Makefile.in |
5462 |
|
|
|
5463 |
chrisfen |
3131 |
2005-02-13 12:05 tim |
5464 |
tim |
2102 |
|
5465 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5466 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
5467 |
|
|
applications/staticProps/StaticProps.cpp, |
5468 |
|
|
applications/staticProps/StaticProps.ggo, |
5469 |
|
|
applications/staticProps/StaticPropsCmd.c, |
5470 |
|
|
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
5471 |
|
|
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
5472 |
|
|
defaults to the cutoff radius |
5473 |
|
|
|
5474 |
chrisfen |
3131 |
2005-02-13 11:14 tim |
5475 |
tim |
2102 |
|
5476 |
|
|
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
5477 |
|
|
|
5478 |
chrisfen |
3131 |
2005-02-13 11:10 tim |
5479 |
tim |
2102 |
|
5480 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5481 |
|
|
applications/dynamicProps/CorrelationFunction.cpp, |
5482 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
5483 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
5484 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5485 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
5486 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
5487 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
5488 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
5489 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
5490 |
|
|
visitors/OtherVisitor.cpp: dynamicProps get built |
5491 |
|
|
|
5492 |
chrisfen |
3131 |
2005-02-13 07:56 tim |
5493 |
tim |
2102 |
|
5494 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5495 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5496 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
5497 |
|
|
progress |
5498 |
|
|
|
5499 |
chrisfen |
3131 |
2005-02-13 00:04 tim |
5500 |
tim |
2102 |
|
5501 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
5502 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5503 |
|
|
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
5504 |
|
|
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
5505 |
|
|
work in dynamicProps |
5506 |
|
|
|
5507 |
chrisfen |
3131 |
2005-02-12 23:25 tim |
5508 |
tim |
2102 |
|
5509 |
|
|
* src/applications/dynamicProps/DynamicProps.cpp: adding |
5510 |
|
|
dynamicProps |
5511 |
|
|
|
5512 |
chrisfen |
3131 |
2005-02-12 23:14 tim |
5513 |
tim |
2102 |
|
5514 |
|
|
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
5515 |
|
|
DynamicPropsCmd.h: adding command line option to DynamicProps |
5516 |
|
|
|
5517 |
chrisfen |
3131 |
2005-02-12 23:13 tim |
5518 |
tim |
2102 |
|
5519 |
|
|
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
5520 |
|
|
adding command line option for DynamicProps |
5521 |
|
|
|
5522 |
chrisfen |
3131 |
2005-02-12 22:57 tim |
5523 |
tim |
2102 |
|
5524 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5525 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
5526 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
5527 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
5528 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
5529 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
5530 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
5531 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
5532 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
5533 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5534 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
5535 |
|
|
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
5536 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
5537 |
|
|
dynamicProps |
5538 |
|
|
|
5539 |
chrisfen |
3131 |
2005-02-12 12:09 tim |
5540 |
tim |
2102 |
|
5541 |
|
|
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
5542 |
|
|
|
5543 |
chrisfen |
3131 |
2005-02-11 14:41 tim |
5544 |
tim |
2102 |
|
5545 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
5546 |
|
|
more constructor to Snapshot to create customized DataStorage |
5547 |
|
|
|
5548 |
chrisfen |
3131 |
2005-02-11 14:39 tim |
5549 |
tim |
2102 |
|
5550 |
|
|
* src/selection/: DistanceFinder.hpp, Makefile, |
5551 |
|
|
SelectionManager.hpp: adding beginSelected, nextSelected method to |
5552 |
|
|
SelectionManager |
5553 |
|
|
|
5554 |
chrisfen |
3131 |
2005-02-11 14:36 tim |
5555 |
tim |
2102 |
|
5556 |
|
|
* src/config.h.in, configure: adding support for physmem |
5557 |
|
|
|
5558 |
chrisfen |
3131 |
2005-02-11 14:35 tim |
5559 |
tim |
2102 |
|
5560 |
|
|
* ac-tools/configure.in: adding supprot for physmem |
5561 |
|
|
|
5562 |
chrisfen |
3131 |
2005-02-11 14:35 tim |
5563 |
tim |
2102 |
|
5564 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
5565 |
|
|
physmem |
5566 |
|
|
|
5567 |
chrisfen |
3131 |
2005-02-10 14:37 tim |
5568 |
tim |
2102 |
|
5569 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
5570 |
|
|
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
5571 |
|
|
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
5572 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
5573 |
|
|
StaticPropsCmd.h: more work in StaticProps |
5574 |
|
|
|
5575 |
chrisfen |
3131 |
2005-02-10 10:14 tim |
5576 |
tim |
2102 |
|
5577 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
5578 |
|
|
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
5579 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
5580 |
|
|
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
5581 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
5582 |
|
|
StaticPropsCmd.h: change the filenames |
5583 |
|
|
|
5584 |
chrisfen |
3131 |
2005-02-10 06:15 tim |
5585 |
tim |
2102 |
|
5586 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
5587 |
|
|
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
5588 |
|
|
RadialDistrFunc.hpp: adding GofRAngle |
5589 |
|
|
|
5590 |
chrisfen |
3131 |
2005-02-09 10:21 tim |
5591 |
tim |
2102 |
|
5592 |
|
|
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
5593 |
|
|
useless files |
5594 |
|
|
|
5595 |
chrisfen |
3131 |
2005-02-09 10:12 tim |
5596 |
tim |
2102 |
|
5597 |
|
|
* src/applications/staticProps/: GofR.cpp, Makefile, |
5598 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
5599 |
|
|
|
5600 |
chrisfen |
3131 |
2005-02-09 09:08 tim |
5601 |
tim |
2102 |
|
5602 |
|
|
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
5603 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
5604 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
5605 |
|
|
|
5606 |
chrisfen |
3131 |
2005-02-07 14:39 tim |
5607 |
tim |
2102 |
|
5608 |
|
|
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
5609 |
|
|
Molecule class |
5610 |
|
|
|
5611 |
chrisfen |
3131 |
2005-02-07 14:38 tim |
5612 |
tim |
2102 |
|
5613 |
|
|
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
5614 |
|
|
|
5615 |
chrisfen |
3131 |
2005-02-07 14:36 tim |
5616 |
tim |
2102 |
|
5617 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5618 |
|
|
SelectionCompiler.cpp: support select internal index selection, for |
5619 |
|
|
example, select DMPC.3 |
5620 |
|
|
|
5621 |
chrisfen |
3131 |
2005-02-07 13:11 tim |
5622 |
tim |
2102 |
|
5623 |
|
|
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
5624 |
|
|
help info for Dump2XYZ |
5625 |
|
|
|
5626 |
chrisfen |
3131 |
2005-02-07 12:39 chrisfen |
5627 |
tim |
2102 |
|
5628 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
5629 |
|
|
selection librarys added |
5630 |
|
|
|
5631 |
chrisfen |
3131 |
2005-02-07 12:31 tim |
5632 |
tim |
2102 |
|
5633 |
|
|
* src/selection/Makefile, make/Makefile.in: adding Makefile |
5634 |
|
|
|
5635 |
chrisfen |
3131 |
2005-02-07 12:20 chrisfen |
5636 |
tim |
2102 |
|
5637 |
|
|
* src/utils/wildcards.hpp: issue commented out in wildcards |
5638 |
|
|
|
5639 |
chrisfen |
3131 |
2005-02-07 12:06 tim |
5640 |
tim |
2102 |
|
5641 |
|
|
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
5642 |
|
|
which cause reevaluate return NULL |
5643 |
|
|
|
5644 |
chrisfen |
3131 |
2005-02-07 11:14 tim |
5645 |
tim |
2102 |
|
5646 |
|
|
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
5647 |
|
|
SimSnapshotManager.hpp: fix a bug in determing the global index for |
5648 |
|
|
rigidbodies |
5649 |
|
|
|
5650 |
chrisfen |
3131 |
2005-02-07 11:13 tim |
5651 |
tim |
2102 |
|
5652 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
5653 |
|
|
in Bitset |
5654 |
|
|
|
5655 |
chrisfen |
3131 |
2005-02-07 11:13 tim |
5656 |
tim |
2102 |
|
5657 |
|
|
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
5658 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5659 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
5660 |
|
|
TokenMap.cpp: selection library is working |
5661 |
|
|
|
5662 |
chrisfen |
3131 |
2005-02-04 14:46 tim |
5663 |
tim |
2102 |
|
5664 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
5665 |
|
|
|
5666 |
chrisfen |
3131 |
2005-02-04 14:45 tim |
5667 |
tim |
2102 |
|
5668 |
|
|
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
5669 |
|
|
and XYZVisitor now use selection library |
5670 |
|
|
|
5671 |
chrisfen |
3131 |
2005-02-04 14:44 tim |
5672 |
tim |
2102 |
|
5673 |
|
|
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
5674 |
|
|
adding SelectionManager into SimInfo |
5675 |
|
|
|
5676 |
chrisfen |
3131 |
2005-02-04 14:43 tim |
5677 |
tim |
2102 |
|
5678 |
|
|
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
5679 |
|
|
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
5680 |
|
|
selection library |
5681 |
|
|
|
5682 |
chrisfen |
3131 |
2005-02-04 14:42 tim |
5683 |
tim |
2102 |
|
5684 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
5685 |
|
|
in BitSet |
5686 |
|
|
|
5687 |
chrisfen |
3131 |
2005-02-04 14:41 tim |
5688 |
tim |
2102 |
|
5689 |
|
|
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
5690 |
|
|
implementation |
5691 |
|
|
|
5692 |
chrisfen |
3131 |
2005-02-04 14:39 tim |
5693 |
tim |
2102 |
|
5694 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5695 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5696 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
5697 |
|
|
SelectionManager.hpp, Token.hpp: half of the selection utility is |
5698 |
|
|
working need to debug within keyword and atomproperty keyword |
5699 |
|
|
|
5700 |
chrisfen |
3131 |
2005-02-03 21:42 tim |
5701 |
tim |
2102 |
|
5702 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
5703 |
|
|
get built |
5704 |
|
|
|
5705 |
chrisfen |
3131 |
2005-02-03 21:42 tim |
5706 |
tim |
2102 |
|
5707 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
5708 |
|
|
|
5709 |
chrisfen |
3131 |
2005-02-03 21:26 tim |
5710 |
tim |
2102 |
|
5711 |
|
|
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
5712 |
|
|
remove some useless files |
5713 |
|
|
|
5714 |
chrisfen |
3131 |
2005-02-03 20:57 tim |
5715 |
tim |
2102 |
|
5716 |
|
|
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
5717 |
|
|
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
5718 |
|
|
adding wildcard class; NameFinder is finished |
5719 |
|
|
|
5720 |
chrisfen |
3131 |
2005-02-03 15:14 tim |
5721 |
tim |
2102 |
|
5722 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5723 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5724 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
5725 |
|
|
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
5726 |
|
|
selection library |
5727 |
|
|
|
5728 |
chrisfen |
3131 |
2005-02-03 06:04 tim |
5729 |
tim |
2102 |
|
5730 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
5731 |
|
|
selection in progress |
5732 |
|
|
|
5733 |
chrisfen |
3131 |
2005-02-02 15:13 tim |
5734 |
tim |
2102 |
|
5735 |
|
|
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
5736 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
5737 |
|
|
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
5738 |
|
|
progress, except SelectionEvaluator, other files are compiled |
5739 |
|
|
|
5740 |
chrisfen |
3131 |
2005-02-02 15:12 tim |
5741 |
tim |
2102 |
|
5742 |
|
|
* src/utils/: Makefile.in, any.hpp: adding boost::any |
5743 |
|
|
|
5744 |
chrisfen |
3131 |
2005-02-02 04:51 tim |
5745 |
tim |
2102 |
|
5746 |
|
|
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
5747 |
|
|
|
5748 |
chrisfen |
3131 |
2005-02-01 14:49 tim |
5749 |
tim |
2102 |
|
5750 |
|
|
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
5751 |
|
|
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
5752 |
|
|
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
5753 |
|
|
selection/Token.hpp: Selection in progress |
5754 |
|
|
|
5755 |
chrisfen |
3131 |
2005-01-31 22:55 tim |
5756 |
tim |
2102 |
|
5757 |
|
|
* src/: selection/SelectionCompiler.hpp, |
5758 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
5759 |
|
|
selection/SelectionManager.hpp, selection/Token.hpp, |
5760 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
5761 |
|
|
|
5762 |
chrisfen |
3131 |
2005-01-26 07:26 tim |
5763 |
tim |
2102 |
|
5764 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, |
5765 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
5766 |
|
|
to add eorWriter |
5767 |
|
|
|
5768 |
chrisfen |
3131 |
2005-01-26 07:15 tim |
5769 |
tim |
2102 |
|
5770 |
|
|
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
5771 |
|
|
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
5772 |
|
|
wrong column of electroframe |
5773 |
|
|
|
5774 |
chrisfen |
3131 |
2005-01-25 13:59 tim |
5775 |
tim |
2102 |
|
5776 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
5777 |
|
|
SimInfo, use number of cutoff stamp as counter to loop over |
5778 |
|
|
rigidbody stamp |
5779 |
|
|
|
5780 |
chrisfen |
3131 |
2005-01-25 09:45 tim |
5781 |
tim |
2102 |
|
5782 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5783 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
5784 |
|
|
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
5785 |
|
|
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
5786 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
5787 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
5788 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
5789 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
5790 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
5791 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
5792 |
|
|
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
5793 |
|
|
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
5794 |
|
|
primitives/GhostTorsion.hpp, primitives/Makefile, |
5795 |
|
|
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
5796 |
|
|
section parser's error message (2) add GhostTorsion (3) accumulate |
5797 |
|
|
inertial tensor from the directional atoms before calculate |
5798 |
|
|
rigidbody's inertial tensor |
5799 |
|
|
|
5800 |
chrisfen |
3131 |
2005-01-17 14:17 tim |
5801 |
tim |
2102 |
|
5802 |
|
|
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
5803 |
|
|
|
5804 |
chrisfen |
3131 |
2005-01-17 08:58 tim |
5805 |
tim |
2102 |
|
5806 |
|
|
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
5807 |
|
|
system parameters |
5808 |
|
|
|
5809 |
chrisfen |
3131 |
2005-01-17 08:05 tim |
5810 |
tim |
2102 |
|
5811 |
|
|
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
5812 |
|
|
|
5813 |
chrisfen |
3131 |
2005-01-14 14:02 tim |
5814 |
tim |
2102 |
|
5815 |
|
|
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
5816 |
|
|
|
5817 |
chrisfen |
3131 |
2005-01-14 13:37 tim |
5818 |
tim |
2102 |
|
5819 |
|
|
* forceFields/Makefile: sync Makefile |
5820 |
|
|
|
5821 |
chrisfen |
3131 |
2005-01-14 13:13 gezelter |
5822 |
tim |
2102 |
|
5823 |
|
|
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
5824 |
|
|
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
5825 |
|
|
src/applications/dump2Xyz/Makefile, |
5826 |
|
|
src/applications/oopse/Makefile, |
5827 |
|
|
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
5828 |
|
|
src/constraints/Makefile, src/integrators/Makefile, |
5829 |
|
|
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
5830 |
|
|
src/primitives/Makefile, src/profiling/Makefile, |
5831 |
|
|
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
5832 |
|
|
src/visitors/Makefile: moved Package variable into subdirectory |
5833 |
|
|
makefiles to speed up the building process |
5834 |
|
|
|
5835 |
chrisfen |
3131 |
2005-01-14 12:48 gezelter |
5836 |
tim |
2102 |
|
5837 |
|
|
* src/applications/oopse/oopse.cpp: Fixed publication details in |
5838 |
|
|
banner |
5839 |
|
|
|
5840 |
chrisfen |
3131 |
2005-01-14 12:48 gezelter |
5841 |
tim |
2102 |
|
5842 |
|
|
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
5843 |
|
|
simParallel_interface.h: added dummy subroutine to avoid empty |
5844 |
|
|
unit, synchronized this dummy routine between C and fortran |
5845 |
|
|
|
5846 |
chrisfen |
3131 |
2005-01-14 12:31 gezelter |
5847 |
tim |
2102 |
|
5848 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
5849 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
5850 |
|
|
DarkSide/Makefile, DarkSide/atype.F90, |
5851 |
|
|
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
5852 |
|
|
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
5853 |
|
|
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
5854 |
|
|
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
5855 |
|
|
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
5856 |
|
|
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
5857 |
|
|
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
5858 |
|
|
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
5859 |
|
|
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
5860 |
|
|
modules and C/Fortran interface subroutines |
5861 |
|
|
|
5862 |
chrisfen |
3131 |
2005-01-14 12:15 gezelter |
5863 |
tim |
2102 |
|
5864 |
|
|
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
5865 |
|
|
|
5866 |
chrisfen |
3131 |
2005-01-14 12:09 gezelter |
5867 |
tim |
2102 |
|
5868 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
5869 |
|
|
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
5870 |
|
|
|
5871 |
chrisfen |
3131 |
2005-01-14 08:49 tim |
5872 |
tim |
2102 |
|
5873 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
5874 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
5875 |
|
|
utils/StringUtils.hpp: using c library to do conversion instead of |
5876 |
|
|
using iostream due to a bug in libstdc++(GCC 3.2) |
5877 |
|
|
|
5878 |
chrisfen |
3131 |
2005-01-13 18:40 tim |
5879 |
tim |
2102 |
|
5880 |
|
|
* src/brains/SimSetup.cpp: no message |
5881 |
|
|
|
5882 |
chrisfen |
3131 |
2005-01-13 17:56 tim |
5883 |
tim |
2102 |
|
5884 |
|
|
* src/primitives/Molecule.hpp: fix a bug in global index |
5885 |
|
|
|
5886 |
chrisfen |
3131 |
2005-01-13 17:04 tim |
5887 |
tim |
2102 |
|
5888 |
|
|
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
5889 |
|
|
Integrator.hpp in Minimizer |
5890 |
|
|
|
5891 |
chrisfen |
3131 |
2005-01-13 14:14 gezelter |
5892 |
tim |
2102 |
|
5893 |
|
|
* src/utils/Makefile: compile getopt and getopt1 if we need to |
5894 |
|
|
|
5895 |
chrisfen |
3131 |
2005-01-13 13:56 gezelter |
5896 |
tim |
2102 |
|
5897 |
|
|
* make/Makefile.in: template flags |
5898 |
|
|
|
5899 |
chrisfen |
3131 |
2005-01-13 13:48 gezelter |
5900 |
tim |
2102 |
|
5901 |
|
|
* src/applications/oopse/Makefile: formatting |
5902 |
|
|
|
5903 |
chrisfen |
3131 |
2005-01-13 13:48 gezelter |
5904 |
tim |
2102 |
|
5905 |
|
|
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
5906 |
|
|
target |
5907 |
|
|
|
5908 |
chrisfen |
3131 |
2005-01-13 11:40 tim |
5909 |
tim |
2102 |
|
5910 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
5911 |
|
|
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
5912 |
|
|
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
5913 |
|
|
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
5914 |
|
|
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
5915 |
|
|
|
5916 |
chrisfen |
3131 |
2005-01-13 10:26 tim |
5917 |
tim |
2102 |
|
5918 |
|
|
* make/Makefile.in: change the order of linking (object file comes |
5919 |
|
|
first and then follow by user built library) |
5920 |
|
|
|
5921 |
chrisfen |
3131 |
2005-01-12 15:24 tim |
5922 |
tim |
2102 |
|
5923 |
|
|
* src/io/DumpWriter.cpp: remove useless debug info |
5924 |
|
|
|
5925 |
chrisfen |
3131 |
2005-01-12 15:21 tim |
5926 |
tim |
2102 |
|
5927 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
5928 |
|
|
|
5929 |
chrisfen |
3131 |
2005-01-12 15:17 tim |
5930 |
tim |
2102 |
|
5931 |
|
|
* make/: Makefile.in, Makefile.in: missing tab |
5932 |
|
|
|
5933 |
chrisfen |
3131 |
2005-01-12 15:15 tim |
5934 |
tim |
2102 |
|
5935 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
5936 |
|
|
get fixed |
5937 |
|
|
|
5938 |
chrisfen |
3131 |
2005-01-12 14:40 gezelter |
5939 |
tim |
2102 |
|
5940 |
|
|
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
5941 |
|
|
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
5942 |
|
|
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
5943 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
5944 |
|
|
src/UseTheForce/ForceFieldCreator.hpp, |
5945 |
|
|
src/UseTheForce/ForceFieldFactory.cpp, |
5946 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
5947 |
|
|
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
5948 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
5949 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
5950 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
5951 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
5952 |
|
|
src/UseTheForce/notifyCutoffs.F90, |
5953 |
|
|
src/UseTheForce/notifyCutoffs_interface.h, |
5954 |
|
|
src/UseTheForce/DarkSide/LJ.F90, |
5955 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
5956 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
5957 |
|
|
src/UseTheForce/DarkSide/charge.F90, |
5958 |
|
|
src/UseTheForce/DarkSide/charge_interface.h, |
5959 |
|
|
src/UseTheForce/DarkSide/dipole.F90, |
5960 |
|
|
src/UseTheForce/DarkSide/dipole_interface.h, |
5961 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
5962 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
5963 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
5964 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
5965 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
5966 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
5967 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
5968 |
|
|
src/UseTheForce/DarkSide/reactionField.F90, |
5969 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
5970 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
5971 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
5972 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
5973 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
5974 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
5975 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
5976 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
5977 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
5978 |
|
|
src/applications/Makedepend, src/applications/quickLate.c, |
5979 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
5980 |
|
|
src/applications/oopse/oopse.cpp, |
5981 |
|
|
src/applications/simpleBuilder/BaseLattice.cpp, |
5982 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
5983 |
|
|
src/applications/simpleBuilder/Lattice.cpp, |
5984 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
5985 |
|
|
src/applications/simpleBuilder/LatticeCreator.cpp, |
5986 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
5987 |
|
|
src/applications/simpleBuilder/LatticeFactory.cpp, |
5988 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
5989 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
5990 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
5991 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
5992 |
|
|
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
5993 |
|
|
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
5994 |
|
|
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
5995 |
|
|
src/brains/Makefile, src/brains/Migrator.hpp, |
5996 |
|
|
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
5997 |
|
|
src/brains/Register.cpp, src/brains/Register.hpp, |
5998 |
|
|
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
5999 |
|
|
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
6000 |
|
|
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
6001 |
|
|
src/brains/SimSnapshotManager.cpp, |
6002 |
|
|
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
6003 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
6004 |
|
|
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
6005 |
|
|
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
6006 |
|
|
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
6007 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
6008 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
6009 |
|
|
src/constraints/AbstractClasses.hpp, |
6010 |
|
|
src/constraints/ConstraintElem.hpp, |
6011 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
6012 |
|
|
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
6013 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
6014 |
|
|
src/constraints/ZconsStruct.hpp, |
6015 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
6016 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
6017 |
|
|
src/integrators/AbstractClasses.hpp, |
6018 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
6019 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
6020 |
|
|
src/integrators/Integrator.hpp, |
6021 |
|
|
src/integrators/IntegratorCreator.hpp, |
6022 |
|
|
src/integrators/IntegratorFactory.cpp, |
6023 |
|
|
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
6024 |
|
|
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
6025 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
6026 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
6027 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
6028 |
|
|
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
6029 |
|
|
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
6030 |
|
|
src/integrators/RotationAlgorithm.hpp, |
6031 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
6032 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
6033 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
6034 |
|
|
src/io/AtomTypesSectionParser.cpp, |
6035 |
|
|
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
6036 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
6037 |
|
|
src/io/BendTypesSectionParser.cpp, |
6038 |
|
|
src/io/BendTypesSectionParser.hpp, |
6039 |
|
|
src/io/BondTypesSectionParser.cpp, |
6040 |
|
|
src/io/BondTypesSectionParser.hpp, |
6041 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
6042 |
|
|
src/io/DirectionalAtomTypesSectionParser.hpp, |
6043 |
|
|
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
6044 |
|
|
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
6045 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
6046 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, |
6047 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
6048 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
6049 |
|
|
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
6050 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
6051 |
|
|
src/io/LennardJonesAtomTypesSectionParser.hpp, |
6052 |
|
|
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
6053 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
6054 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
6055 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
6056 |
|
|
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
6057 |
|
|
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
6058 |
|
|
src/io/StickyAtomTypesSectionParser.hpp, |
6059 |
|
|
src/io/TorsionTypesSectionParser.cpp, |
6060 |
|
|
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
6061 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
6062 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
6063 |
|
|
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
6064 |
|
|
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
6065 |
|
|
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
6066 |
|
|
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
6067 |
|
|
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
6068 |
|
|
src/math/MatVec3.h, src/math/Polynomial.hpp, |
6069 |
|
|
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
6070 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
6071 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
6072 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
6073 |
|
|
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
6074 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
6075 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
6076 |
|
|
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
6077 |
|
|
src/minimizers/MinimizerCreator.hpp, |
6078 |
|
|
src/minimizers/MinimizerFactory.cpp, |
6079 |
|
|
src/minimizers/MinimizerFactory.hpp, |
6080 |
|
|
src/minimizers/MinimizerParameterSet.cpp, |
6081 |
|
|
src/minimizers/MinimizerParameterSet.hpp, |
6082 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
6083 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
6084 |
|
|
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
6085 |
|
|
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
6086 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
6087 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
6088 |
|
|
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
6089 |
|
|
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
6090 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
6091 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
6092 |
|
|
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
6093 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
6094 |
|
|
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
6095 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
6096 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
6097 |
|
|
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
6098 |
|
|
src/primitives/UreyBradleyBend.cpp, |
6099 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
6100 |
|
|
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
6101 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
6102 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
6103 |
|
|
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
6104 |
|
|
src/types/BendType.hpp, src/types/BondStamp.cpp, |
6105 |
|
|
src/types/BondStamp.hpp, src/types/BondType.hpp, |
6106 |
|
|
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
6107 |
|
|
src/types/Component.cpp, src/types/Component.hpp, |
6108 |
|
|
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
6109 |
|
|
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
6110 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
6111 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
6112 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
6113 |
|
|
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
6114 |
|
|
src/types/Makefile, src/types/MoleculeStamp.cpp, |
6115 |
|
|
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
6116 |
|
|
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
6117 |
|
|
src/types/PolynomialBondType.hpp, |
6118 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
6119 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
6120 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
6121 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
6122 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
6123 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
6124 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
6125 |
|
|
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
6126 |
|
|
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
6127 |
|
|
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
6128 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
6129 |
|
|
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
6130 |
|
|
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
6131 |
|
|
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
6132 |
|
|
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
6133 |
|
|
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
6134 |
|
|
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
6135 |
|
|
src/utils/Utility.cpp, src/utils/Utility.hpp, |
6136 |
|
|
src/utils/definitions.F90, src/utils/fError.c, |
6137 |
|
|
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
6138 |
|
|
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
6139 |
|
|
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
6140 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
6141 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
6142 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
6143 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
6144 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
6145 |
|
|
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
6146 |
|
|
OOPSE-2.0 |
6147 |
|
|
|
6148 |
chrisfen |
3131 |
2005-01-12 10:13 tim |
6149 |
tim |
2102 |
|
6150 |
|
|
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
6151 |
|
|
utils/TypeContainer.hpp: forget to include <algorithm> |
6152 |
|
|
|
6153 |
chrisfen |
3131 |
2005-01-12 09:25 tim |
6154 |
tim |
2102 |
|
6155 |
|
|
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
6156 |
|
|
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
6157 |
|
|
fields |
6158 |
|
|
|
6159 |
chrisfen |
3131 |
2005-01-12 09:14 tim |
6160 |
tim |
2102 |
|
6161 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6162 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
6163 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
6164 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
6165 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
6166 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
6167 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
6168 |
|
|
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
6169 |
|
|
UseTheForce/notifyCutoffs.F90, |
6170 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
6171 |
|
|
UseTheForce/DarkSide/atype.F90, |
6172 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
6173 |
|
|
UseTheForce/DarkSide/charge.F90, |
6174 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
6175 |
|
|
UseTheForce/DarkSide/dipole.F90, |
6176 |
|
|
UseTheForce/DarkSide/dipole_interface.h, |
6177 |
|
|
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
6178 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
6179 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
6180 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
6181 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
6182 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
6183 |
|
|
UseTheForce/DarkSide/shapes.F90, |
6184 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
6185 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
6186 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
6187 |
|
|
UseTheForce/DarkSide/simulation.F90, |
6188 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
6189 |
|
|
UseTheForce/DarkSide/sticky.F90, |
6190 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
6191 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
6192 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
6193 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
6194 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
6195 |
|
|
applications/simpleBuilder/Lattice.cpp, |
6196 |
|
|
applications/simpleBuilder/Lattice.hpp, |
6197 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
6198 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
6199 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
6200 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
6201 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
6202 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
6203 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
6204 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
6205 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
6206 |
|
|
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
6207 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6208 |
|
|
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
6209 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6210 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
6211 |
|
|
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
6212 |
|
|
brains/Snapshot.cpp, brains/Snapshot.hpp, |
6213 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
6214 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
6215 |
|
|
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
6216 |
|
|
constraints/Rattle.cpp, constraints/Rattle.hpp, |
6217 |
|
|
constraints/ZconsStruct.hpp, |
6218 |
|
|
constraints/ZconstraintForceManager.cpp, |
6219 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
6220 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
6221 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
6222 |
|
|
integrators/IntegratorFactory.cpp, |
6223 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
6224 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
6225 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
6226 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
6227 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
6228 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
6229 |
|
|
integrators/Velocitizer.hpp, |
6230 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
6231 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
6232 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
6233 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
6234 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
6235 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
6236 |
|
|
io/BondTypesSectionParser.hpp, |
6237 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
6238 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
6239 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
6240 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
6241 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
6242 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
6243 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
6244 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
6245 |
|
|
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
6246 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
6247 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
6248 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
6249 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
6250 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
6251 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
6252 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
6253 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
6254 |
|
|
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
6255 |
|
|
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
6256 |
|
|
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
6257 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
6258 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, |
6259 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
6260 |
|
|
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
6261 |
|
|
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
6262 |
|
|
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
6263 |
|
|
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
6264 |
|
|
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
6265 |
|
|
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
6266 |
|
|
minimizers/MinimizerParameterSet.cpp, |
6267 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
6268 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
6269 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
6270 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
6271 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
6272 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
6273 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
6274 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
6275 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
6276 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
6277 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
6278 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
6279 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
6280 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
6281 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
6282 |
|
|
types/AtomType.hpp, types/AtomTypeProperties.h, |
6283 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
6284 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
6285 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
6286 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
6287 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
6288 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
6289 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
6290 |
|
|
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
6291 |
|
|
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
6292 |
|
|
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
6293 |
|
|
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
6294 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
6295 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
6296 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
6297 |
|
|
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
6298 |
|
|
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
6299 |
|
|
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
6300 |
|
|
types/TorsionStamp.hpp, types/TorsionType.hpp, |
6301 |
|
|
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
6302 |
|
|
types/ZconStamp.hpp, utils/GenericData.hpp, |
6303 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
6304 |
|
|
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
6305 |
|
|
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
6306 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
6307 |
|
|
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
6308 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
6309 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
6310 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
6311 |
|
|
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
6312 |
|
|
utils/simError.c, utils/simError.h, utils/status.F90, |
6313 |
|
|
utils/vector_class.F90, visitors/AtomData.hpp, |
6314 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
6315 |
|
|
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
6316 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
6317 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6318 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
6319 |
|
|
visitors/ZconsVisitor.hpp: change license |
6320 |
|
|
|
6321 |
chrisfen |
3131 |
2005-01-12 09:14 tim |
6322 |
tim |
2102 |
|
6323 |
|
|
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
6324 |
|
|
branch new_design. |
6325 |
|
|
|
6326 |
chrisfen |
3131 |
2005-01-11 13:03 tim |
6327 |
tim |
2102 |
|
6328 |
|
|
* src/: constraints/ZconstraintForceManager.cpp, |
6329 |
|
|
constraints/ZconstraintForceManager.hpp, |
6330 |
|
|
minimizers/MinimizerParameterSet.cpp, |
6331 |
|
|
minimizers/MinimizerParameterSet.hpp: change const static double |
6332 |
|
|
data member to const double |
6333 |
|
|
|
6334 |
chrisfen |
3131 |
2005-01-11 12:50 tim |
6335 |
tim |
2102 |
|
6336 |
|
|
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
6337 |
|
|
|
6338 |
chrisfen |
3131 |
2005-01-11 12:39 tim |
6339 |
tim |
2102 |
|
6340 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
6341 |
|
|
change data type from logical to integer in AtomTypeProperties.h |
6342 |
|
|
|
6343 |
chrisfen |
3131 |
2005-01-11 08:36 tim |
6344 |
tim |
2102 |
|
6345 |
|
|
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
6346 |
|
|
new format of EAM force field |
6347 |
|
|
|
6348 |
chrisfen |
3131 |
2005-01-11 08:24 tim |
6349 |
tim |
2102 |
|
6350 |
|
|
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
6351 |
|
|
to DUFF2.frc |
6352 |
|
|
|
6353 |
chrisfen |
3131 |
2005-01-11 08:23 tim |
6354 |
tim |
2102 |
|
6355 |
|
|
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
6356 |
|
|
DUFF2.frc |
6357 |
|
|
|
6358 |
chrisfen |
3131 |
2005-01-11 08:09 tim |
6359 |
tim |
2102 |
|
6360 |
|
|
* make/Makefile.in: adding constraints and minimizers into |
6361 |
|
|
Makefile.in |
6362 |
|
|
|
6363 |
chrisfen |
3131 |
2005-01-11 08:03 tim |
6364 |
tim |
2102 |
|
6365 |
|
|
* src/io/: ChargeAtomTypesSectionParser.cpp, |
6366 |
|
|
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
6367 |
|
|
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
6368 |
|
|
files |
6369 |
|
|
|
6370 |
chrisfen |
3131 |
2005-01-11 07:59 tim |
6371 |
tim |
2102 |
|
6372 |
|
|
* src/io/ZConsWriter.cpp: [no log message] |
6373 |
|
|
|
6374 |
chrisfen |
3131 |
2005-01-11 07:53 tim |
6375 |
tim |
2102 |
|
6376 |
|
|
* src/UseTheForce/EAM.cpp: minor fix |
6377 |
|
|
|
6378 |
chrisfen |
3131 |
2005-01-11 07:52 tim |
6379 |
tim |
2102 |
|
6380 |
tim |
2116 |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
6381 |
|
|
on branch new_design. |
6382 |
|
|
|
6383 |
chrisfen |
3131 |
2005-01-11 07:52 tim |
6384 |
tim |
2116 |
|
6385 |
tim |
2102 |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
6386 |
|
|
on branch new_design. |
6387 |
|
|
|
6388 |
chrisfen |
3131 |
2005-01-11 07:52 tim |
6389 |
tim |
2102 |
|
6390 |
|
|
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
6391 |
|
|
|
6392 |
chrisfen |
3131 |
2005-01-11 07:47 tim |
6393 |
tim |
2102 |
|
6394 |
|
|
* make/Makefile.in: forget a '$' sign |
6395 |
|
|
|
6396 |
chrisfen |
3131 |
2005-01-11 07:46 tim |
6397 |
tim |
2102 |
|
6398 |
|
|
* make/Makefile.in: missing tab in rules |
6399 |
|
|
|
6400 |
chrisfen |
3131 |
2005-01-10 14:04 tim |
6401 |
tim |
2102 |
|
6402 |
|
|
* src/: UseTheForce/ForceFieldCreator.cpp, |
6403 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
6404 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
6405 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
6406 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
6407 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
6408 |
|
|
brains/Register.cpp, brains/Register.hpp, |
6409 |
|
|
integrators/IntegratorCreator.cpp, |
6410 |
|
|
integrators/IntegratorCreator.hpp, |
6411 |
|
|
integrators/IntegratorFactory.cpp, |
6412 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
6413 |
|
|
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
6414 |
|
|
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
6415 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
6416 |
|
|
minimizers/MinimizerFactory.hpp: create a register module to |
6417 |
|
|
register force fields, integrators and minimizers |
6418 |
|
|
|
6419 |
chrisfen |
3131 |
2005-01-10 14:04 tim |
6420 |
tim |
2102 |
|
6421 |
|
|
* src/brains/Register.cpp: file Register.cpp was initially added on |
6422 |
|
|
branch new_design. |
6423 |
|
|
|
6424 |
chrisfen |
3131 |
2005-01-10 14:04 tim |
6425 |
tim |
2102 |
|
6426 |
|
|
* src/brains/Register.hpp: file Register.hpp was initially added on |
6427 |
|
|
branch new_design. |
6428 |
|
|
|
6429 |
chrisfen |
3131 |
2005-01-10 12:52 tim |
6430 |
tim |
2102 |
|
6431 |
|
|
* src/: UseTheForce/ForceFieldFactory.cpp, |
6432 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
6433 |
|
|
constraints/ZconstraintForceManager.cpp, |
6434 |
|
|
constraints/ZconstraintForceManager.hpp, |
6435 |
|
|
integrators/IntegratorFactory.cpp, |
6436 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
6437 |
|
|
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
6438 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
6439 |
|
|
method is working now |
6440 |
|
|
|
6441 |
chrisfen |
3131 |
2005-01-10 10:05 tim |
6442 |
tim |
2102 |
|
6443 |
|
|
* src/: constraints/ConstraintElem.hpp, |
6444 |
|
|
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
6445 |
|
|
constraints/ZconstraintForceManager.cpp, |
6446 |
|
|
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
6447 |
|
|
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
6448 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
6449 |
|
|
zconstraint |
6450 |
|
|
|
6451 |
chrisfen |
3131 |
2005-01-10 10:05 tim |
6452 |
tim |
2102 |
|
6453 |
|
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
6454 |
|
|
initially added on branch new_design. |
6455 |
|
|
|
6456 |
chrisfen |
3131 |
2005-01-07 13:50 tim |
6457 |
tim |
2102 |
|
6458 |
tim |
2116 |
* src/constraints/ZconstraintForceManager.cpp: file |
6459 |
|
|
ZconstraintForceManager.cpp was initially added on branch |
6460 |
|
|
new_design. |
6461 |
|
|
|
6462 |
chrisfen |
3131 |
2005-01-07 13:50 tim |
6463 |
tim |
2116 |
|
6464 |
|
|
* src/constraints/ZconstraintForceManager.hpp: file |
6465 |
|
|
ZconstraintForceManager.hpp was initially added on branch |
6466 |
|
|
new_design. |
6467 |
|
|
|
6468 |
chrisfen |
3131 |
2005-01-07 13:50 tim |
6469 |
tim |
2116 |
|
6470 |
tim |
2102 |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
6471 |
|
|
applications/simpleBuilder/Lattice.hpp, |
6472 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
6473 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
6474 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
6475 |
|
|
constraints/ConstraintElem.hpp, constraints/Makefile, |
6476 |
|
|
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
6477 |
|
|
constraints/ZconstraintForceManager.cpp, |
6478 |
|
|
constraints/ZconstraintForceManager.hpp, |
6479 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
6480 |
|
|
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
6481 |
|
|
|
6482 |
chrisfen |
3131 |
2005-01-07 13:50 tim |
6483 |
tim |
2102 |
|
6484 |
|
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
6485 |
|
|
initially added on branch new_design. |
6486 |
|
|
|
6487 |
chrisfen |
3131 |
2005-01-06 14:31 tim |
6488 |
tim |
2102 |
|
6489 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6490 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6491 |
|
|
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
6492 |
|
|
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
6493 |
|
|
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
6494 |
|
|
constraint is almost working |
6495 |
|
|
|
6496 |
chrisfen |
3131 |
2005-01-05 16:36 tim |
6497 |
tim |
2102 |
|
6498 |
|
|
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
6499 |
|
|
working |
6500 |
|
|
|
6501 |
chrisfen |
3131 |
2005-01-05 16:16 tim |
6502 |
tim |
2102 |
|
6503 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
6504 |
|
|
applications/oopse/oopse.cpp, |
6505 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
6506 |
|
|
applications/simpleBuilder/Lattice.cpp, |
6507 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
6508 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
6509 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
6510 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
6511 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
6512 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
6513 |
|
|
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
6514 |
|
|
in progress |
6515 |
|
|
|
6516 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6517 |
tim |
2102 |
|
6518 |
|
|
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
6519 |
|
|
was initially added on branch new_design. |
6520 |
|
|
|
6521 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6522 |
tim |
2102 |
|
6523 |
tim |
2116 |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
6524 |
|
|
added on branch new_design. |
6525 |
|
|
|
6526 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6527 |
tim |
2116 |
|
6528 |
tim |
2102 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
6529 |
|
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
6530 |
|
|
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
6531 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
6532 |
|
|
SDMinimizer.hpp: minimizer in progress |
6533 |
|
|
|
6534 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6535 |
tim |
2102 |
|
6536 |
tim |
2116 |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
6537 |
|
|
was initially added on branch new_design. |
6538 |
tim |
2102 |
|
6539 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6540 |
tim |
2102 |
|
6541 |
tim |
2116 |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
6542 |
tim |
2102 |
was initially added on branch new_design. |
6543 |
|
|
|
6544 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6545 |
tim |
2102 |
|
6546 |
tim |
2116 |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
6547 |
tim |
2102 |
was initially added on branch new_design. |
6548 |
|
|
|
6549 |
chrisfen |
3131 |
2005-01-05 09:35 tim |
6550 |
tim |
2102 |
|
6551 |
|
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
6552 |
|
|
added on branch new_design. |
6553 |
|
|
|
6554 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6555 |
tim |
2102 |
|
6556 |
|
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
6557 |
|
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
6558 |
|
|
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
6559 |
|
|
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
6560 |
|
|
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
6561 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
6562 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
6563 |
|
|
progress |
6564 |
|
|
|
6565 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6566 |
tim |
2102 |
|
6567 |
tim |
2116 |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
6568 |
|
|
initially added on branch new_design. |
6569 |
tim |
2102 |
|
6570 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6571 |
tim |
2102 |
|
6572 |
|
|
* src/minimizers/MinimizerParameterSet.cpp: file |
6573 |
|
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
6574 |
|
|
|
6575 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6576 |
tim |
2102 |
|
6577 |
|
|
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
6578 |
|
|
initially added on branch new_design. |
6579 |
|
|
|
6580 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6581 |
tim |
2102 |
|
6582 |
tim |
2116 |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
6583 |
|
|
was initially added on branch new_design. |
6584 |
|
|
|
6585 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6586 |
tim |
2116 |
|
6587 |
|
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
6588 |
|
|
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
6589 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
6590 |
|
|
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
6591 |
|
|
|
6592 |
chrisfen |
3131 |
2005-01-04 14:18 tim |
6593 |
tim |
2116 |
|
6594 |
tim |
2102 |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
6595 |
|
|
branch new_design. |
6596 |
|
|
|
6597 |
chrisfen |
3131 |
2004-12-20 12:50 chuckv |
6598 |
tim |
2102 |
|
6599 |
|
|
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
6600 |
|
|
other BSD's, replaced test -f *.mod with ls function since BSD test |
6601 |
|
|
apparently doesn't support wildcards. |
6602 |
|
|
|
6603 |
chrisfen |
3131 |
2004-12-20 12:36 tim |
6604 |
tim |
2102 |
|
6605 |
|
|
* make/Makefile.in: fix a test command incompatiable problem |
6606 |
|
|
|
6607 |
chrisfen |
3131 |
2004-12-20 11:49 tim |
6608 |
tim |
2102 |
|
6609 |
|
|
* src/integrators/NPTi.cpp: NPT is working now |
6610 |
|
|
|
6611 |
chrisfen |
3131 |
2004-12-16 11:20 tim |
6612 |
tim |
2102 |
|
6613 |
|
|
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
6614 |
|
|
invalid stamp id |
6615 |
|
|
|
6616 |
chrisfen |
3131 |
2004-12-16 11:00 tim |
6617 |
tim |
2102 |
|
6618 |
|
|
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
6619 |
|
|
newEAM.u6.frc: adding new EAM force field files |
6620 |
|
|
|
6621 |
chrisfen |
3131 |
2004-12-16 10:55 tim |
6622 |
tim |
2102 |
|
6623 |
|
|
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
6624 |
|
|
in EAM parameter file is incorrect |
6625 |
|
|
|
6626 |
chrisfen |
3131 |
2004-12-16 09:27 tim |
6627 |
tim |
2102 |
|
6628 |
|
|
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
6629 |
|
|
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
6630 |
|
|
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
6631 |
|
|
|
6632 |
chrisfen |
3131 |
2004-12-15 14:34 tim |
6633 |
tim |
2102 |
|
6634 |
|
|
* src/: applications/simpleBuilder/BaseLattice.cpp, |
6635 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
6636 |
|
|
applications/simpleBuilder/Lattice.cpp, |
6637 |
|
|
applications/simpleBuilder/Lattice.hpp, |
6638 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
6639 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
6640 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
6641 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
6642 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
6643 |
|
|
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
6644 |
|
|
|
6645 |
chrisfen |
3131 |
2004-12-15 13:07 tim |
6646 |
tim |
2102 |
|
6647 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6648 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
6649 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
6650 |
|
|
add EAM Force Field |
6651 |
|
|
|
6652 |
chrisfen |
3131 |
2004-12-15 11:40 tim |
6653 |
tim |
2102 |
|
6654 |
|
|
* src/applications/oopse/oopse.cpp: add more force fields |
6655 |
|
|
|
6656 |
chrisfen |
3131 |
2004-12-15 08:44 tim |
6657 |
tim |
2102 |
|
6658 |
|
|
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
6659 |
|
|
to call All_reduce in MPI version) |
6660 |
|
|
|
6661 |
chrisfen |
3131 |
2004-12-15 08:13 tim |
6662 |
tim |
2102 |
|
6663 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
6664 |
|
|
io/DumpReader.cpp: MPI in NVE is working |
6665 |
|
|
|
6666 |
chrisfen |
3131 |
2004-12-14 13:57 tim |
6667 |
tim |
2102 |
|
6668 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
6669 |
|
|
Master nodes does not brocast the total number of frames |
6670 |
|
|
|
6671 |
chrisfen |
3131 |
2004-12-14 11:08 tim |
6672 |
tim |
2102 |
|
6673 |
|
|
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
6674 |
|
|
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
6675 |
|
|
minimizers/CGFamilyMinimizer.cpp, |
6676 |
|
|
minimizers/MinimizerParameterSet.hpp, |
6677 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
6678 |
|
|
minimizers/SDMinimizer.cpp: more fix in MPI version |
6679 |
|
|
|
6680 |
chrisfen |
3131 |
2004-12-13 14:30 tim |
6681 |
tim |
2102 |
|
6682 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, |
6683 |
|
|
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
6684 |
|
|
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
6685 |
|
|
integrators/DLM.cpp, integrators/Integrator.cpp, |
6686 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
6687 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
6688 |
|
|
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
6689 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
6690 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
6691 |
|
|
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
6692 |
|
|
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
6693 |
|
|
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
6694 |
|
|
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
6695 |
|
|
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
6696 |
|
|
is built |
6697 |
|
|
|
6698 |
chrisfen |
3131 |
2004-12-10 10:41 tim |
6699 |
tim |
2102 |
|
6700 |
|
|
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
6701 |
|
|
|
6702 |
chrisfen |
3131 |
2004-12-10 08:14 tim |
6703 |
tim |
2102 |
|
6704 |
|
|
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
6705 |
|
|
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
6706 |
|
|
and Dipole is working now |
6707 |
|
|
|
6708 |
chrisfen |
3131 |
2004-12-09 15:15 tim |
6709 |
tim |
2102 |
|
6710 |
|
|
* src/: UseTheForce/DarkSide/dipole.F90, |
6711 |
|
|
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
6712 |
|
|
fix an index problem in eFrame matrix |
6713 |
|
|
|
6714 |
chrisfen |
3131 |
2004-12-09 15:09 tim |
6715 |
tim |
2102 |
|
6716 |
|
|
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
6717 |
|
|
initializing the new Charge AtomType |
6718 |
|
|
|
6719 |
chrisfen |
3131 |
2004-12-09 13:15 tim |
6720 |
tim |
2102 |
|
6721 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
6722 |
|
|
types/DirectionalAtomType.cpp: sticky module get compiled |
6723 |
|
|
|
6724 |
chrisfen |
3131 |
2004-12-09 12:43 gezelter |
6725 |
tim |
2102 |
|
6726 |
|
|
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
6727 |
|
|
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
6728 |
|
|
GB |
6729 |
|
|
|
6730 |
chrisfen |
3131 |
2004-12-09 12:42 gezelter |
6731 |
tim |
2102 |
|
6732 |
|
|
* src/UseTheForce/doForces.F90: u_l -> eFrame |
6733 |
|
|
|
6734 |
chrisfen |
3131 |
2004-12-09 12:27 gezelter |
6735 |
tim |
2102 |
|
6736 |
|
|
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
6737 |
|
|
module now has the option for multiple sticky types |
6738 |
|
|
|
6739 |
chrisfen |
3131 |
2004-12-09 12:27 gezelter |
6740 |
tim |
2102 |
|
6741 |
|
|
* src/UseTheForce/doForces.F90: sticky |
6742 |
|
|
|
6743 |
chrisfen |
3131 |
2004-12-09 08:22 tim |
6744 |
tim |
2102 |
|
6745 |
|
|
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
6746 |
|
|
inconsistency in lab2Bidy |
6747 |
|
|
|
6748 |
chrisfen |
3131 |
2004-12-09 07:45 tim |
6749 |
tim |
2102 |
|
6750 |
|
|
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
6751 |
|
|
in calculating torque in rigid body |
6752 |
|
|
|
6753 |
chrisfen |
3131 |
2004-12-08 12:37 tim |
6754 |
tim |
2102 |
|
6755 |
|
|
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
6756 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, |
6757 |
|
|
integrators/Integrator.cpp, |
6758 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
6759 |
|
|
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
6760 |
|
|
|
6761 |
chrisfen |
3131 |
2004-12-08 09:03 tim |
6762 |
tim |
2102 |
|
6763 |
|
|
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
6764 |
|
|
in NVT is working |
6765 |
|
|
|
6766 |
chrisfen |
3131 |
2004-12-07 15:08 tim |
6767 |
tim |
2102 |
|
6768 |
|
|
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
6769 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
6770 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
6771 |
|
|
io/DumpWriter.cpp: NPT in progress |
6772 |
|
|
|
6773 |
chrisfen |
3131 |
2004-12-07 06:43 tim |
6774 |
tim |
2102 |
|
6775 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
6776 |
|
|
message] |
6777 |
|
|
|
6778 |
chrisfen |
3131 |
2004-12-06 21:12 tim |
6779 |
tim |
2102 |
|
6780 |
|
|
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
6781 |
|
|
UseInitXSstate |
6782 |
|
|
|
6783 |
chrisfen |
3131 |
2004-12-06 21:00 tim |
6784 |
tim |
2102 |
|
6785 |
|
|
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
6786 |
|
|
|
6787 |
chrisfen |
3131 |
2004-12-06 20:47 tim |
6788 |
tim |
2102 |
|
6789 |
|
|
* src/types/DirectionalAtomType.cpp: [no log message] |
6790 |
|
|
|
6791 |
chrisfen |
3131 |
2004-12-06 18:18 tim |
6792 |
tim |
2102 |
|
6793 |
|
|
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
6794 |
|
|
|
6795 |
chrisfen |
3131 |
2004-12-06 17:33 tim |
6796 |
tim |
2102 |
|
6797 |
|
|
* forceFields/newDUFF.frc: change the force constant of bonds |
6798 |
|
|
|
6799 |
chrisfen |
3131 |
2004-12-06 15:29 tim |
6800 |
tim |
2102 |
|
6801 |
|
|
* src/: UseTheForce/DarkSide/charge.F90, |
6802 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
6803 |
|
|
UseTheForce/DarkSide/dipole.F90, |
6804 |
|
|
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
6805 |
|
|
fix atom type ident in Charge and Dipole Module |
6806 |
|
|
|
6807 |
chrisfen |
3131 |
2004-12-06 14:56 tim |
6808 |
tim |
2102 |
|
6809 |
|
|
* src/primitives/Torsion.cpp: butane is working now |
6810 |
|
|
|
6811 |
chrisfen |
3131 |
2004-12-06 12:15 tim |
6812 |
tim |
2102 |
|
6813 |
|
|
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
6814 |
|
|
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
6815 |
|
|
interaction for butane is correct.Still something wrong with long |
6816 |
|
|
range one |
6817 |
|
|
|
6818 |
chrisfen |
3131 |
2004-12-05 20:49 tim |
6819 |
tim |
2102 |
|
6820 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
6821 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6822 |
|
|
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
6823 |
|
|
primitives/Atom.hpp, utils/NumericConstant.hpp, |
6824 |
|
|
utils/TypeContainer.hpp: fix a bug in Exclude List |
6825 |
|
|
|
6826 |
chrisfen |
3131 |
2004-12-05 14:21 tim |
6827 |
tim |
2102 |
|
6828 |
|
|
* forceFields/newDUFF.frc: minor fix in DUFF |
6829 |
|
|
|
6830 |
chrisfen |
3131 |
2004-12-05 14:02 tim |
6831 |
tim |
2102 |
|
6832 |
|
|
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
6833 |
|
|
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
6834 |
|
|
fix a bug in filling MolMembership |
6835 |
|
|
|
6836 |
chrisfen |
3131 |
2004-12-05 09:12 tim |
6837 |
tim |
2102 |
|
6838 |
|
|
* forceFields/newDUFF.frc: minor fix in force field file |
6839 |
|
|
|
6840 |
chrisfen |
3131 |
2004-12-05 09:09 tim |
6841 |
tim |
2102 |
|
6842 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
6843 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
6844 |
|
|
|
6845 |
chrisfen |
3131 |
2004-12-04 12:09 tim |
6846 |
tim |
2102 |
|
6847 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
6848 |
|
|
math/Vector3.hpp: NVE is working now, get the same result as |
6849 |
|
|
OOPSE-1.0 |
6850 |
|
|
|
6851 |
chrisfen |
3131 |
2004-12-04 11:29 tim |
6852 |
tim |
2102 |
|
6853 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
6854 |
|
|
|
6855 |
chrisfen |
3131 |
2004-12-04 11:24 gezelter |
6856 |
tim |
2102 |
|
6857 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
6858 |
|
|
|
6859 |
chrisfen |
3131 |
2004-12-04 11:24 gezelter |
6860 |
tim |
2102 |
|
6861 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
6862 |
|
|
|
6863 |
chrisfen |
3131 |
2004-12-03 21:24 tim |
6864 |
tim |
2102 |
|
6865 |
|
|
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
6866 |
|
|
integrators/Integrator.hpp, |
6867 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
6868 |
|
|
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
6869 |
|
|
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
6870 |
|
|
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
6871 |
|
|
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
6872 |
|
|
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
6873 |
|
|
|
6874 |
chrisfen |
3131 |
2004-12-03 16:01 tim |
6875 |
tim |
2102 |
|
6876 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
6877 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
6878 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
6879 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
6880 |
|
|
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
6881 |
|
|
energy of NVE is not conserved |
6882 |
|
|
|
6883 |
chrisfen |
3131 |
2004-12-03 14:36 tim |
6884 |
tim |
2102 |
|
6885 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
6886 |
|
|
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
6887 |
|
|
|
6888 |
chrisfen |
3131 |
2004-12-03 13:30 tim |
6889 |
tim |
2102 |
|
6890 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
6891 |
|
|
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
6892 |
|
|
integrators/NVE.cpp, primitives/Molecule.cpp, |
6893 |
|
|
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
6894 |
|
|
primitives/Torsion.hpp: more missing function get implemented |
6895 |
|
|
|
6896 |
chrisfen |
3131 |
2004-12-03 12:30 tim |
6897 |
tim |
2102 |
|
6898 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
6899 |
|
|
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
6900 |
|
|
|
6901 |
chrisfen |
3131 |
2004-12-03 09:59 tim |
6902 |
tim |
2102 |
|
6903 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
6904 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6905 |
|
|
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
6906 |
|
|
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
6907 |
|
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
6908 |
|
|
utils/TypeContainer.hpp: begin to fix bugs |
6909 |
|
|
|
6910 |
chrisfen |
3131 |
2004-12-02 16:26 tim |
6911 |
tim |
2102 |
|
6912 |
tim |
2116 |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
6913 |
|
|
new_design. |
6914 |
|
|
|
6915 |
chrisfen |
3131 |
2004-12-02 16:26 tim |
6916 |
tim |
2116 |
|
6917 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6918 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
6919 |
|
|
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
6920 |
|
|
integrators/IntegratorCreator.cpp, |
6921 |
|
|
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
6922 |
|
|
io/SectionParserManager.hpp, utils/Makefile, |
6923 |
|
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
6924 |
|
|
bug in countTokens in StringTokenizer |
6925 |
|
|
|
6926 |
chrisfen |
3131 |
2004-12-02 16:06 tim |
6927 |
tim |
2102 |
|
6928 |
|
|
* forceFields/newDUFF.frc: minor fix |
6929 |
|
|
|
6930 |
chrisfen |
3131 |
2004-12-02 15:15 tim |
6931 |
tim |
2102 |
|
6932 |
|
|
* forceFields/newDUFF.frc: new ForceField format |
6933 |
|
|
|
6934 |
chrisfen |
3131 |
2004-12-02 14:15 tim |
6935 |
tim |
2102 |
|
6936 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6937 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
6938 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
6939 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
6940 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
6941 |
|
|
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
6942 |
|
|
integrators/IntegratorCreator.hpp, |
6943 |
|
|
integrators/IntegratorFactory.cpp, |
6944 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
6945 |
|
|
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
6946 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
6947 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
6948 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
6949 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
6950 |
|
|
types/Makefile: refine factory pattern to make it initialized |
6951 |
|
|
correctly |
6952 |
|
|
|
6953 |
chrisfen |
3131 |
2004-12-02 14:15 tim |
6954 |
tim |
2102 |
|
6955 |
|
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
6956 |
|
|
was initially added on branch new_design. |
6957 |
|
|
|
6958 |
chrisfen |
3131 |
2004-12-02 14:15 tim |
6959 |
tim |
2102 |
|
6960 |
tim |
2116 |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
6961 |
|
|
was initially added on branch new_design. |
6962 |
|
|
|
6963 |
chrisfen |
3131 |
2004-12-02 14:15 tim |
6964 |
tim |
2116 |
|
6965 |
|
|
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
6966 |
|
|
was initially added on branch new_design. |
6967 |
|
|
|
6968 |
chrisfen |
3131 |
2004-12-02 14:15 tim |
6969 |
tim |
2116 |
|
6970 |
|
|
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
6971 |
|
|
was initially added on branch new_design. |
6972 |
|
|
|
6973 |
chrisfen |
3131 |
2004-12-02 08:53 tim |
6974 |
tim |
2116 |
|
6975 |
tim |
2102 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
6976 |
|
|
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
6977 |
|
|
|
6978 |
chrisfen |
3131 |
2004-12-02 08:04 tim |
6979 |
tim |
2102 |
|
6980 |
|
|
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
6981 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
6982 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
6983 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
6984 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
6985 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
6986 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
6987 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
6988 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, |
6989 |
|
|
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
6990 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
6991 |
|
|
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
6992 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
6993 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
6994 |
|
|
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
6995 |
|
|
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
6996 |
|
|
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
6997 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
6998 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6999 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
7000 |
|
|
have two linking problem |
7001 |
|
|
|
7002 |
chrisfen |
3131 |
2004-12-01 21:17 tim |
7003 |
tim |
2102 |
|
7004 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
7005 |
|
|
applications/simpleBuilder/Lattice.cpp, |
7006 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
7007 |
|
|
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
7008 |
|
|
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
7009 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
7010 |
|
|
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
7011 |
|
|
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
7012 |
|
|
visitors/ZconsVisitor.cpp: change endl to std::endl |
7013 |
|
|
|
7014 |
chrisfen |
3131 |
2004-12-01 21:14 tim |
7015 |
tim |
2102 |
|
7016 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
7017 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
7018 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
7019 |
|
|
applications/simpleBuilder/Lattice.hpp, |
7020 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
7021 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
7022 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
7023 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
7024 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
7025 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
7026 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
7027 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
7028 |
|
|
visitors/RigidBodyVisitor.hpp: minor fix |
7029 |
|
|
|
7030 |
chrisfen |
3131 |
2004-12-01 21:09 tim |
7031 |
tim |
2102 |
|
7032 |
|
|
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
7033 |
|
|
remove StreamTokenizer |
7034 |
|
|
|
7035 |
chrisfen |
3131 |
2004-12-01 21:06 tim |
7036 |
tim |
2102 |
|
7037 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
7038 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
7039 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
7040 |
|
|
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
7041 |
|
|
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
7042 |
|
|
namespace std in .cpp file |
7043 |
|
|
|
7044 |
chrisfen |
3131 |
2004-12-01 21:04 tim |
7045 |
tim |
2102 |
|
7046 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
7047 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
7048 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
7049 |
|
|
applications/simpleBuilder/Lattice.cpp, |
7050 |
|
|
applications/simpleBuilder/Lattice.hpp, |
7051 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
7052 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
7053 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
7054 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
7055 |
|
|
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
7056 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
7057 |
|
|
minimizers/MinimizerParameterSet.hpp, |
7058 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
7059 |
|
|
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
7060 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
7061 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
7062 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
7063 |
|
|
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
7064 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
7065 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
7066 |
|
|
qulified name prefix std |
7067 |
|
|
|
7068 |
chrisfen |
3131 |
2004-12-01 20:55 tim |
7069 |
tim |
2102 |
|
7070 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
7071 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
7072 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
7073 |
|
|
applications/simpleBuilder/Lattice.hpp, |
7074 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
7075 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
7076 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
7077 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
7078 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
7079 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
7080 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
7081 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
7082 |
|
|
visitors/RigidBodyVisitor.hpp: replace string by std::string |
7083 |
|
|
|
7084 |
chrisfen |
3131 |
2004-12-01 19:12 tim |
7085 |
tim |
2102 |
|
7086 |
|
|
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
7087 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
7088 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
7089 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
7090 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
7091 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
7092 |
|
|
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
7093 |
|
|
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
7094 |
|
|
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
7095 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
7096 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
7097 |
|
|
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
7098 |
|
|
src/utils/Makefile, src/utils/StringUtils.cpp, |
7099 |
|
|
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
7100 |
|
|
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
7101 |
|
|
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
7102 |
|
|
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
7103 |
|
|
header files |
7104 |
|
|
|
7105 |
chrisfen |
3131 |
2004-12-01 18:23 tim |
7106 |
tim |
2102 |
|
7107 |
|
|
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
7108 |
|
|
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
7109 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
7110 |
|
|
begin to fix linking problem |
7111 |
|
|
|
7112 |
chrisfen |
3131 |
2004-12-01 18:08 tim |
7113 |
tim |
2102 |
|
7114 |
|
|
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
7115 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
7116 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
7117 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
7118 |
|
|
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
7119 |
|
|
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
7120 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
7121 |
|
|
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
7122 |
|
|
still has some linking problem |
7123 |
|
|
|
7124 |
chrisfen |
3131 |
2004-12-01 16:26 tim |
7125 |
tim |
2102 |
|
7126 |
|
|
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
7127 |
|
|
utils/OOPSEConstant.hpp: NVT get built |
7128 |
|
|
|
7129 |
chrisfen |
3131 |
2004-12-01 16:09 tim |
7130 |
tim |
2102 |
|
7131 |
tim |
2116 |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
7132 |
|
|
branch new_design. |
7133 |
tim |
2102 |
|
7134 |
chrisfen |
3131 |
2004-12-01 16:09 tim |
7135 |
tim |
2102 |
|
7136 |
tim |
2116 |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
7137 |
|
|
branch new_design. |
7138 |
|
|
|
7139 |
chrisfen |
3131 |
2004-12-01 16:09 tim |
7140 |
tim |
2116 |
|
7141 |
tim |
2102 |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
7142 |
|
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
7143 |
|
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
7144 |
|
|
integrators/Integrator.hpp, integrators/Makefile, |
7145 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, |
7146 |
|
|
integrators/RotationAlgorithm.hpp, |
7147 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
7148 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
7149 |
|
|
get built |
7150 |
|
|
|
7151 |
chrisfen |
3131 |
2004-12-01 16:09 tim |
7152 |
tim |
2102 |
|
7153 |
tim |
2116 |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
7154 |
|
|
was initially added on branch new_design. |
7155 |
tim |
2102 |
|
7156 |
chrisfen |
3131 |
2004-12-01 14:45 tim |
7157 |
tim |
2102 |
|
7158 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
7159 |
|
|
integrators/IntegratorFactory.cpp, |
7160 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
7161 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
7162 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
7163 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
7164 |
|
|
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
7165 |
|
|
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
7166 |
|
|
|
7167 |
chrisfen |
3131 |
2004-12-01 14:45 tim |
7168 |
tim |
2102 |
|
7169 |
|
|
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
7170 |
|
|
branch new_design. |
7171 |
|
|
|
7172 |
chrisfen |
3131 |
2004-12-01 12:05 tim |
7173 |
tim |
2102 |
|
7174 |
|
|
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
7175 |
|
|
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
7176 |
|
|
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
7177 |
|
|
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
7178 |
|
|
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
7179 |
|
|
visitors/ZconsVisitor.hpp: visitors get built |
7180 |
|
|
|
7181 |
chrisfen |
3131 |
2004-12-01 11:32 chrisfen |
7182 |
tim |
2102 |
|
7183 |
|
|
* samples/water/tip3p_ice/tp3.md: fixed a sample |
7184 |
|
|
|
7185 |
chrisfen |
3131 |
2004-12-01 11:10 tim |
7186 |
tim |
2102 |
|
7187 |
|
|
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
7188 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
7189 |
|
|
src/types/AtomType.hpp, src/utils/Utility.hpp, |
7190 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
7191 |
|
|
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
7192 |
|
|
spell check |
7193 |
|
|
|
7194 |
chrisfen |
3131 |
2004-12-01 10:42 tim |
7195 |
tim |
2102 |
|
7196 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
7197 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
7198 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
7199 |
|
|
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
7200 |
|
|
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
7201 |
|
|
and constraint, other directories get built |
7202 |
|
|
|
7203 |
chrisfen |
3131 |
2004-12-01 09:38 tim |
7204 |
tim |
2102 |
|
7205 |
|
|
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
7206 |
|
|
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
7207 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
7208 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
7209 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
7210 |
|
|
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
7211 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
7212 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
7213 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
7214 |
|
|
refactory AtomType |
7215 |
|
|
|
7216 |
chrisfen |
3131 |
2004-11-30 19:11 tim |
7217 |
tim |
2102 |
|
7218 |
|
|
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
7219 |
|
|
|
7220 |
chrisfen |
3131 |
2004-11-30 18:30 tim |
7221 |
tim |
2102 |
|
7222 |
|
|
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
7223 |
|
|
NumericConstant |
7224 |
|
|
|
7225 |
chrisfen |
3131 |
2004-11-30 18:24 tim |
7226 |
tim |
2102 |
|
7227 |
|
|
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
7228 |
|
|
primitives/RigidBody.cpp: minor fix |
7229 |
|
|
|
7230 |
chrisfen |
3131 |
2004-11-30 15:14 tim |
7231 |
tim |
2102 |
|
7232 |
|
|
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
7233 |
|
|
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
7234 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
7235 |
|
|
get built, next is integrator |
7236 |
|
|
|
7237 |
chrisfen |
3131 |
2004-11-30 14:43 tim |
7238 |
tim |
2102 |
|
7239 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7240 |
|
|
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
7241 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
7242 |
|
|
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
7243 |
|
|
utils/StringUtils.hpp: brains get built |
7244 |
|
|
|
7245 |
chrisfen |
3131 |
2004-11-30 12:50 tim |
7246 |
tim |
2102 |
|
7247 |
|
|
* src/: brains/ForceManager.cpp, brains/Makefile, |
7248 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
7249 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
7250 |
|
|
utils/StringUtils.hpp: brains get built, io is next |
7251 |
|
|
|
7252 |
chrisfen |
3131 |
2004-11-30 11:58 tim |
7253 |
tim |
2102 |
|
7254 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
7255 |
|
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
7256 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
7257 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
7258 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
7259 |
|
|
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
7260 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
7261 |
|
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
7262 |
|
|
|
7263 |
chrisfen |
3131 |
2004-11-30 11:58 tim |
7264 |
tim |
2102 |
|
7265 |
tim |
2116 |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
7266 |
|
|
added on branch new_design. |
7267 |
|
|
|
7268 |
chrisfen |
3131 |
2004-11-30 09:54 tim |
7269 |
tim |
2116 |
|
7270 |
tim |
2102 |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
7271 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
7272 |
|
|
utils/LocalIndexManager.hpp: more get fixed |
7273 |
|
|
|
7274 |
chrisfen |
3131 |
2004-11-29 21:03 tim |
7275 |
tim |
2102 |
|
7276 |
tim |
2116 |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
7277 |
|
|
initially added on branch new_design. |
7278 |
|
|
|
7279 |
chrisfen |
3131 |
2004-11-29 21:03 tim |
7280 |
tim |
2116 |
|
7281 |
tim |
2102 |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
7282 |
|
|
LocalndexManager.hpp to LocalIndexManager.hpp |
7283 |
|
|
|
7284 |
chrisfen |
3131 |
2004-11-29 20:43 tim |
7285 |
tim |
2102 |
|
7286 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
7287 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
7288 |
|
|
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
7289 |
|
|
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
7290 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
7291 |
|
|
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
7292 |
|
|
|
7293 |
chrisfen |
3131 |
2004-11-29 20:14 tim |
7294 |
tim |
2102 |
|
7295 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
7296 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
7297 |
|
|
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
7298 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
7299 |
|
|
fixed |
7300 |
|
|
|
7301 |
chrisfen |
3131 |
2004-11-29 19:49 tim |
7302 |
tim |
2102 |
|
7303 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
7304 |
|
|
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
7305 |
|
|
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
7306 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
7307 |
|
|
types/QuarticTorsionType.hpp: minor fixed |
7308 |
|
|
|
7309 |
chrisfen |
3131 |
2004-11-29 19:32 tim |
7310 |
tim |
2102 |
|
7311 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
7312 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
7313 |
|
|
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
7314 |
|
|
embedded |
7315 |
|
|
|
7316 |
chrisfen |
3131 |
2004-11-29 13:42 tim |
7317 |
tim |
2102 |
|
7318 |
|
|
* test/math/: Makefile, PolynomialTestCase.cpp, |
7319 |
|
|
PolynomialTestCase.hpp: add PolynomialTestCase |
7320 |
|
|
|
7321 |
chrisfen |
3131 |
2004-11-29 13:42 tim |
7322 |
tim |
2102 |
|
7323 |
|
|
* src/math/Polynomial.hpp: Polynomial passes unit test |
7324 |
|
|
|
7325 |
chrisfen |
3131 |
2004-11-29 12:03 tim |
7326 |
tim |
2102 |
|
7327 |
|
|
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
7328 |
|
|
QuarticTorsion.hpp to QuarticTorsionType.hpp |
7329 |
|
|
|
7330 |
chrisfen |
3131 |
2004-11-29 12:03 tim |
7331 |
tim |
2102 |
|
7332 |
|
|
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
7333 |
|
|
initially added on branch new_design. |
7334 |
|
|
|
7335 |
chrisfen |
3131 |
2004-11-29 11:56 tim |
7336 |
tim |
2102 |
|
7337 |
|
|
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
7338 |
|
|
initially added on branch new_design. |
7339 |
|
|
|
7340 |
chrisfen |
3131 |
2004-11-29 11:56 tim |
7341 |
tim |
2102 |
|
7342 |
|
|
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
7343 |
|
|
CubicTorsionType and QuarticTorsionType |
7344 |
|
|
|
7345 |
chrisfen |
3131 |
2004-11-29 11:56 tim |
7346 |
tim |
2102 |
|
7347 |
|
|
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
7348 |
|
|
initially added on branch new_design. |
7349 |
|
|
|
7350 |
chrisfen |
3131 |
2004-11-29 10:00 tim |
7351 |
tim |
2102 |
|
7352 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
7353 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
7354 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
7355 |
|
|
fixed |
7356 |
|
|
|
7357 |
chrisfen |
3131 |
2004-11-29 09:59 tim |
7358 |
tim |
2102 |
|
7359 |
|
|
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
7360 |
|
|
new_design. |
7361 |
|
|
|
7362 |
chrisfen |
3131 |
2004-11-29 09:59 tim |
7363 |
tim |
2102 |
|
7364 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
7365 |
|
|
Algorithm for std::string |
7366 |
|
|
|
7367 |
chrisfen |
3131 |
2004-11-29 07:52 tim |
7368 |
tim |
2102 |
|
7369 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
7370 |
|
|
some useless files |
7371 |
|
|
|
7372 |
chrisfen |
3131 |
2004-11-29 07:50 tim |
7373 |
tim |
2102 |
|
7374 |
|
|
* src/io/: BondTypesSectionParser.cpp, |
7375 |
|
|
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
7376 |
|
|
ElectrostaticAtomTypesSectionParser.cpp, |
7377 |
|
|
HarmonicBondTypesSectionParser.cpp, |
7378 |
|
|
HarmonicBondTypesSectionParser.hpp, |
7379 |
|
|
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
7380 |
|
|
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
7381 |
|
|
StickyAtomTypesSectionParser.hpp: more files get fixed |
7382 |
|
|
|
7383 |
chrisfen |
3131 |
2004-11-29 07:27 tim |
7384 |
tim |
2102 |
|
7385 |
|
|
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
7386 |
|
|
DirectionalAtomTypesSectionParser.cpp, |
7387 |
|
|
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
7388 |
|
|
Makefile, SectionParser.cpp, SectionParser.hpp, |
7389 |
|
|
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
7390 |
|
|
built |
7391 |
|
|
|
7392 |
chrisfen |
3131 |
2004-11-29 06:49 tim |
7393 |
tim |
2102 |
|
7394 |
|
|
* src/types/UreyBradleyBendType.hpp: types get built |
7395 |
|
|
|
7396 |
chrisfen |
3131 |
2004-11-29 06:40 tim |
7397 |
tim |
2102 |
|
7398 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
7399 |
|
|
types get built |
7400 |
|
|
|
7401 |
chrisfen |
3131 |
2004-11-25 18:13 tim |
7402 |
tim |
2102 |
|
7403 |
|
|
* src/: UseTheForce/ForceField.hpp, |
7404 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
7405 |
|
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
7406 |
|
|
files |
7407 |
|
|
|
7408 |
chrisfen |
3131 |
2004-11-25 12:18 tim |
7409 |
tim |
2102 |
|
7410 |
tim |
2116 |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
7411 |
|
|
initially added on branch new_design. |
7412 |
|
|
|
7413 |
chrisfen |
3131 |
2004-11-25 12:18 tim |
7414 |
tim |
2116 |
|
7415 |
tim |
2102 |
* src/: io/AtomTypesSectionParser.cpp, |
7416 |
|
|
io/BondTypesSectionParser.cpp, |
7417 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
7418 |
|
|
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
7419 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
7420 |
|
|
files |
7421 |
|
|
|
7422 |
chrisfen |
3131 |
2004-11-25 12:18 tim |
7423 |
tim |
2102 |
|
7424 |
|
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
7425 |
|
|
initially added on branch new_design. |
7426 |
|
|
|
7427 |
chrisfen |
3131 |
2004-11-24 14:12 tim |
7428 |
tim |
2102 |
|
7429 |
|
|
* src/: io/AtomTypesSectionParser.cpp, |
7430 |
|
|
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
7431 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
7432 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
7433 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
7434 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
7435 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
7436 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
7437 |
|
|
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
7438 |
|
|
io/EAMAtomTypesSectionParser.hpp, |
7439 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
7440 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
7441 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
7442 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
7443 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
7444 |
|
|
io/SectionParser.hpp, io/SectionParserManager.hpp, |
7445 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
7446 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
7447 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
7448 |
|
|
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
7449 |
|
|
|
7450 |
chrisfen |
3131 |
2004-11-24 13:33 tim |
7451 |
tim |
2102 |
|
7452 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
7453 |
|
|
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
7454 |
|
|
LJFF.cpp, Makefile: UseTheForce get built |
7455 |
|
|
|
7456 |
chrisfen |
3131 |
2004-11-24 12:55 tim |
7457 |
tim |
2102 |
|
7458 |
|
|
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
7459 |
|
|
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
7460 |
|
|
primitives/Makefile, primitives/Molecule.cpp, |
7461 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
7462 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
7463 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
7464 |
|
|
primitives/UreyBradleyBend.hpp: types and primitives get built |
7465 |
|
|
|
7466 |
chrisfen |
3131 |
2004-11-24 11:49 tim |
7467 |
tim |
2102 |
|
7468 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
7469 |
|
|
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
7470 |
|
|
StringTokenizerTestCase |
7471 |
|
|
|
7472 |
chrisfen |
3131 |
2004-11-24 11:49 tim |
7473 |
tim |
2102 |
|
7474 |
|
|
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
7475 |
|
|
StringTokenizer.hpp: StringTokenizer passes unit test |
7476 |
|
|
|
7477 |
chrisfen |
3131 |
2004-11-24 10:20 tim |
7478 |
tim |
2102 |
|
7479 |
|
|
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
7480 |
|
|
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
7481 |
|
|
change Makefile |
7482 |
|
|
|
7483 |
chrisfen |
3131 |
2004-11-24 10:06 chrisfen |
7484 |
tim |
2102 |
|
7485 |
|
|
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
7486 |
|
|
fine |
7487 |
|
|
|
7488 |
chrisfen |
3131 |
2004-11-24 10:06 chrisfen |
7489 |
tim |
2102 |
|
7490 |
|
|
* src/integrators/Integrator.cpp: improved restraints |
7491 |
|
|
|
7492 |
chrisfen |
3131 |
2004-11-24 10:05 chrisfen |
7493 |
tim |
2102 |
|
7494 |
|
|
* samples/water/tip3p_ice/tp3.md: oops... |
7495 |
|
|
|
7496 |
chrisfen |
3131 |
2004-11-24 09:42 tim |
7497 |
tim |
1779 |
|
7498 |
|
|
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
7499 |
|
|
brains/DataStorage.hpp, brains/SimCreator.cpp, |
7500 |
|
|
brains/SimCreator.hpp, integrators/Integrator.hpp, |
7501 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
7502 |
|
|
primitives/DirectionalAtom.cpp: add SetForceManager method to |
7503 |
|
|
integrator |
7504 |
|
|
|
7505 |
chrisfen |
3131 |
2004-11-23 15:12 tim |
7506 |
tim |
1779 |
|
7507 |
|
|
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
7508 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
7509 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
7510 |
|
|
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
7511 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
7512 |
|
|
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
7513 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
7514 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
7515 |
|
|
types/UreyBradleyBendType.hpp: refactory NPT integrator |
7516 |
|
|
|
7517 |
chrisfen |
3131 |
2004-11-23 14:50 chrisfen |
7518 |
tim |
1779 |
|
7519 |
|
|
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
7520 |
|
|
Restraints should work in parallel now |
7521 |
|
|
|
7522 |
chrisfen |
3131 |
2004-11-23 14:48 chrisfen |
7523 |
tim |
1779 |
|
7524 |
|
|
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
7525 |
|
|
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
7526 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
7527 |
|
|
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
7528 |
|
|
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
7529 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
7530 |
|
|
to restraints |
7531 |
|
|
|
7532 |
chrisfen |
3131 |
2004-11-23 14:47 chrisfen |
7533 |
tim |
1779 |
|
7534 |
|
|
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
7535 |
|
|
return to the original on next commit |
7536 |
|
|
|
7537 |
chrisfen |
3131 |
2004-11-23 09:53 tim |
7538 |
tim |
1779 |
|
7539 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7540 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
7541 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
7542 |
|
|
io/ChargeAtomTypesSectionParser.cpp, |
7543 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
7544 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
7545 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
7546 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
7547 |
|
|
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
7548 |
|
|
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
7549 |
|
|
|
7550 |
chrisfen |
3131 |
2004-11-23 09:53 tim |
7551 |
tim |
1779 |
|
7552 |
|
|
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
7553 |
|
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
7554 |
|
|
branch new_design. |
7555 |
|
|
|
7556 |
chrisfen |
3131 |
2004-11-23 09:53 tim |
7557 |
tim |
1779 |
|
7558 |
tim |
2116 |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
7559 |
|
|
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
7560 |
|
|
branch new_design. |
7561 |
tim |
1779 |
|
7562 |
chrisfen |
3131 |
2004-11-22 22:03 tim |
7563 |
tim |
1779 |
|
7564 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
7565 |
|
|
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
7566 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
7567 |
|
|
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
7568 |
|
|
|
7569 |
chrisfen |
3131 |
2004-11-22 22:03 tim |
7570 |
tim |
1779 |
|
7571 |
tim |
2116 |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
7572 |
|
|
was initially added on branch new_design. |
7573 |
|
|
|
7574 |
chrisfen |
3131 |
2004-11-22 22:03 tim |
7575 |
tim |
2116 |
|
7576 |
tim |
1779 |
* src/io/EAMAtomTypesSectionParser.hpp: file |
7577 |
|
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
7578 |
|
|
new_design. |
7579 |
|
|
|
7580 |
chrisfen |
3131 |
2004-11-22 22:03 tim |
7581 |
tim |
1779 |
|
7582 |
tim |
2116 |
* src/io/EAMAtomTypesSectionParser.cpp: file |
7583 |
|
|
EAMAtomTypesSectionParser.cpp was initially added on branch |
7584 |
|
|
new_design. |
7585 |
tim |
1779 |
|
7586 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7587 |
tim |
1779 |
|
7588 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.hpp: file |
7589 |
|
|
TorsionTypesSectionParser.hpp was initially added on branch |
7590 |
tim |
1779 |
new_design. |
7591 |
|
|
|
7592 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7593 |
tim |
1779 |
|
7594 |
|
|
* src/io/BendTypesSectionParser.hpp: file |
7595 |
|
|
BendTypesSectionParser.hpp was initially added on branch |
7596 |
|
|
new_design. |
7597 |
|
|
|
7598 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7599 |
tim |
1779 |
|
7600 |
|
|
* src/io/BondTypesSectionParser.hpp: file |
7601 |
|
|
BondTypesSectionParser.hpp was initially added on branch |
7602 |
|
|
new_design. |
7603 |
|
|
|
7604 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7605 |
tim |
1779 |
|
7606 |
tim |
2116 |
* src/io/BondTypesSectionParser.cpp: file |
7607 |
|
|
BondTypesSectionParser.cpp was initially added on branch |
7608 |
tim |
1779 |
new_design. |
7609 |
|
|
|
7610 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7611 |
tim |
1779 |
|
7612 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.cpp: file |
7613 |
|
|
TorsionTypesSectionParser.cpp was initially added on branch |
7614 |
tim |
1779 |
new_design. |
7615 |
|
|
|
7616 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7617 |
tim |
1779 |
|
7618 |
|
|
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
7619 |
|
|
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
7620 |
|
|
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
7621 |
|
|
BondTypesSectionParser, BendTypesSectionParser and |
7622 |
|
|
TorsionTypeSectionParser |
7623 |
|
|
|
7624 |
chrisfen |
3131 |
2004-11-22 20:35 tim |
7625 |
tim |
1779 |
|
7626 |
tim |
2116 |
* src/io/BendTypesSectionParser.cpp: file |
7627 |
|
|
BendTypesSectionParser.cpp was initially added on branch |
7628 |
|
|
new_design. |
7629 |
|
|
|
7630 |
chrisfen |
3131 |
2004-11-22 15:04 tim |
7631 |
tim |
2116 |
|
7632 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
7633 |
|
|
DUFF and EAM |
7634 |
|
|
|
7635 |
chrisfen |
3131 |
2004-11-22 15:02 tim |
7636 |
tim |
1779 |
|
7637 |
tim |
2116 |
* src/io/: DirectionalAtomTypesParser.hpp, |
7638 |
|
|
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
7639 |
|
|
|
7640 |
chrisfen |
3131 |
2004-11-22 15:02 tim |
7641 |
tim |
2116 |
|
7642 |
tim |
1779 |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
7643 |
|
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
7644 |
|
|
new_design. |
7645 |
|
|
|
7646 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7647 |
tim |
1779 |
|
7648 |
tim |
2116 |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
7649 |
|
|
DipoleAtomTypesSectionParser.hpp was initially added on branch |
7650 |
|
|
new_design. |
7651 |
tim |
1779 |
|
7652 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7653 |
tim |
1779 |
|
7654 |
tim |
2116 |
* src/io/AtomTypesSectionParser.hpp: file |
7655 |
|
|
AtomTypesSectionParser.hpp was initially added on branch |
7656 |
tim |
1779 |
new_design. |
7657 |
|
|
|
7658 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7659 |
tim |
1779 |
|
7660 |
|
|
* src/io/HarmonicBondTypesSectionParser.hpp: file |
7661 |
|
|
HarmonicBondTypesSectionParser.hpp was initially added on branch |
7662 |
|
|
new_design. |
7663 |
|
|
|
7664 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7665 |
tim |
1779 |
|
7666 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.cpp: file |
7667 |
|
|
StickyAtomTypesSectionParser.cpp was initially added on branch |
7668 |
tim |
1779 |
new_design. |
7669 |
|
|
|
7670 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7671 |
tim |
1779 |
|
7672 |
tim |
2116 |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
7673 |
|
|
LennardJonesAtomTypesSectionParser.hpp was initially added on |
7674 |
|
|
branch new_design. |
7675 |
|
|
|
7676 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7677 |
tim |
2116 |
|
7678 |
|
|
* src/io/HarmonicBondTypesSectionParser.cpp: file |
7679 |
|
|
HarmonicBondTypesSectionParser.cpp was initially added on branch |
7680 |
|
|
new_design. |
7681 |
|
|
|
7682 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7683 |
tim |
2116 |
|
7684 |
tim |
2102 |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
7685 |
|
|
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
7686 |
|
|
new_design. |
7687 |
|
|
|
7688 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7689 |
tim |
2102 |
|
7690 |
tim |
2116 |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
7691 |
|
|
was initially added on branch new_design. |
7692 |
|
|
|
7693 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7694 |
tim |
2116 |
|
7695 |
|
|
* src/io/AtomTypesSectionParser.cpp: file |
7696 |
|
|
AtomTypesSectionParser.cpp was initially added on branch |
7697 |
|
|
new_design. |
7698 |
|
|
|
7699 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7700 |
tim |
2116 |
|
7701 |
|
|
* src/io/ChargeAtomTypesSectionParser.cpp: file |
7702 |
|
|
ChargeAtomTypesSectionParser.cpp was initially added on branch |
7703 |
|
|
new_design. |
7704 |
|
|
|
7705 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7706 |
tim |
2116 |
|
7707 |
|
|
* src/io/DipoleAtomTypesSectionParser.cpp: file |
7708 |
|
|
DipoleAtomTypesSectionParser.cpp was initially added on branch |
7709 |
|
|
new_design. |
7710 |
|
|
|
7711 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7712 |
tim |
2116 |
|
7713 |
tim |
2102 |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
7714 |
|
|
LennardJonesAtomTypesSectionParser.cpp was initially added on |
7715 |
tim |
1779 |
branch new_design. |
7716 |
|
|
|
7717 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7718 |
tim |
1779 |
|
7719 |
tim |
2116 |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
7720 |
|
|
ChargeAtomTypesSectionParser.hpp was initially added on branch |
7721 |
tim |
1779 |
new_design. |
7722 |
|
|
|
7723 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7724 |
tim |
1779 |
|
7725 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.hpp: file |
7726 |
|
|
StickyAtomTypesSectionParser.hpp was initially added on branch |
7727 |
|
|
new_design. |
7728 |
|
|
|
7729 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7730 |
tim |
2116 |
|
7731 |
|
|
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
7732 |
|
|
added on branch new_design. |
7733 |
|
|
|
7734 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7735 |
tim |
2116 |
|
7736 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
7737 |
|
|
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
7738 |
|
|
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
7739 |
|
|
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
7740 |
|
|
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
7741 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
7742 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
7743 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
7744 |
|
|
io/DirectionalAtomTypesParser.hpp, |
7745 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
7746 |
|
|
io/HarmonicBondTypesSectionParser.cpp, |
7747 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
7748 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
7749 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
7750 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
7751 |
|
|
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
7752 |
|
|
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
7753 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
7754 |
|
|
utils/GenericData.hpp: adding section parsers |
7755 |
|
|
|
7756 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7757 |
tim |
2102 |
|
7758 |
tim |
2116 |
* src/io/DirectionalAtomTypesParser.hpp: file |
7759 |
|
|
DirectionalAtomTypesParser.hpp was initially added on branch |
7760 |
tim |
1779 |
new_design. |
7761 |
|
|
|
7762 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7763 |
tim |
1779 |
|
7764 |
tim |
2102 |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
7765 |
tim |
1779 |
was initially added on branch new_design. |
7766 |
|
|
|
7767 |
chrisfen |
3131 |
2004-11-22 12:55 tim |
7768 |
tim |
1779 |
|
7769 |
tim |
2116 |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
7770 |
|
|
added on branch new_design. |
7771 |
tim |
1779 |
|
7772 |
chrisfen |
3131 |
2004-11-19 14:12 tim |
7773 |
tim |
1779 |
|
7774 |
tim |
2116 |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
7775 |
tim |
1779 |
added on branch new_design. |
7776 |
|
|
|
7777 |
chrisfen |
3131 |
2004-11-19 14:12 tim |
7778 |
tim |
1779 |
|
7779 |
|
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
7780 |
|
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
7781 |
|
|
types/FixedBondType.hpp: remove more useless files |
7782 |
|
|
|
7783 |
chrisfen |
3131 |
2004-11-19 13:47 tim |
7784 |
tim |
2102 |
|
7785 |
tim |
1779 |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
7786 |
|
|
integrators/Integrator.cpp, applications/Makedepend: remove more |
7787 |
|
|
useless files |
7788 |
|
|
|
7789 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7790 |
tim |
1779 |
|
7791 |
tim |
2116 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7792 |
|
|
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
7793 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
7794 |
|
|
integrators/NVT.hpp: refactory integrator |
7795 |
|
|
|
7796 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7797 |
tim |
2116 |
|
7798 |
tim |
1779 |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
7799 |
|
|
branch new_design. |
7800 |
|
|
|
7801 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7802 |
tim |
1779 |
|
7803 |
tim |
2116 |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
7804 |
|
|
branch new_design. |
7805 |
tim |
1779 |
|
7806 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7807 |
tim |
1779 |
|
7808 |
|
|
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
7809 |
|
|
branch new_design. |
7810 |
|
|
|
7811 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7812 |
tim |
1779 |
|
7813 |
tim |
2116 |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
7814 |
|
|
on branch new_design. |
7815 |
tim |
1779 |
|
7816 |
chrisfen |
3131 |
2004-11-19 13:38 tim |
7817 |
tim |
1779 |
|
7818 |
tim |
2116 |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
7819 |
tim |
1779 |
branch new_design. |
7820 |
|
|
|
7821 |
chrisfen |
3131 |
2004-11-19 12:37 tim |
7822 |
tim |
2102 |
|
7823 |
tim |
2116 |
* forceFields/newDUFF.frc: new DUFF forcefield |
7824 |
tim |
2102 |
|
7825 |
chrisfen |
3131 |
2004-11-19 12:23 tim |
7826 |
tim |
1779 |
|
7827 |
tim |
2116 |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
7828 |
|
|
branch new_design. |
7829 |
tim |
1779 |
|
7830 |
chrisfen |
3131 |
2004-11-19 12:23 tim |
7831 |
tim |
1779 |
|
7832 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
7833 |
|
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
7834 |
|
|
utils/TypeContainer.hpp: add EAM |
7835 |
|
|
|
7836 |
chrisfen |
3131 |
2004-11-19 12:23 tim |
7837 |
tim |
1779 |
|
7838 |
|
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
7839 |
|
|
branch new_design. |
7840 |
|
|
|
7841 |
chrisfen |
3131 |
2004-11-19 10:02 tim |
7842 |
tim |
2102 |
|
7843 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
7844 |
|
|
error checking |
7845 |
|
|
|
7846 |
chrisfen |
3131 |
2004-11-19 09:56 tim |
7847 |
tim |
1779 |
|
7848 |
tim |
2116 |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
7849 |
tim |
1779 |
was initially added on branch new_design. |
7850 |
|
|
|
7851 |
chrisfen |
3131 |
2004-11-19 09:56 tim |
7852 |
tim |
1779 |
|
7853 |
tim |
2116 |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
7854 |
tim |
1779 |
was initially added on branch new_design. |
7855 |
|
|
|
7856 |
chrisfen |
3131 |
2004-11-19 09:56 tim |
7857 |
tim |
1779 |
|
7858 |
|
|
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
7859 |
|
|
added on branch new_design. |
7860 |
|
|
|
7861 |
chrisfen |
3131 |
2004-11-19 09:56 tim |
7862 |
tim |
1779 |
|
7863 |
|
|
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
7864 |
|
|
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
7865 |
|
|
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
7866 |
|
|
integrators/IntegratorFactory.cpp, |
7867 |
|
|
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
7868 |
|
|
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
7869 |
|
|
utils/StringTokenizer.cpp: DUFF is almost done except error |
7870 |
|
|
checking |
7871 |
|
|
|
7872 |
chrisfen |
3131 |
2004-11-18 16:11 tim |
7873 |
tim |
1779 |
|
7874 |
|
|
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
7875 |
|
|
|
7876 |
chrisfen |
3131 |
2004-11-18 15:26 tim |
7877 |
tim |
1779 |
|
7878 |
tim |
2116 |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
7879 |
|
|
initially added on branch new_design. |
7880 |
|
|
|
7881 |
chrisfen |
3131 |
2004-11-18 15:26 tim |
7882 |
tim |
2116 |
|
7883 |
tim |
1779 |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
7884 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
7885 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
7886 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
7887 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
7888 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
7889 |
|
|
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
7890 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
7891 |
|
|
DUFF parser |
7892 |
|
|
|
7893 |
chrisfen |
3131 |
2004-11-18 13:42 tim |
7894 |
tim |
2102 |
|
7895 |
tim |
1779 |
* forceFields/newDUFF.frc: adding new format DUFF force field |
7896 |
|
|
|
7897 |
chrisfen |
3131 |
2004-11-18 07:57 chrisfen |
7898 |
tim |
1779 |
|
7899 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
7900 |
|
|
slowed down the force loop |
7901 |
|
|
|
7902 |
chrisfen |
3131 |
2004-11-17 21:42 tim |
7903 |
tim |
1779 |
|
7904 |
tim |
2116 |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
7905 |
tim |
1779 |
initially added on branch new_design. |
7906 |
|
|
|
7907 |
chrisfen |
3131 |
2004-11-17 21:42 tim |
7908 |
tim |
1779 |
|
7909 |
tim |
2116 |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
7910 |
tim |
1779 |
initially added on branch new_design. |
7911 |
|
|
|
7912 |
chrisfen |
3131 |
2004-11-17 21:42 tim |
7913 |
tim |
1779 |
|
7914 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
7915 |
|
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
7916 |
|
|
utils/NumericConstant.hpp: Adding NumericConstant class |
7917 |
|
|
|
7918 |
chrisfen |
3131 |
2004-11-17 20:16 tim |
7919 |
tim |
1779 |
|
7920 |
|
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
7921 |
|
|
UseTheForce/ForceFields.hpp: remove more junk files |
7922 |
|
|
|
7923 |
chrisfen |
3131 |
2004-11-17 20:12 tim |
7924 |
tim |
1779 |
|
7925 |
|
|
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
7926 |
|
|
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
7927 |
|
|
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
7928 |
|
|
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
7929 |
|
|
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
7930 |
|
|
primitives/TorsionExtensions.cpp: remove some junk files |
7931 |
|
|
|
7932 |
chrisfen |
3131 |
2004-11-17 20:07 tim |
7933 |
tim |
1779 |
|
7934 |
|
|
* src/primitives/BendExtensions.cpp: remove some junk files |
7935 |
|
|
|
7936 |
chrisfen |
3131 |
2004-11-17 20:04 tim |
7937 |
tim |
1779 |
|
7938 |
|
|
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
7939 |
|
|
QuadraticBondType.hpp: refine QudraticBond |
7940 |
|
|
|
7941 |
chrisfen |
3131 |
2004-11-17 19:57 tim |
7942 |
tim |
1779 |
|
7943 |
|
|
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
7944 |
|
|
|
7945 |
chrisfen |
3131 |
2004-11-17 19:57 tim |
7946 |
tim |
1779 |
|
7947 |
|
|
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
7948 |
|
|
initially added on branch new_design. |
7949 |
|
|
|
7950 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7951 |
tim |
1779 |
|
7952 |
tim |
2116 |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
7953 |
|
|
was initially added on branch new_design. |
7954 |
|
|
|
7955 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7956 |
tim |
2116 |
|
7957 |
tim |
1779 |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
7958 |
|
|
added on branch new_design. |
7959 |
|
|
|
7960 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7961 |
tim |
1779 |
|
7962 |
tim |
2116 |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
7963 |
|
|
added on branch new_design. |
7964 |
|
|
|
7965 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7966 |
tim |
2116 |
|
7967 |
tim |
1779 |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
7968 |
|
|
initially added on branch new_design. |
7969 |
|
|
|
7970 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7971 |
tim |
1779 |
|
7972 |
tim |
2116 |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
7973 |
tim |
1779 |
initially added on branch new_design. |
7974 |
|
|
|
7975 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7976 |
tim |
1779 |
|
7977 |
tim |
2116 |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
7978 |
tim |
1779 |
initially added on branch new_design. |
7979 |
|
|
|
7980 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7981 |
tim |
1779 |
|
7982 |
|
|
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
7983 |
|
|
added on branch new_design. |
7984 |
|
|
|
7985 |
chrisfen |
3131 |
2004-11-17 13:47 tim |
7986 |
tim |
1779 |
|
7987 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
7988 |
|
|
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
7989 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
7990 |
|
|
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
7991 |
|
|
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
7992 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
7993 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
7994 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
7995 |
|
|
UreyBradleyBend and GhostBend |
7996 |
|
|
|
7997 |
chrisfen |
3131 |
2004-11-17 10:58 tim |
7998 |
tim |
2102 |
|
7999 |
tim |
1779 |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
8000 |
|
|
was initially added on branch new_design. |
8001 |
|
|
|
8002 |
chrisfen |
3131 |
2004-11-17 10:58 tim |
8003 |
tim |
1779 |
|
8004 |
|
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
8005 |
|
|
was initially added on branch new_design. |
8006 |
|
|
|
8007 |
chrisfen |
3131 |
2004-11-17 10:58 tim |
8008 |
tim |
1779 |
|
8009 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
8010 |
|
|
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
8011 |
|
|
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
8012 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
8013 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
8014 |
|
|
stuff and Chebyshev Polynomial |
8015 |
|
|
|
8016 |
chrisfen |
3131 |
2004-11-17 10:58 tim |
8017 |
tim |
1779 |
|
8018 |
tim |
2116 |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
8019 |
tim |
1779 |
initially added on branch new_design. |
8020 |
|
|
|
8021 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8022 |
tim |
1779 |
|
8023 |
tim |
2116 |
* src/types/PolynomialTorsionType.hpp: file |
8024 |
|
|
PolynomialTorsionType.hpp was initially added on branch new_design. |
8025 |
tim |
1779 |
|
8026 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8027 |
tim |
1779 |
|
8028 |
|
|
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
8029 |
|
|
initially added on branch new_design. |
8030 |
|
|
|
8031 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8032 |
tim |
1779 |
|
8033 |
|
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
8034 |
|
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
8035 |
|
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
8036 |
|
|
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
8037 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
8038 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
8039 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
8040 |
|
|
utils/StringTokenizer.hpp: add PolynomialBondType, |
8041 |
|
|
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
8042 |
|
|
CharmmTorsionType. Need to refine the design and add document for |
8043 |
|
|
them |
8044 |
|
|
|
8045 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8046 |
tim |
1779 |
|
8047 |
tim |
2116 |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
8048 |
|
|
initially added on branch new_design. |
8049 |
|
|
|
8050 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8051 |
tim |
2116 |
|
8052 |
|
|
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
8053 |
|
|
initially added on branch new_design. |
8054 |
|
|
|
8055 |
chrisfen |
3131 |
2004-11-16 22:37 tim |
8056 |
tim |
2116 |
|
8057 |
|
|
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
8058 |
|
|
initially added on branch new_design. |
8059 |
|
|
|
8060 |
chrisfen |
3131 |
2004-11-16 17:11 tim |
8061 |
tim |
2116 |
|
8062 |
tim |
1779 |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
8063 |
|
|
TorsionType.hpp: add PolynomialBondType |
8064 |
|
|
|
8065 |
chrisfen |
3131 |
2004-11-16 17:11 tim |
8066 |
tim |
1779 |
|
8067 |
|
|
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
8068 |
|
|
initially added on branch new_design. |
8069 |
|
|
|
8070 |
chrisfen |
3131 |
2004-11-16 15:20 tim |
8071 |
tim |
1779 |
|
8072 |
|
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
8073 |
|
|
on branch new_design. |
8074 |
|
|
|
8075 |
chrisfen |
3131 |
2004-11-16 15:20 tim |
8076 |
tim |
1779 |
|
8077 |
tim |
2116 |
* src/math/Polynomial.hpp: Adding Polynomial class |
8078 |
tim |
1779 |
|
8079 |
chrisfen |
3131 |
2004-11-16 14:04 gezelter |
8080 |
tim |
1779 |
|
8081 |
|
|
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
8082 |
|
|
added on branch new_design. |
8083 |
|
|
|
8084 |
chrisfen |
3131 |
2004-11-16 14:04 gezelter |
8085 |
tim |
1779 |
|
8086 |
tim |
2116 |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
8087 |
|
|
initially added on branch new_design. |
8088 |
|
|
|
8089 |
chrisfen |
3131 |
2004-11-16 14:04 gezelter |
8090 |
tim |
2116 |
|
8091 |
tim |
1779 |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
8092 |
|
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
8093 |
|
|
|
8094 |
chrisfen |
3131 |
2004-11-16 12:36 tim |
8095 |
tim |
1779 |
|
8096 |
|
|
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
8097 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
8098 |
|
|
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
8099 |
|
|
TorsionType |
8100 |
|
|
|
8101 |
chrisfen |
3131 |
2004-11-15 18:07 tim |
8102 |
tim |
1779 |
|
8103 |
tim |
2116 |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
8104 |
|
|
branch new_design. |
8105 |
|
|
|
8106 |
chrisfen |
3131 |
2004-11-15 18:07 tim |
8107 |
tim |
2116 |
|
8108 |
tim |
1779 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
8109 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
8110 |
|
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
8111 |
|
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
8112 |
|
|
|
8113 |
chrisfen |
3131 |
2004-11-15 15:00 tim |
8114 |
tim |
1779 |
|
8115 |
tim |
2116 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
8116 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
8117 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
8118 |
|
|
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
8119 |
|
|
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
8120 |
tim |
1779 |
|
8121 |
chrisfen |
3131 |
2004-11-15 15:00 tim |
8122 |
tim |
1779 |
|
8123 |
|
|
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
8124 |
|
|
was initially added on branch new_design. |
8125 |
|
|
|
8126 |
chrisfen |
3131 |
2004-11-15 15:00 tim |
8127 |
tim |
1779 |
|
8128 |
tim |
2116 |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
8129 |
|
|
was initially added on branch new_design. |
8130 |
|
|
|
8131 |
chrisfen |
3131 |
2004-11-15 15:00 tim |
8132 |
tim |
2116 |
|
8133 |
tim |
2102 |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
8134 |
|
|
branch new_design. |
8135 |
tim |
1779 |
|
8136 |
chrisfen |
3131 |
2004-11-15 10:02 tim |
8137 |
tim |
1779 |
|
8138 |
tim |
2116 |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
8139 |
|
|
initially added on branch new_design. |
8140 |
tim |
1779 |
|
8141 |
chrisfen |
3131 |
2004-11-15 10:02 tim |
8142 |
tim |
1779 |
|
8143 |
|
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
8144 |
|
|
branch new_design. |
8145 |
|
|
|
8146 |
chrisfen |
3131 |
2004-11-15 10:02 tim |
8147 |
tim |
1779 |
|
8148 |
|
|
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
8149 |
|
|
branch new_design. |
8150 |
|
|
|
8151 |
chrisfen |
3131 |
2004-11-15 10:02 tim |
8152 |
tim |
1779 |
|
8153 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
8154 |
|
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
8155 |
|
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
8156 |
|
|
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
8157 |
|
|
DumpWriter.Next Step is LJFF and integrators |
8158 |
|
|
|
8159 |
chrisfen |
3131 |
2004-11-12 21:08 tim |
8160 |
tim |
1779 |
|
8161 |
|
|
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
8162 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
8163 |
|
|
brains/SimInfo.hpp, primitives/Molecule.cpp, |
8164 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
8165 |
|
|
refactory, refactory |
8166 |
|
|
|
8167 |
chrisfen |
3131 |
2004-11-12 14:43 tim |
8168 |
tim |
1779 |
|
8169 |
|
|
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
8170 |
|
|
StringTokenizer.cpp: bug fix in hasMoreTokens |
8171 |
|
|
|
8172 |
chrisfen |
3131 |
2004-11-12 14:28 tim |
8173 |
tim |
1779 |
|
8174 |
|
|
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
8175 |
|
|
initially added on branch new_design. |
8176 |
|
|
|
8177 |
chrisfen |
3131 |
2004-11-12 14:28 tim |
8178 |
tim |
1779 |
|
8179 |
|
|
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
8180 |
|
|
StringUtils, a c-style strtok like class, need unit test |
8181 |
|
|
|
8182 |
chrisfen |
3131 |
2004-11-12 09:40 tim |
8183 |
tim |
1779 |
|
8184 |
|
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
8185 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
8186 |
|
|
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
8187 |
|
|
|
8188 |
chrisfen |
3131 |
2004-11-11 23:05 tim |
8189 |
tim |
1779 |
|
8190 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
8191 |
|
|
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
8192 |
|
|
MoleculeCreator forget to create CutoffGroups for free atoms |
8193 |
|
|
|
8194 |
chrisfen |
3131 |
2004-11-11 22:19 tim |
8195 |
tim |
1779 |
|
8196 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
8197 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
8198 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
8199 |
|
|
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
8200 |
|
|
OOPSE = Object-Obfuscated Parallel Simulation Engine |
8201 |
|
|
|
8202 |
chrisfen |
3131 |
2004-11-11 13:48 chrisfen |
8203 |
tim |
1779 |
|
8204 |
|
|
* samples/water/tip3p_ice/tp3.md: working sample |
8205 |
|
|
|
8206 |
chrisfen |
3131 |
2004-11-11 13:47 chrisfen |
8207 |
tim |
1779 |
|
8208 |
|
|
* src/restraints/Restraints.cpp: working towards parallel |
8209 |
|
|
restraints |
8210 |
|
|
|
8211 |
chrisfen |
3131 |
2004-11-11 13:47 chrisfen |
8212 |
tim |
1779 |
|
8213 |
|
|
* src/integrators/Integrator.cpp: Commented out some write |
8214 |
|
|
statements |
8215 |
|
|
|
8216 |
chrisfen |
3131 |
2004-11-11 13:46 chrisfen |
8217 |
tim |
1779 |
|
8218 |
|
|
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
8219 |
|
|
write statements |
8220 |
|
|
|
8221 |
chrisfen |
3131 |
2004-11-11 13:46 chrisfen |
8222 |
tim |
1779 |
|
8223 |
|
|
* samples/water/tip3p_ice/tp3.md: Fun with ice |
8224 |
|
|
|
8225 |
chrisfen |
3131 |
2004-11-11 08:41 tim |
8226 |
tim |
1779 |
|
8227 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
8228 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
8229 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
8230 |
|
|
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
8231 |
|
|
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
8232 |
|
|
useless mpiSimulation |
8233 |
|
|
|
8234 |
chrisfen |
3131 |
2004-11-11 08:41 tim |
8235 |
tim |
1779 |
|
8236 |
|
|
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
8237 |
|
|
branch new_design. |
8238 |
|
|
|
8239 |
chrisfen |
3131 |
2004-11-10 14:50 tim |
8240 |
tim |
1779 |
|
8241 |
|
|
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
8242 |
|
|
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
8243 |
|
|
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
8244 |
|
|
|
8245 |
chrisfen |
3131 |
2004-11-10 14:01 tim |
8246 |
tim |
1779 |
|
8247 |
|
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
8248 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
8249 |
|
|
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
8250 |
|
|
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
8251 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
8252 |
|
|
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
8253 |
|
|
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
8254 |
|
|
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
8255 |
|
|
File will be removed) (3) ForceField (at least LJ) and BondType, |
8256 |
|
|
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
8257 |
|
|
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
8258 |
|
|
|
8259 |
chrisfen |
3131 |
2004-11-10 06:52 tim |
8260 |
tim |
1779 |
|
8261 |
|
|
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
8262 |
|
|
configurable StatWriter |
8263 |
|
|
|
8264 |
chrisfen |
3131 |
2004-11-10 06:52 tim |
8265 |
tim |
1779 |
|
8266 |
|
|
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
8267 |
|
|
branch new_design. |
8268 |
|
|
|
8269 |
chrisfen |
3131 |
2004-11-09 18:58 tim |
8270 |
tim |
1779 |
|
8271 |
|
|
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
8272 |
|
|
in progress |
8273 |
|
|
|
8274 |
chrisfen |
3131 |
2004-11-09 15:11 tim |
8275 |
tim |
1779 |
|
8276 |
tim |
2116 |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
8277 |
|
|
added on branch new_design. |
8278 |
|
|
|
8279 |
chrisfen |
3131 |
2004-11-09 15:11 tim |
8280 |
tim |
2116 |
|
8281 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: file |
8282 |
|
|
VelocityVerletIntegrator.cpp was initially added on branch |
8283 |
|
|
new_design. |
8284 |
|
|
|
8285 |
chrisfen |
3131 |
2004-11-09 15:11 tim |
8286 |
tim |
2116 |
|
8287 |
tim |
1779 |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
8288 |
|
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
8289 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
8290 |
|
|
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
8291 |
|
|
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
8292 |
|
|
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
8293 |
|
|
|
8294 |
chrisfen |
3131 |
2004-11-09 15:11 tim |
8295 |
tim |
1779 |
|
8296 |
|
|
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
8297 |
|
|
added on branch new_design. |
8298 |
|
|
|
8299 |
chrisfen |
3131 |
2004-11-09 15:11 tim |
8300 |
tim |
1779 |
|
8301 |
|
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
8302 |
|
|
branch new_design. |
8303 |
|
|
|
8304 |
chrisfen |
3131 |
2004-11-08 17:08 tim |
8305 |
tim |
2102 |
|
8306 |
tim |
1779 |
* src/integrators/VelocityVerletIntegrator.hpp: file |
8307 |
|
|
VelocityVerletIntegrator.hpp was initially added on branch |
8308 |
|
|
new_design. |
8309 |
|
|
|
8310 |
chrisfen |
3131 |
2004-11-08 17:08 tim |
8311 |
tim |
1779 |
|
8312 |
tim |
2116 |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
8313 |
|
|
branch new_design. |
8314 |
|
|
|
8315 |
chrisfen |
3131 |
2004-11-08 17:08 tim |
8316 |
tim |
2116 |
|
8317 |
tim |
1779 |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
8318 |
|
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
8319 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
8320 |
|
|
utils/TypeContainer.hpp: More to break |
8321 |
|
|
|
8322 |
chrisfen |
3131 |
2004-11-05 21:21 tim |
8323 |
tim |
2102 |
|
8324 |
tim |
1779 |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
8325 |
|
|
added on branch new_design. |
8326 |
|
|
|
8327 |
chrisfen |
3131 |
2004-11-05 21:21 tim |
8328 |
tim |
1779 |
|
8329 |
|
|
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
8330 |
|
|
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
8331 |
|
|
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
8332 |
|
|
ForceField and TypeContainer classes |
8333 |
|
|
|
8334 |
chrisfen |
3131 |
2004-11-05 15:38 tim |
8335 |
tim |
1779 |
|
8336 |
tim |
2116 |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
8337 |
|
|
initially added on branch new_design. |
8338 |
|
|
|
8339 |
chrisfen |
3131 |
2004-11-05 15:38 tim |
8340 |
tim |
2116 |
|
8341 |
tim |
1779 |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
8342 |
|
|
initially added on branch new_design. |
8343 |
|
|
|
8344 |
chrisfen |
3131 |
2004-11-05 15:38 tim |
8345 |
tim |
1779 |
|
8346 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
8347 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
8348 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
8349 |
|
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
8350 |
|
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
8351 |
|
|
|
8352 |
chrisfen |
3131 |
2004-11-05 13:45 chrisfen |
8353 |
tim |
2102 |
|
8354 |
tim |
1779 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
8355 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
8356 |
|
|
linear visitor |
8357 |
|
|
|
8358 |
chrisfen |
3131 |
2004-11-05 13:04 chrisfen |
8359 |
tim |
1779 |
|
8360 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
8361 |
|
|
debugging process |
8362 |
|
|
|
8363 |
chrisfen |
3131 |
2004-11-05 13:04 chrisfen |
8364 |
tim |
1779 |
|
8365 |
|
|
* make/Makefile.in: included visitors and minimizer |
8366 |
|
|
|
8367 |
chrisfen |
3131 |
2004-11-05 13:03 chrisfen |
8368 |
tim |
1779 |
|
8369 |
|
|
* ChangeLog: new changes |
8370 |
|
|
|
8371 |
chrisfen |
3131 |
2004-11-04 18:56 tim |
8372 |
tim |
1701 |
|
8373 |
chrisfen |
1714 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
8374 |
|
|
primitives/Molecule.hpp: Pain...... |
8375 |
tim |
1712 |
|
8376 |
chrisfen |
3131 |
2004-11-04 12:55 tim |
8377 |
chrisfen |
1714 |
|
8378 |
|
|
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
8379 |
|
|
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
8380 |
|
|
src/brains/Stats.hpp: time to break SimSetup |
8381 |
|
|
|
8382 |
chrisfen |
3131 |
2004-11-04 12:51 gezelter |
8383 |
chrisfen |
1714 |
|
8384 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
8385 |
|
|
classes in progress |
8386 |
|
|
|
8387 |
chrisfen |
3131 |
2004-11-04 11:48 tim |
8388 |
tim |
1712 |
|
8389 |
|
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
8390 |
tim |
1701 |
branch new_design. |
8391 |
|
|
|
8392 |
chrisfen |
3131 |
2004-11-04 11:48 tim |
8393 |
tim |
1712 |
|
8394 |
|
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
8395 |
|
|
branch new_design. |
8396 |
|
|
|
8397 |
chrisfen |
3131 |
2004-11-04 11:48 tim |
8398 |
tim |
1712 |
|
8399 |
tim |
2116 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
8400 |
|
|
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
8401 |
|
|
class |
8402 |
|
|
|
8403 |
chrisfen |
3131 |
2004-11-04 08:22 gezelter |
8404 |
tim |
2116 |
|
8405 |
tim |
1712 |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
8406 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
8407 |
|
|
linearAxis are virtual in StuntDouble, but are implemented by |
8408 |
|
|
DirectionalAtom and RigidBody In StuntDouble, they should return |
8409 |
|
|
false and "-1" but there should be logic to figure them out in the |
8410 |
|
|
other two classes |
8411 |
|
|
|
8412 |
chrisfen |
3131 |
2004-11-04 08:20 gezelter |
8413 |
tim |
1712 |
|
8414 |
|
|
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
8415 |
|
|
remember what I did |
8416 |
|
|
|
8417 |
chrisfen |
3131 |
2004-11-04 08:20 gezelter |
8418 |
tim |
1712 |
|
8419 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
8420 |
|
|
|
8421 |
chrisfen |
3131 |
2004-11-04 08:20 gezelter |
8422 |
tim |
1712 |
|
8423 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
8424 |
|
|
in the entry_plug so that it only is set if the atoms really are in |
8425 |
|
|
the simulation |
8426 |
|
|
|
8427 |
chrisfen |
3131 |
2004-11-04 08:20 gezelter |
8428 |
tim |
1712 |
|
8429 |
|
|
* samples/water/ssd/ssd.md: testing force fields |
8430 |
|
|
|
8431 |
chrisfen |
3131 |
2004-11-04 08:19 gezelter |
8432 |
tim |
1712 |
|
8433 |
|
|
* samples/shape/linear.in: testing shapes |
8434 |
|
|
|
8435 |
chrisfen |
3131 |
2004-11-03 11:56 tim |
8436 |
tim |
1712 |
|
8437 |
|
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
8438 |
|
|
class(similar as SimSetup) |
8439 |
|
|
|
8440 |
chrisfen |
3131 |
2004-11-03 11:56 tim |
8441 |
tim |
1712 |
|
8442 |
|
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
8443 |
|
|
added on branch new_design. |
8444 |
|
|
|
8445 |
chrisfen |
3131 |
2004-11-03 11:56 tim |
8446 |
chrisfen |
1714 |
|
8447 |
|
|
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
8448 |
|
|
added on branch new_design. |
8449 |
|
|
|
8450 |
chrisfen |
3131 |
2004-11-03 10:00 tim |
8451 |
tim |
1712 |
|
8452 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8453 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
8454 |
|
|
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
8455 |
|
|
brains/DataStorage.hpp, primitives/Atom.hpp, |
8456 |
|
|
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
8457 |
|
|
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
8458 |
|
|
compiled. Still a long way to go ...... |
8459 |
|
|
|
8460 |
chrisfen |
3131 |
2004-11-03 08:08 tim |
8461 |
tim |
1712 |
|
8462 |
|
|
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
8463 |
|
|
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
8464 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
8465 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
8466 |
|
|
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
8467 |
|
|
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
8468 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
8469 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
8470 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
8471 |
|
|
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
8472 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
8473 |
|
|
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
8474 |
|
|
|
8475 |
chrisfen |
3131 |
2004-11-02 14:41 tim |
8476 |
tim |
1712 |
|
8477 |
tim |
2116 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
8478 |
|
|
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
8479 |
|
|
Need unit test |
8480 |
chrisfen |
1714 |
|
8481 |
chrisfen |
3131 |
2004-11-02 14:41 tim |
8482 |
chrisfen |
1714 |
|
8483 |
tim |
1712 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
8484 |
|
|
initially added on branch new_design. |
8485 |
|
|
|
8486 |
chrisfen |
3131 |
2004-11-02 14:41 tim |
8487 |
tim |
1712 |
|
8488 |
tim |
2116 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
8489 |
|
|
branch new_design. |
8490 |
tim |
1712 |
|
8491 |
chrisfen |
3131 |
2004-11-02 08:59 tim |
8492 |
tim |
1712 |
|
8493 |
tim |
2116 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
8494 |
|
|
branch new_design. |
8495 |
|
|
|
8496 |
chrisfen |
3131 |
2004-11-02 08:59 tim |
8497 |
tim |
2116 |
|
8498 |
tim |
2102 |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
8499 |
|
|
SimSnapshotManager.hpp: SimModel in progress |
8500 |
tim |
1712 |
|
8501 |
chrisfen |
3131 |
2004-11-02 07:28 chrisfen |
8502 |
tim |
1701 |
|
8503 |
|
|
* src/: UseTheForce/DarkSide/shapes.F90, |
8504 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
8505 |
|
|
looks like it's working |
8506 |
|
|
|
8507 |
chrisfen |
3131 |
2004-11-02 07:27 tim |
8508 |
tim |
1701 |
|
8509 |
tim |
2116 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
8510 |
|
|
functions for dealing with memory issue |
8511 |
|
|
|
8512 |
chrisfen |
3131 |
2004-11-02 07:27 tim |
8513 |
tim |
2116 |
|
8514 |
tim |
2102 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
8515 |
|
|
added on branch new_design. |
8516 |
tim |
1701 |
|
8517 |
chrisfen |
3131 |
2004-11-02 07:23 tim |
8518 |
tim |
1701 |
|
8519 |
|
|
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
8520 |
|
|
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
8521 |
|
|
SimModel(something similar as SimInfo) |
8522 |
|
|
|
8523 |
chrisfen |
3131 |
2004-11-01 14:52 tim |
8524 |
tim |
1701 |
|
8525 |
|
|
* src/: applications/simpleBuilder/MoLocator.hpp, |
8526 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
8527 |
|
|
brains/DataStorage.hpp, brains/ForceFields.cpp, |
8528 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
8529 |
|
|
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
8530 |
|
|
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
8531 |
|
|
math/SquareMatrix3.hpp, math/Vector3.hpp, |
8532 |
|
|
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
8533 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
8534 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
8535 |
|
|
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
8536 |
|
|
restraints/Restraints.cpp, types/TorsionType.hpp, |
8537 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
8538 |
|
|
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
8539 |
|
|
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
8540 |
|
|
RigidBody and StuntDouble classes get compiled |
8541 |
|
|
|
8542 |
chrisfen |
3131 |
2004-11-01 13:40 tim |
8543 |
tim |
1701 |
|
8544 |
tim |
2116 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
8545 |
|
|
on branch new_design. |
8546 |
|
|
|
8547 |
chrisfen |
3131 |
2004-11-01 13:40 tim |
8548 |
tim |
2116 |
|
8549 |
tim |
2102 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
8550 |
|
|
branch new_design. |
8551 |
tim |
1701 |
|
8552 |
chrisfen |
3131 |
2004-11-01 13:40 tim |
8553 |
tim |
1701 |
|
8554 |
|
|
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
8555 |
|
|
branch new_design. |
8556 |
|
|
|
8557 |
chrisfen |
3131 |
2004-11-01 13:40 tim |
8558 |
tim |
1701 |
|
8559 |
tim |
2116 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
8560 |
|
|
version of Bond, Bend and Torsion. |
8561 |
tim |
1701 |
|
8562 |
chrisfen |
3131 |
2004-11-01 13:37 tim |
8563 |
tim |
1701 |
|
8564 |
|
|
* src/types/BendType.hpp: file BendType.hpp was initially added on |
8565 |
|
|
branch new_design. |
8566 |
|
|
|
8567 |
chrisfen |
3131 |
2004-11-01 13:37 tim |
8568 |
tim |
1701 |
|
8569 |
tim |
2116 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
8570 |
|
|
BondType, BendType, TorsionType |
8571 |
tim |
1701 |
|
8572 |
chrisfen |
3131 |
2004-11-01 13:37 tim |
8573 |
tim |
1701 |
|
8574 |
|
|
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
8575 |
|
|
added on branch new_design. |
8576 |
|
|
|
8577 |
chrisfen |
3131 |
2004-11-01 13:37 tim |
8578 |
tim |
1701 |
|
8579 |
tim |
2116 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
8580 |
|
|
branch new_design. |
8581 |
tim |
1701 |
|
8582 |
chrisfen |
3131 |
2004-11-01 12:15 tim |
8583 |
tim |
1701 |
|
8584 |
|
|
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
8585 |
|
|
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
8586 |
|
|
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
8587 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
8588 |
|
|
break, break and break..... |
8589 |
|
|
|
8590 |
chrisfen |
3131 |
2004-11-01 11:57 tim |
8591 |
tim |
1701 |
|
8592 |
|
|
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
8593 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
8594 |
|
|
StuntDouble.hpp: these core classes get compiled |
8595 |
|
|
|
8596 |
chrisfen |
3131 |
2004-10-29 15:37 tim |
8597 |
tim |
1701 |
|
8598 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
8599 |
|
|
class |
8600 |
|
|
|
8601 |
chrisfen |
3131 |
2004-10-29 15:28 chrisfen |
8602 |
tim |
1701 |
|
8603 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
8604 |
|
|
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
8605 |
|
|
types/ShapeAtomType.cpp: still debugging |
8606 |
|
|
|
8607 |
chrisfen |
3131 |
2004-10-29 15:28 chrisfen |
8608 |
tim |
1701 |
|
8609 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
8610 |
|
|
shapes rcut calculator added |
8611 |
|
|
|
8612 |
chrisfen |
3131 |
2004-10-29 15:27 chrisfen |
8613 |
tim |
1701 |
|
8614 |
|
|
* samples/shape/linear.md: shorter run |
8615 |
|
|
|
8616 |
chrisfen |
3131 |
2004-10-29 13:54 tim |
8617 |
tim |
1701 |
|
8618 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
8619 |
|
|
|
8620 |
chrisfen |
3131 |
2004-10-29 09:22 tim |
8621 |
tim |
1701 |
|
8622 |
|
|
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
8623 |
|
|
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
8624 |
|
|
some deprecated files |
8625 |
|
|
|
8626 |
chrisfen |
3131 |
2004-10-29 09:20 tim |
8627 |
tim |
1701 |
|
8628 |
|
|
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
8629 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
8630 |
|
|
More painful reconstruction is coming !!! |
8631 |
|
|
|
8632 |
chrisfen |
3131 |
2004-10-28 15:34 tim |
8633 |
tim |
1701 |
|
8634 |
|
|
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
8635 |
|
|
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
8636 |
|
|
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
8637 |
|
|
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
8638 |
|
|
DirectionalAtom and RigidBody |
8639 |
|
|
|
8640 |
chrisfen |
3131 |
2004-10-28 15:26 tim |
8641 |
tim |
1701 |
|
8642 |
|
|
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
8643 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
8644 |
|
|
src/applications/simpleBuilder/Vector3d.hpp, |
8645 |
|
|
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
8646 |
|
|
remove old Vector3d.hpp from application/simpleBuilder |
8647 |
|
|
|
8648 |
chrisfen |
3131 |
2004-10-28 14:42 tim |
8649 |
tim |
1701 |
|
8650 |
|
|
* src/utils/next_combination.hpp: Minor change in next_combination |
8651 |
|
|
|
8652 |
chrisfen |
3131 |
2004-10-28 14:28 tim |
8653 |
tim |
1681 |
|
8654 |
|
|
* src/utils/next_combination.hpp, |
8655 |
|
|
test/utils/NextCombinationTestCase.cpp, |
8656 |
|
|
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
8657 |
|
|
|
8658 |
chrisfen |
3131 |
2004-10-28 14:11 tim |
8659 |
tim |
1681 |
|
8660 |
|
|
* src/utils/next_combination.hpp: change documentation of |
8661 |
|
|
next_combination.hpp |
8662 |
|
|
|
8663 |
chrisfen |
3131 |
2004-10-28 13:41 tim |
8664 |
tim |
1681 |
|
8665 |
|
|
* ChangeLog, src/utils/next_combination.hpp, |
8666 |
|
|
test/utils/NextCombinationTestCase.cpp, |
8667 |
|
|
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
8668 |
|
|
|
8669 |
chrisfen |
3131 |
2004-10-28 13:01 tim |
8670 |
tim |
1681 |
|
8671 |
|
|
* src/utils/next_combination.hpp: adding replace wildcard function |
8672 |
|
|
|
8673 |
chrisfen |
3131 |
2004-10-28 12:33 tim |
8674 |
tim |
1681 |
|
8675 |
|
|
* src/utils/next_combination.hpp: Minor change |
8676 |
|
|
|
8677 |
chrisfen |
3131 |
2004-10-28 12:06 tim |
8678 |
tim |
1677 |
|
8679 |
|
|
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
8680 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
8681 |
|
|
src/utils/next_combination.hpp, test/utils/Makefile, |
8682 |
|
|
test/utils/NextCombinationTestCase.cpp, |
8683 |
|
|
test/utils/ReplaceWildCardTestCase.cpp, |
8684 |
|
|
test/utils/next_combination.hpp: STL next_permutation like |
8685 |
|
|
next_combination is working |
8686 |
|
|
|
8687 |
chrisfen |
3131 |
2004-10-28 10:22 chrisfen |
8688 |
tim |
1677 |
|
8689 |
|
|
* src/UseTheForce/WATER.cpp: fix of setDipoles |
8690 |
|
|
|
8691 |
chrisfen |
3131 |
2004-10-28 10:20 gezelter |
8692 |
tim |
1677 |
|
8693 |
|
|
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
8694 |
|
|
shapeFile |
8695 |
|
|
|
8696 |
chrisfen |
3131 |
2004-10-28 10:20 gezelter |
8697 |
tim |
1677 |
|
8698 |
|
|
* samples/shape/linear.md: forgot the orientation line |
8699 |
|
|
|
8700 |
chrisfen |
3131 |
2004-10-28 09:56 gezelter |
8701 |
tim |
1677 |
|
8702 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8703 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
8704 |
|
|
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
8705 |
|
|
declaration foo |
8706 |
|
|
|
8707 |
chrisfen |
3131 |
2004-10-28 09:55 gezelter |
8708 |
tim |
1677 |
|
8709 |
|
|
* samples/lipid/5x5.md: uncommented .in line |
8710 |
|
|
|
8711 |
chrisfen |
3131 |
2004-10-28 08:42 tim |
8712 |
tim |
1677 |
|
8713 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
8714 |
|
|
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
8715 |
|
|
in progress |
8716 |
|
|
|
8717 |
chrisfen |
3131 |
2004-10-28 08:15 tim |
8718 |
tim |
1677 |
|
8719 |
|
|
* test/utils/: NextCombinationTestCase.cpp, |
8720 |
|
|
NextCombinationTestCase.hpp: adding next_combination test case |
8721 |
|
|
|
8722 |
chrisfen |
3131 |
2004-10-28 08:02 tim |
8723 |
tim |
1677 |
|
8724 |
|
|
* test/utils/next_combination.hpp: STL Compatible combination |
8725 |
|
|
sequence generator |
8726 |
|
|
|
8727 |
chrisfen |
3131 |
2004-10-27 23:23 tim |
8728 |
tim |
1677 |
|
8729 |
|
|
* test/utils/: GenerateCombination.hpp, |
8730 |
|
|
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
8731 |
|
|
|
8732 |
chrisfen |
3131 |
2004-10-27 23:16 tim |
8733 |
tim |
1677 |
|
8734 |
|
|
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
8735 |
|
|
next_combination function. |
8736 |
|
|
|
8737 |
chrisfen |
3131 |
2004-10-27 20:27 tim |
8738 |
tim |
1677 |
|
8739 |
|
|
* test/utils/ReplaceWildCard.hpp: no message |
8740 |
|
|
|
8741 |
chrisfen |
3131 |
2004-10-27 20:14 tim |
8742 |
tim |
1677 |
|
8743 |
|
|
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
8744 |
|
|
ReplaceWildCard(recursive version) is working, need refactoring. An |
8745 |
|
|
iterative version is on the way |
8746 |
|
|
|
8747 |
chrisfen |
3131 |
2004-10-27 19:28 tim |
8748 |
tim |
1677 |
|
8749 |
|
|
* test/utils/: Makefile, ReplaceWildCard.hpp, |
8750 |
|
|
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
8751 |
|
|
|
8752 |
chrisfen |
3131 |
2004-10-27 19:08 tim |
8753 |
tim |
1677 |
|
8754 |
|
|
* test/utils/: ReplaceWildCardTestCase.cpp, |
8755 |
|
|
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
8756 |
|
|
|
8757 |
chrisfen |
3131 |
2004-10-27 16:17 tim |
8758 |
tim |
1677 |
|
8759 |
|
|
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
8760 |
|
|
test |
8761 |
|
|
|
8762 |
chrisfen |
3131 |
2004-10-26 23:25 tim |
8763 |
tim |
1677 |
|
8764 |
|
|
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
8765 |
|
|
char matching is on the way |
8766 |
|
|
|
8767 |
chrisfen |
3131 |
2004-10-26 23:07 tim |
8768 |
tim |
1677 |
|
8769 |
|
|
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
8770 |
|
|
|
8771 |
chrisfen |
3131 |
2004-10-26 20:00 gezelter |
8772 |
tim |
1674 |
|
8773 |
|
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
8774 |
|
|
|
8775 |
chrisfen |
3131 |
2004-10-26 19:20 gezelter |
8776 |
tim |
1674 |
|
8777 |
|
|
* src/UseTheForce/ForceFields.hpp: subclass foo |
8778 |
|
|
|
8779 |
chrisfen |
3131 |
2004-10-26 19:16 gezelter |
8780 |
tim |
1674 |
|
8781 |
|
|
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
8782 |
|
|
string conversion |
8783 |
|
|
|
8784 |
chrisfen |
3131 |
2004-10-26 17:01 gezelter |
8785 |
tim |
1674 |
|
8786 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8787 |
|
|
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
8788 |
|
|
brains/SimSetup.hpp: char* -> string |
8789 |
|
|
|
8790 |
chrisfen |
3131 |
2004-10-26 15:25 gezelter |
8791 |
tim |
1674 |
|
8792 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
8793 |
|
|
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
8794 |
|
|
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
8795 |
|
|
isXXX |
8796 |
|
|
|
8797 |
chrisfen |
3131 |
2004-10-26 15:25 gezelter |
8798 |
tim |
1674 |
|
8799 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
8800 |
|
|
define name collision |
8801 |
|
|
|
8802 |
chrisfen |
3131 |
2004-10-26 15:24 gezelter |
8803 |
tim |
1674 |
|
8804 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8805 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
8806 |
|
|
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
8807 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8808 |
|
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
8809 |
|
|
forcefield refactoring for shapes |
8810 |
|
|
|
8811 |
chrisfen |
3131 |
2004-10-26 15:24 gezelter |
8812 |
tim |
1677 |
|
8813 |
|
|
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
8814 |
|
|
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
8815 |
|
|
linear.md, linear.shape, toluene.shape: adding sample shape |
8816 |
|
|
directory |
8817 |
|
|
|
8818 |
chrisfen |
3131 |
2004-10-26 15:19 tim |
8819 |
tim |
1674 |
|
8820 |
|
|
* ChangeLog, src/brains/DataStorage.cpp, |
8821 |
|
|
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
8822 |
|
|
test/brains/DataStorageTestCase.cpp, |
8823 |
|
|
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
8824 |
|
|
DataStorage passes unit test |
8825 |
|
|
|
8826 |
chrisfen |
3131 |
2004-10-26 11:03 chrisfen |
8827 |
tim |
1674 |
|
8828 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
8829 |
|
|
Changes to help advance shapes |
8830 |
|
|
|
8831 |
chrisfen |
3131 |
2004-10-26 11:02 chrisfen |
8832 |
tim |
1674 |
|
8833 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
8834 |
|
|
Shapes force field reader |
8835 |
|
|
|
8836 |
chrisfen |
3131 |
2004-10-26 10:28 tim |
8837 |
tim |
1674 |
|
8838 |
|
|
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
8839 |
|
|
SnapshotTestCase in progress |
8840 |
|
|
|
8841 |
chrisfen |
3131 |
2004-10-25 15:46 tim |
8842 |
tim |
1648 |
|
8843 |
|
|
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
8844 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
8845 |
|
|
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
8846 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
8847 |
|
|
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
8848 |
|
|
and Vector classes |
8849 |
|
|
|
8850 |
chrisfen |
3131 |
2004-10-25 10:03 tim |
8851 |
tim |
1644 |
|
8852 |
|
|
* ChangeLog, src/utils/GenericFactory.hpp, |
8853 |
|
|
test/utils/GenericFactoryTestCase.cpp, |
8854 |
|
|
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
8855 |
|
|
GenericFactory Test Case. GenericFactory now can bed used to creat |
8856 |
|
|
ForcefieldFactory and IntegratorFactory etc. |
8857 |
|
|
|
8858 |
chrisfen |
3131 |
2004-10-24 21:08 tim |
8859 |
tim |
1644 |
|
8860 |
|
|
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
8861 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
8862 |
|
|
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
8863 |
|
|
get reconstructed |
8864 |
|
|
|
8865 |
chrisfen |
3131 |
2004-10-24 00:55 tim |
8866 |
tim |
1644 |
|
8867 |
|
|
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
8868 |
|
|
|
8869 |
chrisfen |
3131 |
2004-10-23 16:09 tim |
8870 |
tim |
1644 |
|
8871 |
|
|
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
8872 |
|
|
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
8873 |
|
|
RigidBody.cpp: Refactoring in progress |
8874 |
|
|
|
8875 |
chrisfen |
3131 |
2004-10-22 16:09 tim |
8876 |
tim |
1643 |
|
8877 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
8878 |
|
|
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
8879 |
|
|
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
8880 |
|
|
test/brains/StuntDouble.hpp: more work in Snapshot |
8881 |
|
|
|
8882 |
chrisfen |
3131 |
2004-10-22 15:59 chrisfen |
8883 |
tim |
1643 |
|
8884 |
|
|
* src/: UseTheForce/LJFF.cpp, |
8885 |
|
|
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
8886 |
|
|
god! It runs and conserves energy! |
8887 |
|
|
|
8888 |
chrisfen |
3131 |
2004-10-22 15:54 chrisfen |
8889 |
tim |
1643 |
|
8890 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
8891 |
|
|
|
8892 |
chrisfen |
3131 |
2004-10-22 15:53 chrisfen |
8893 |
tim |
1643 |
|
8894 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8895 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
8896 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8897 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
8898 |
|
|
breakey |
8899 |
|
|
|
8900 |
chrisfen |
3131 |
2004-10-22 15:53 chrisfen |
8901 |
tim |
1643 |
|
8902 |
|
|
* make/Makefile.in: compiler flags |
8903 |
|
|
|
8904 |
chrisfen |
3131 |
2004-10-22 14:20 gezelter |
8905 |
tim |
1643 |
|
8906 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8907 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
8908 |
|
|
brains/fSimulation.h, types/AtomType.hpp, |
8909 |
|
|
types/DirectionalAtomType.hpp: fixey fixey |
8910 |
|
|
|
8911 |
chrisfen |
3131 |
2004-10-22 13:22 gezelter |
8912 |
tim |
1643 |
|
8913 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
8914 |
|
|
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
8915 |
|
|
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
8916 |
|
|
fortran files and c/Fortran interfaces |
8917 |
|
|
|
8918 |
chrisfen |
3131 |
2004-10-22 13:21 gezelter |
8919 |
tim |
1643 |
|
8920 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
8921 |
|
|
DirectionalAtomType.hpp, Makefile: More on AtomType and |
8922 |
|
|
DirectionalAtomType |
8923 |
|
|
|
8924 |
chrisfen |
3131 |
2004-10-22 07:47 gezelter |
8925 |
tim |
1639 |
|
8926 |
|
|
* src/types/AtomType.hpp: Adding AtomType |
8927 |
|
|
|
8928 |
chrisfen |
3131 |
2004-10-21 14:31 tim |
8929 |
tim |
1639 |
|
8930 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
8931 |
|
|
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
8932 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
8933 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
8934 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
8935 |
|
|
Snapshot and SnapshotManager in progress |
8936 |
|
|
|
8937 |
chrisfen |
3131 |
2004-10-21 14:30 tim |
8938 |
tim |
1639 |
|
8939 |
|
|
* test/brains/: BrainsTest.cpp, Makefile, |
8940 |
|
|
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
8941 |
|
|
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
8942 |
|
|
Snapshot and snapshotManager. |
8943 |
|
|
|
8944 |
chrisfen |
3131 |
2004-10-21 13:15 gezelter |
8945 |
tim |
1630 |
|
8946 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8947 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
8948 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
8949 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8950 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
8951 |
|
|
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
8952 |
|
|
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
8953 |
|
|
Fixey Fixey. |
8954 |
|
|
|
8955 |
chrisfen |
3131 |
2004-10-21 09:32 tim |
8956 |
tim |
1630 |
|
8957 |
|
|
* src/utils/GenericData.cpp, src/utils/Makefile, |
8958 |
|
|
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
8959 |
|
|
|
8960 |
chrisfen |
3131 |
2004-10-21 09:24 tim |
8961 |
tim |
1630 |
|
8962 |
|
|
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
8963 |
|
|
|
8964 |
chrisfen |
3131 |
2004-10-21 09:22 tim |
8965 |
tim |
1630 |
|
8966 |
|
|
* ChangeLog, src/brains/SimSetup.cpp, |
8967 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
8968 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
8969 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
8970 |
|
|
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
8971 |
|
|
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
8972 |
|
|
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
8973 |
|
|
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
8974 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
8975 |
|
|
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
8976 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
8977 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
8978 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
8979 |
|
|
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
8980 |
|
|
GenericData |
8981 |
|
|
|
8982 |
chrisfen |
3131 |
2004-10-21 08:25 chuckv |
8983 |
tim |
1630 |
|
8984 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
8985 |
|
|
module. |
8986 |
|
|
|
8987 |
chrisfen |
3131 |
2004-10-21 08:24 chuckv |
8988 |
tim |
1630 |
|
8989 |
|
|
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
8990 |
|
|
fortran lj module. |
8991 |
|
|
|
8992 |
chrisfen |
3131 |
2004-10-20 15:54 tim |
8993 |
tim |
1625 |
|
8994 |
|
|
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
8995 |
|
|
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
8996 |
|
|
test/utils/PropertyMapTestCase.cpp, |
8997 |
|
|
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
8998 |
|
|
GenericData and PropertyMap pass unit test. |
8999 |
|
|
|
9000 |
chrisfen |
3131 |
2004-10-20 14:52 gezelter |
9001 |
tim |
1622 |
|
9002 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
9003 |
|
|
DarkSide/sticky_interface.h: fixed a fortran name problem |
9004 |
|
|
|
9005 |
chrisfen |
3131 |
2004-10-20 14:38 tim |
9006 |
tim |
1622 |
|
9007 |
|
|
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
9008 |
|
|
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
9009 |
|
|
UtilTest, UtilTest.cpp: adding generic data test case |
9010 |
|
|
|
9011 |
chrisfen |
3131 |
2004-10-20 14:16 chuckv |
9012 |
tim |
1622 |
|
9013 |
|
|
* configure, ac-tools/aclocal.m4, |
9014 |
|
|
src/UseTheForce/DarkSide/Makefile, |
9015 |
|
|
src/UseTheForce/DarkSide/mpiSimulation.F90, |
9016 |
|
|
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
9017 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
9018 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
9019 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
9020 |
|
|
Fortran/C++ interface de-obfuscation project appears to be |
9021 |
|
|
complete! Woo hoo! |
9022 |
|
|
|
9023 |
chrisfen |
3131 |
2004-10-20 13:47 chuckv |
9024 |
tim |
1622 |
|
9025 |
|
|
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
9026 |
|
|
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
9027 |
|
|
continues |
9028 |
|
|
|
9029 |
chrisfen |
3131 |
2004-10-20 13:46 chuckv |
9030 |
tim |
1622 |
|
9031 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
9032 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
9033 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
9034 |
|
|
UseTheForce/doForces_interface.h, |
9035 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
9036 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
9037 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
9038 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
9039 |
|
|
UseTheForce/DarkSide/mpiSimulation_interface.h, |
9040 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
9041 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
9042 |
|
|
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
9043 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
9044 |
|
|
de-obfuscation project (It is a very long story) |
9045 |
|
|
|
9046 |
chrisfen |
3131 |
2004-10-20 11:07 tim |
9047 |
tim |
1622 |
|
9048 |
|
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
9049 |
|
|
test/math/SquareMatrix3TestCase.cpp, |
9050 |
|
|
test/math/SquareMatrixTestCase.cpp, |
9051 |
|
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
9052 |
|
|
|
9053 |
chrisfen |
3131 |
2004-10-19 22:52 tim |
9054 |
tim |
1616 |
|
9055 |
|
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
9056 |
|
|
SnapshotManager in design phase |
9057 |
|
|
|
9058 |
chrisfen |
3131 |
2004-10-19 21:54 gezelter |
9059 |
tim |
1616 |
|
9060 |
|
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
9061 |
|
|
problem prevented linking |
9062 |
|
|
|
9063 |
chrisfen |
3131 |
2004-10-19 21:54 gezelter |
9064 |
tim |
1616 |
|
9065 |
|
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
9066 |
|
|
|
9067 |
chrisfen |
3131 |
2004-10-19 21:26 gezelter |
9068 |
tim |
1616 |
|
9069 |
|
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
9070 |
|
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
9071 |
|
|
more fortran name mangling |
9072 |
|
|
|
9073 |
chrisfen |
3131 |
2004-10-19 21:23 gezelter |
9074 |
tim |
1616 |
|
9075 |
|
|
* src/profiling/timing.F90: yet more fortran renaming |
9076 |
|
|
|
9077 |
chrisfen |
3131 |
2004-10-19 21:19 gezelter |
9078 |
tim |
1616 |
|
9079 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
9080 |
|
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
9081 |
|
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
9082 |
|
|
wrappers.F90: Fortran name cleanup continues |
9083 |
|
|
|
9084 |
chrisfen |
3131 |
2004-10-19 21:12 gezelter |
9085 |
tim |
1616 |
|
9086 |
|
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
9087 |
|
|
broken fortran stuff |
9088 |
|
|
|
9089 |
chrisfen |
3131 |
2004-10-19 21:02 gezelter |
9090 |
tim |
1616 |
|
9091 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
9092 |
|
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
9093 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
9094 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
9095 |
|
|
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
9096 |
|
|
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
9097 |
|
|
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
9098 |
|
|
mpiSimulation_interface.h, mpiSimulation_module.F90, |
9099 |
|
|
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
9100 |
|
|
shapes_interface.h, shapes_module.h, simulation.F90, |
9101 |
|
|
simulation_interface.h, simulation_module.F90, |
9102 |
|
|
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
9103 |
|
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
9104 |
|
|
name sanity on the fortran side |
9105 |
|
|
|
9106 |
chrisfen |
3131 |
2004-10-19 17:18 tim |
9107 |
tim |
1616 |
|
9108 |
|
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
9109 |
|
|
|
9110 |
chrisfen |
3131 |
2004-10-19 16:01 tim |
9111 |
tim |
1616 |
|
9112 |
|
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
9113 |
|
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
9114 |
|
|
except diagonalize(), all of functions in math library pass the |
9115 |
|
|
test |
9116 |
|
|
|
9117 |
chrisfen |
3131 |
2004-10-19 15:43 chuckv |
9118 |
tim |
1616 |
|
9119 |
|
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
9120 |
|
|
C-fortran interface functions. |
9121 |
|
|
|
9122 |
chrisfen |
3131 |
2004-10-19 15:37 chuckv |
9123 |
tim |
1616 |
|
9124 |
|
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
9125 |
|
|
eam_module_inteface.h, gb_module_interface.h, |
9126 |
|
|
mpisimulation_module_interface.h, simulation_module_interface.h, |
9127 |
|
|
sticky_pair_module_interface.h: Added correct prototypes for |
9128 |
|
|
C-fortran interface functions. |
9129 |
|
|
|
9130 |
chrisfen |
3131 |
2004-10-19 14:28 tim |
9131 |
tim |
1616 |
|
9132 |
|
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
9133 |
|
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
9134 |
|
|
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
9135 |
|
|
test/math/RectMatrixTestCase.cpp, |
9136 |
|
|
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
9137 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
9138 |
|
|
bugs get fixed at math library |
9139 |
|
|
|
9140 |
chrisfen |
3131 |
2004-10-19 13:43 chuckv |
9141 |
tim |
1616 |
|
9142 |
|
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
9143 |
|
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
9144 |
|
|
DarkSide/mpisimulation_module_interface.h, |
9145 |
|
|
DarkSide/simulation_module_interface.h, |
9146 |
|
|
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
9147 |
|
|
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
9148 |
|
|
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
9149 |
|
|
DarkSide/simulation_module.F90, do_Forces.F90, |
9150 |
|
|
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
9151 |
|
|
notifycutoffs_module_interface.h: Added new files for fortran |
9152 |
|
|
interface. |
9153 |
|
|
|
9154 |
chrisfen |
3131 |
2004-10-19 13:43 gezelter |
9155 |
tim |
1616 |
|
9156 |
|
|
* src/UseTheForce/Makefile: regressing |
9157 |
|
|
|
9158 |
chrisfen |
3131 |
2004-10-19 13:40 gezelter |
9159 |
tim |
1616 |
|
9160 |
|
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
9161 |
|
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
9162 |
|
|
working on shapes for portability |
9163 |
|
|
|
9164 |
chrisfen |
3131 |
2004-10-19 13:40 gezelter |
9165 |
tim |
1616 |
|
9166 |
|
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
9167 |
|
|
|
9168 |
chrisfen |
3131 |
2004-10-19 11:21 chrisfen |
9169 |
tim |
1616 |
|
9170 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
9171 |
|
|
findBegin |
9172 |
|
|
|
9173 |
chrisfen |
3131 |
2004-10-18 21:34 tim |
9174 |
tim |
1603 |
|
9175 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
9176 |
|
|
are fixed in Vector class |
9177 |
|
|
|
9178 |
chrisfen |
3131 |
2004-10-18 21:28 tim |
9179 |
tim |
1603 |
|
9180 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
9181 |
|
|
some bugs in RectMatrixTestCase |
9182 |
|
|
|
9183 |
chrisfen |
3131 |
2004-10-18 21:21 tim |
9184 |
tim |
1603 |
|
9185 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
9186 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
9187 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
9188 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
9189 |
|
|
|
9190 |
chrisfen |
3131 |
2004-10-18 16:13 tim |
9191 |
tim |
1603 |
|
9192 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
9193 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
9194 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
9195 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
9196 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
9197 |
|
|
tests on math library |
9198 |
|
|
|
9199 |
chrisfen |
3131 |
2004-10-18 14:03 tim |
9200 |
tim |
1603 |
|
9201 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
9202 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
9203 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
9204 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
9205 |
|
|
more testing units |
9206 |
|
|
|
9207 |
chrisfen |
3131 |
2004-10-18 10:07 tim |
9208 |
tim |
1603 |
|
9209 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
9210 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
9211 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
9212 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
9213 |
|
|
|
9214 |
chrisfen |
3131 |
2004-10-18 09:30 gezelter |
9215 |
tim |
1603 |
|
9216 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
9217 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
9218 |
|
|
\phi) |
9219 |
|
|
|
9220 |
chrisfen |
3131 |
2004-10-18 09:29 gezelter |
9221 |
tim |
1603 |
|
9222 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
9223 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
9224 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
9225 |
|
|
Shapes into OOPSE |
9226 |
|
|
|
9227 |
chrisfen |
3131 |
2004-10-18 08:21 gezelter |
9228 |
tim |
1603 |
|
9229 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
9230 |
|
|
|
9231 |
chrisfen |
3131 |
2004-10-17 22:23 tim |
9232 |
tim |
1603 |
|
9233 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
9234 |
|
|
|
9235 |
chrisfen |
3131 |
2004-10-17 22:23 tim |
9236 |
tim |
1603 |
|
9237 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
9238 |
|
|
test case |
9239 |
|
|
|
9240 |
chrisfen |
3131 |
2004-10-16 18:19 tim |
9241 |
tim |
1594 |
|
9242 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
9243 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
9244 |
|
|
progress |
9245 |
|
|
|
9246 |
chrisfen |
3131 |
2004-10-15 18:31 tim |
9247 |
tim |
1594 |
|
9248 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
9249 |
|
|
|
9250 |
chrisfen |
3131 |
2004-10-15 14:11 tim |
9251 |
tim |
1594 |
|
9252 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
9253 |
|
|
IfstrstreamTestCase.hpp: adding test file |
9254 |
|
|
|
9255 |
chrisfen |
3131 |
2004-10-15 14:10 tim |
9256 |
tim |
1594 |
|
9257 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
9258 |
|
|
|
9259 |
chrisfen |
3131 |
2004-10-15 13:42 tim |
9260 |
tim |
1594 |
|
9261 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
9262 |
|
|
|
9263 |
chrisfen |
3131 |
2004-10-15 13:35 tim |
9264 |
tim |
1594 |
|
9265 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
9266 |
|
|
|
9267 |
chrisfen |
3131 |
2004-10-15 13:34 tim |
9268 |
tim |
1594 |
|
9269 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
9270 |
|
|
namespace oopse |
9271 |
|
|
|
9272 |
chrisfen |
3131 |
2004-10-15 12:38 chuckv |
9273 |
tim |
1594 |
|
9274 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
9275 |
|
|
XLF and XLC. |
9276 |
|
|
|
9277 |
chrisfen |
3131 |
2004-10-15 11:28 tim |
9278 |
tim |
1594 |
|
9279 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
9280 |
|
|
adding ifstrstream test case |
9281 |
|
|
|
9282 |
chrisfen |
3131 |
2004-10-15 11:20 tim |
9283 |
tim |
1594 |
|
9284 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
9285 |
|
|
|
9286 |
chrisfen |
3131 |
2004-10-15 11:18 tim |
9287 |
tim |
1594 |
|
9288 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
9289 |
|
|
|
9290 |
chrisfen |
3131 |
2004-10-15 11:17 tim |
9291 |
tim |
1594 |
|
9292 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
9293 |
|
|
|
9294 |
chrisfen |
3131 |
2004-10-15 11:16 tim |
9295 |
tim |
1594 |
|
9296 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
9297 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
9298 |
|
|
|
9299 |
chrisfen |
3131 |
2004-10-15 08:37 tim |
9300 |
tim |
1594 |
|
9301 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
9302 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
9303 |
|
|
|
9304 |
chrisfen |
3131 |
2004-10-15 08:20 tim |
9305 |
tim |
1594 |
|
9306 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
9307 |
|
|
|
9308 |
chrisfen |
3131 |
2004-10-15 08:19 tim |
9309 |
tim |
1594 |
|
9310 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
9311 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
9312 |
|
|
SquareMatrixTestCase class |
9313 |
|
|
|
9314 |
chrisfen |
3131 |
2004-10-15 00:52 tim |
9315 |
tim |
1594 |
|
9316 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
9317 |
|
|
|
9318 |
chrisfen |
3131 |
2004-10-14 16:28 tim |
9319 |
tim |
1594 |
|
9320 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
9321 |
|
|
Vector.hpp: math library in progress |
9322 |
|
|
|
9323 |
chrisfen |
3131 |
2004-10-14 16:27 tim |
9324 |
tim |
1594 |
|
9325 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
9326 |
|
|
|
9327 |
chrisfen |
3131 |
2004-10-13 16:53 tim |
9328 |
tim |
1594 |
|
9329 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
9330 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
9331 |
|
|
|
9332 |
chrisfen |
3131 |
2004-10-13 15:28 tim |
9333 |
tim |
1594 |
|
9334 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
9335 |
|
|
class |
9336 |
|
|
|
9337 |
chrisfen |
3131 |
2004-10-13 15:27 tim |
9338 |
tim |
1594 |
|
9339 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
9340 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
9341 |
|
|
|
9342 |
chrisfen |
3131 |
2004-10-13 15:24 tim |
9343 |
tim |
1594 |
|
9344 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
9345 |
|
|
|
9346 |
chrisfen |
3131 |
2004-10-12 23:51 tim |
9347 |
tim |
1594 |
|
9348 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
9349 |
|
|
Vector3.hpp: refactory vector and matrix classes |
9350 |
|
|
|
9351 |
chrisfen |
3131 |
2004-10-12 23:50 tim |
9352 |
tim |
1594 |
|
9353 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
9354 |
|
|
|
9355 |
chrisfen |
3131 |
2004-10-12 16:57 tim |
9356 |
tim |
1594 |
|
9357 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
9358 |
|
|
Matrix3x3d.hpp |
9359 |
|
|
|
9360 |
chrisfen |
3131 |
2004-10-12 12:08 tim |
9361 |
tim |
1594 |
|
9362 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
9363 |
|
|
|
9364 |
chrisfen |
3131 |
2004-10-11 15:15 tim |
9365 |
tim |
1594 |
|
9366 |
|
|
* src/: constraints/AbstractClasses.hpp, |
9367 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
9368 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
9369 |
|
|
|
9370 |
chrisfen |
3131 |
2004-10-11 14:54 tim |
9371 |
tim |
1594 |
|
9372 |
|
|
* scripts/filepp: fix a bug in filepp |
9373 |
|
|
|
9374 |
chrisfen |
3131 |
2004-10-11 14:13 tim |
9375 |
tim |
1594 |
|
9376 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
9377 |
|
|
of compilers |
9378 |
|
|
|
9379 |
chrisfen |
3131 |
2004-10-11 14:10 tim |
9380 |
tim |
1594 |
|
9381 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
9382 |
|
|
c/c++ now |
9383 |
|
|
|
9384 |
chrisfen |
3131 |
2004-10-11 11:40 tim |
9385 |
tim |
1594 |
|
9386 |
|
|
* make/Makefile.in: remove -module from F90Options |
9387 |
|
|
|
9388 |
chrisfen |
3131 |
2004-10-11 11:01 tim |
9389 |
tim |
1594 |
|
9390 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
9391 |
|
|
target directory |
9392 |
|
|
|
9393 |
chrisfen |
3131 |
2004-10-11 08:43 gezelter |
9394 |
tim |
1594 |
|
9395 |
|
|
* make/Makefile.in: fixed makefile.in |
9396 |
|
|
|
9397 |
chrisfen |
3131 |
2004-10-11 07:51 tim |
9398 |
tim |
1594 |
|
9399 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
9400 |
|
|
machine |
9401 |
|
|
|
9402 |
chrisfen |
3131 |
2004-10-11 07:26 tim |
9403 |
tim |
1594 |
|
9404 |
|
|
* forceFields/Makefile: add Makefile |
9405 |
|
|
|
9406 |
chrisfen |
3131 |
2004-10-11 07:23 tim |
9407 |
tim |
1594 |
|
9408 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
9409 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
9410 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
9411 |
|
|
directory |
9412 |
|
|
|
9413 |
chrisfen |
3131 |
2004-10-11 07:23 tim |
9414 |
tim |
1594 |
|
9415 |
gezelter |
2199 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
9416 |
|
|
Makefile |
9417 |
tim |
1594 |
|
9418 |
chrisfen |
3131 |
2004-10-08 23:01 tim |
9419 |
tim |
1594 |
|
9420 |
gezelter |
2199 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
9421 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
9422 |
|
|
Remove some Makefile.in |
9423 |
|
|
|
9424 |
chrisfen |
3131 |
2004-10-08 16:15 tim |
9425 |
gezelter |
2199 |
|
9426 |
tim |
1594 |
* make/Makefile.in: [no log message] |
9427 |
|
|
|
9428 |
chrisfen |
3131 |
2004-10-08 15:51 tim |
9429 |
tim |
1594 |
|
9430 |
|
|
* make/Makefile.in: fix make install |
9431 |
|
|
|
9432 |
chrisfen |
3131 |
2004-10-08 15:10 tim |
9433 |
tim |
1594 |
|
9434 |
|
|
* make/Makefile.in: adding make install |
9435 |
|
|
|
9436 |
chrisfen |
3131 |
2004-10-08 15:04 tim |
9437 |
tim |
1594 |
|
9438 |
gezelter |
2199 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
9439 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
9440 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
9441 |
tim |
1594 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
9442 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
9443 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
9444 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
9445 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
9446 |
|
|
|
9447 |
chrisfen |
3131 |
2004-10-06 16:03 gezelter |
9448 |
tim |
1594 |
|
9449 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
9450 |
|
|
stuff |
9451 |
|
|
|
9452 |
chrisfen |
3131 |
2004-10-06 16:03 gezelter |
9453 |
tim |
1594 |
|
9454 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
9455 |
|
|
make/Doxyfile, src/applications/getopt.c, |
9456 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
9457 |
|
|
build fixes |
9458 |
|
|
|
9459 |
chrisfen |
3131 |
2004-10-06 15:20 tim |
9460 |
tim |
1594 |
|
9461 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
9462 |
|
|
|
9463 |
chrisfen |
3131 |
2004-10-06 15:19 tim |
9464 |
tim |
1594 |
|
9465 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
9466 |
|
|
and suffix |
9467 |
|
|
|
9468 |
chrisfen |
3131 |
2004-10-06 14:27 gezelter |
9469 |
tim |
1594 |
|
9470 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
9471 |
|
|
OOPSE-2.0 directory structure yet |
9472 |
|
|
|
9473 |
chrisfen |
3131 |
2004-10-06 14:27 gezelter |
9474 |
tim |
1594 |
|
9475 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
9476 |
|
|
|
9477 |
chrisfen |
3131 |
2004-10-06 14:22 gezelter |
9478 |
gezelter |
1490 |
|
9479 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
9480 |
|
|
make/Makefile.in: cleaning up build process |
9481 |
gezelter |
1490 |
|
9482 |
chrisfen |
3131 |
2004-10-06 13:01 chrisfen |
9483 |
tim |
1594 |
|
9484 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
9485 |
|
|
restraints more intelligent - no longer gives uninformative seg |
9486 |
|
|
faults |
9487 |
|
|
|
9488 |
chrisfen |
3131 |
2004-10-06 12:55 gezelter |
9489 |
tim |
1594 |
|
9490 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
9491 |
|
|
|
9492 |
chrisfen |
3131 |
2004-10-06 12:51 gezelter |
9493 |
gezelter |
1490 |
|
9494 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
9495 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
9496 |
gezelter |
1490 |
|
9497 |
chrisfen |
3131 |
2004-10-06 11:53 tim |
9498 |
tim |
1594 |
|
9499 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
9500 |
|
|
|
9501 |
chrisfen |
3131 |
2004-10-06 11:18 tim |
9502 |
tim |
1594 |
|
9503 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
9504 |
|
|
combine all of the static libraries to a big library |
9505 |
|
|
|
9506 |
chrisfen |
3131 |
2004-10-05 15:57 tim |
9507 |
tim |
1594 |
|
9508 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
9509 |
|
|
|
9510 |
chrisfen |
3131 |
2004-10-05 12:37 tim |
9511 |
tim |
1594 |
|
9512 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
9513 |
|
|
UseTheForce/mpiSimulation_module.F90, |
9514 |
|
|
UseTheForce/DarkSide/Makefile, |
9515 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
9516 |
|
|
mpiSimulation_module to DarkSide |
9517 |
|
|
|
9518 |
chrisfen |
3131 |
2004-10-05 12:35 tim |
9519 |
tim |
1594 |
|
9520 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
9521 |
|
|
library instead of shared library |
9522 |
|
|
|
9523 |
chrisfen |
3131 |
2004-10-05 07:14 tim |
9524 |
tim |
1594 |
|
9525 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
9526 |
|
|
to filepp |
9527 |
|
|
|
9528 |
chrisfen |
3131 |
2004-10-04 13:56 tim |
9529 |
tim |
1594 |
|
9530 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
9531 |
|
|
|
9532 |
chrisfen |
3131 |
2004-10-04 09:24 gezelter |
9533 |
tim |
1594 |
|
9534 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
9535 |
|
|
|
9536 |
chrisfen |
3131 |
2004-10-04 09:06 gezelter |
9537 |
tim |
1594 |
|
9538 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
9539 |
|
|
|
9540 |
chrisfen |
3131 |
2004-10-04 08:27 gezelter |
9541 |
tim |
1594 |
|
9542 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
9543 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
9544 |
|
|
shapes |
9545 |
|
|
|
9546 |
chrisfen |
3131 |
2004-10-01 21:40 tim |
9547 |
tim |
1594 |
|
9548 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
9549 |
|
|
|
9550 |
chrisfen |
3131 |
2004-10-01 21:22 tim |
9551 |
tim |
1594 |
|
9552 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
9553 |
|
|
|
9554 |
chrisfen |
3131 |
2004-10-01 14:59 tim |
9555 |
tim |
1594 |
|
9556 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
9557 |
|
|
|
9558 |
chrisfen |
3131 |
2004-10-01 14:22 gezelter |
9559 |
gezelter |
1490 |
|
9560 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
9561 |
|
|
few minor build changes |
9562 |
gezelter |
1490 |
|
9563 |
chrisfen |
3131 |
2004-10-01 14:11 tim |
9564 |
tim |
1594 |
|
9565 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
9566 |
|
|
|
9567 |
chrisfen |
3131 |
2004-09-30 08:41 tim |
9568 |
tim |
1594 |
|
9569 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
9570 |
|
|
remove object files belong to current package. turn off silent |
9571 |
|
|
mode |
9572 |
|
|
|
9573 |
chrisfen |
3131 |
2004-09-29 14:55 tim |
9574 |
tim |
1594 |
|
9575 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
9576 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
9577 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
9578 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
9579 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
9580 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
9581 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
9582 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
9583 |
|
|
|
9584 |
chrisfen |
3131 |
2004-09-29 14:54 tim |
9585 |
tim |
1594 |
|
9586 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
9587 |
|
|
script |
9588 |
|
|
|
9589 |
chrisfen |
3131 |
2004-09-29 14:32 tim |
9590 |
tim |
1594 |
|
9591 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
9592 |
|
|
|
9593 |
chrisfen |
3131 |
2004-09-29 11:37 tim |
9594 |
tim |
1594 |
|
9595 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
9596 |
|
|
|
9597 |
chrisfen |
3131 |
2004-09-29 10:57 gezelter |
9598 |
gezelter |
1490 |
|
9599 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
9600 |
gezelter |
1490 |
|
9601 |
chrisfen |
3131 |
2004-09-29 10:56 gezelter |
9602 |
tim |
1594 |
|
9603 |
chrisfen |
2727 |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
9604 |
|
|
make stuff |
9605 |
tim |
1594 |
|
9606 |
chrisfen |
3131 |
2004-09-29 10:46 tim |
9607 |
gezelter |
1490 |
|
9608 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
9609 |
gezelter |
1490 |
|
9610 |
chrisfen |
3131 |
2004-09-29 10:12 tim |
9611 |
tim |
1594 |
|
9612 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
9613 |
|
|
|
9614 |
chrisfen |
3131 |
2004-09-29 08:58 gezelter |
9615 |
gezelter |
1490 |
|
9616 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
9617 |
gezelter |
1490 |
|
9618 |
chrisfen |
3131 |
2004-09-29 08:00 tim |
9619 |
tim |
1594 |
|
9620 |
|
|
* make/Makefile: add print statment to rules |
9621 |
|
|
|
9622 |
chrisfen |
3131 |
2004-09-29 07:59 tim |
9623 |
tim |
1594 |
|
9624 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
9625 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
9626 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
9627 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
9628 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
9629 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
9630 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
9631 |
|
|
|
9632 |
chrisfen |
3131 |
2004-09-28 19:55 tim |
9633 |
tim |
1594 |
|
9634 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
9635 |
|
|
which cause headache in bulding libutils |
9636 |
|
|
|
9637 |
chrisfen |
3131 |
2004-09-28 16:24 tim |
9638 |
tim |
1594 |
|
9639 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
9640 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
9641 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
9642 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
9643 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
9644 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
9645 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
9646 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
9647 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
9648 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
9649 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
9650 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
9651 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
9652 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
9653 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
9654 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
9655 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
9656 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
9657 |
|
|
change directory structure of application. Every executable file is |
9658 |
|
|
replaced in seperate directory |
9659 |
|
|
|
9660 |
chrisfen |
3131 |
2004-09-28 15:15 gezelter |
9661 |
tim |
1594 |
|
9662 |
|
|
* lib/dummy: Keep that lib around, please. |
9663 |
|
|
|
9664 |
chrisfen |
3131 |
2004-09-28 15:14 gezelter |
9665 |
gezelter |
1490 |
|
9666 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
9667 |
|
|
starting a configure version |
9668 |
gezelter |
1490 |
|
9669 |
chrisfen |
3131 |
2004-09-28 14:08 tim |
9670 |
tim |
1594 |
|
9671 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
9672 |
|
|
UseTheForce/DarkSide/Makefile, |
9673 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
9674 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
9675 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
9676 |
|
|
around to solve dependency problem |
9677 |
|
|
|
9678 |
chrisfen |
3131 |
2004-09-28 13:43 tim |
9679 |
gezelter |
1490 |
|
9680 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
9681 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
9682 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
9683 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
9684 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
9685 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
9686 |
|
|
src/utils/Makefile: [no log message] |
9687 |
gezelter |
1490 |
|
9688 |
chrisfen |
3131 |
2004-09-28 13:41 tim |
9689 |
tim |
1594 |
|
9690 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
9691 |
|
|
problem |
9692 |
|
|
|
9693 |
chrisfen |
3131 |
2004-09-28 09:13 tim |
9694 |
tim |
1594 |
|
9695 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
9696 |
|
|
src/io/Makefile: add yacc and lex rules |
9697 |
|
|
|
9698 |
chrisfen |
3131 |
2004-09-27 13:24 tim |
9699 |
tim |
1594 |
|
9700 |
|
|
* make/Makefile: adding include path to F90Options |
9701 |
|
|
|
9702 |
chrisfen |
3131 |
2004-09-27 13:13 tim |
9703 |
tim |
1594 |
|
9704 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
9705 |
|
|
|
9706 |
chrisfen |
3131 |
2004-09-24 09:27 tim |
9707 |
tim |
1594 |
|
9708 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
9709 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
9710 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
9711 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
9712 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
9713 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
9714 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
9715 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
9716 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
9717 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
9718 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
9719 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
9720 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
9721 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
9722 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
9723 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
9724 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
9725 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
9726 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
9727 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
9728 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
9729 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
9730 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
9731 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
9732 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
9733 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
9734 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
9735 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
9736 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
9737 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
9738 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
9739 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
9740 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
9741 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
9742 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
9743 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
9744 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
9745 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
9746 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
9747 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
9748 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
9749 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
9750 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
9751 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
9752 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
9753 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
9754 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
9755 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
9756 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
9757 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
9758 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
9759 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
9760 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
9761 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
9762 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
9763 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
9764 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
9765 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
9766 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
9767 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
9768 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
9769 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
9770 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
9771 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
9772 |
|
|
|
9773 |
chrisfen |
3131 |
2004-09-23 21:16 gezelter |
9774 |
gezelter |
1490 |
|
9775 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
9776 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
9777 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
9778 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
9779 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
9780 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
9781 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
9782 |
|
|
src/UseTheForce/fForceField.h, |
9783 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
9784 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
9785 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
9786 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
9787 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
9788 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
9789 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
9790 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
9791 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
9792 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
9793 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
9794 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
9795 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
9796 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
9797 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
9798 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
9799 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
9800 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
9801 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
9802 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
9803 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
9804 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
9805 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
9806 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
9807 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
9808 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
9809 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
9810 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
9811 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
9812 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
9813 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
9814 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
9815 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
9816 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
9817 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
9818 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
9819 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
9820 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
9821 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
9822 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
9823 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
9824 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
9825 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
9826 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
9827 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
9828 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
9829 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
9830 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
9831 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
9832 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
9833 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
9834 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
9835 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
9836 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
9837 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
9838 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
9839 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
9840 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
9841 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
9842 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
9843 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
9844 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
9845 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
9846 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
9847 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
9848 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
9849 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
9850 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
9851 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
9852 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
9853 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
9854 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
9855 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
9856 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
9857 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
9858 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
9859 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
9860 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
9861 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
9862 |
|
|
src/utils/simError.c, src/utils/simError.h, |
9863 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
9864 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
9865 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
9866 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
9867 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
9868 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
9869 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
9870 |
chrisfen |
2727 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
9871 |
|
|
make/_files/style.css, samples/Makefile.in, |
9872 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
9873 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
9874 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
9875 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
9876 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
9877 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
9878 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
9879 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
9880 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
9881 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
9882 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
9883 |
|
|
src/applications/LatticeCreator.cpp, |
9884 |
|
|
src/applications/LatticeCreator.hpp, |
9885 |
|
|
src/applications/LatticeFactory.cpp, |
9886 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
9887 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
9888 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
9889 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
9890 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
9891 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
9892 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
9893 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
9894 |
|
|
src/applications/simpleBuilder.ggo, |
9895 |
|
|
src/applications/simpleBuilderCmd.c, |
9896 |
|
|
src/integrators/AbstractClasses.hpp, |
9897 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
9898 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
9899 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
9900 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
9901 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
9902 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
9903 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
9904 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
9905 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
9906 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
9907 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
9908 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
9909 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
9910 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
9911 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
9912 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
9913 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
9914 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
9915 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
9916 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
9917 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
9918 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
9919 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
9920 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
9921 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
9922 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
9923 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
9924 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
9925 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
9926 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
9927 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
9928 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
9929 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
9930 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
9931 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
9932 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
9933 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
9934 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
9935 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
9936 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
9937 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
9938 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
9939 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
9940 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
9941 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
9942 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
9943 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
9944 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
9945 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
9946 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
9947 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
9948 |
gezelter |
1490 |
|
9949 |
chrisfen |
3131 |
2004-09-23 21:16 gezelter |
9950 |
gezelter |
1490 |
|
9951 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
9952 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
9953 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
9954 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
9955 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
9956 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
9957 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
9958 |
|
|
src/UseTheForce/fForceField.h, |
9959 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
9960 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
9961 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
9962 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
9963 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
9964 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
9965 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
9966 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
9967 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
9968 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
9969 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
9970 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
9971 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
9972 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
9973 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
9974 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
9975 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
9976 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
9977 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
9978 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
9979 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
9980 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
9981 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
9982 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
9983 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
9984 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
9985 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
9986 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
9987 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
9988 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
9989 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
9990 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
9991 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
9992 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
9993 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
9994 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
9995 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
9996 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
9997 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
9998 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
9999 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
10000 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
10001 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
10002 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
10003 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
10004 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
10005 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
10006 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
10007 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
10008 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
10009 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
10010 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
10011 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
10012 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
10013 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
10014 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
10015 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
10016 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
10017 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
10018 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
10019 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
10020 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
10021 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
10022 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
10023 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
10024 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
10025 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
10026 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
10027 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
10028 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
10029 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
10030 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
10031 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
10032 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
10033 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
10034 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
10035 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
10036 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
10037 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
10038 |
|
|
src/utils/simError.c, src/utils/simError.h, |
10039 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
10040 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
10041 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
10042 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
10043 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
10044 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
10045 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
10046 |
chrisfen |
2727 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
10047 |
|
|
make/_files/style.css, samples/Makefile.in, |
10048 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
10049 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
10050 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
10051 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
10052 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
10053 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
10054 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
10055 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
10056 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
10057 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
10058 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
10059 |
|
|
src/applications/LatticeCreator.cpp, |
10060 |
|
|
src/applications/LatticeCreator.hpp, |
10061 |
|
|
src/applications/LatticeFactory.cpp, |
10062 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
10063 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
10064 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
10065 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
10066 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
10067 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
10068 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
10069 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
10070 |
|
|
src/applications/simpleBuilder.ggo, |
10071 |
|
|
src/applications/simpleBuilderCmd.c, |
10072 |
|
|
src/integrators/AbstractClasses.hpp, |
10073 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
10074 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
10075 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
10076 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
10077 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
10078 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
10079 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
10080 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
10081 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
10082 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
10083 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
10084 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
10085 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
10086 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
10087 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
10088 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
10089 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
10090 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
10091 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
10092 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
10093 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
10094 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
10095 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
10096 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
10097 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
10098 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
10099 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
10100 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
10101 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
10102 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
10103 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
10104 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
10105 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
10106 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
10107 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
10108 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
10109 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
10110 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
10111 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
10112 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
10113 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
10114 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
10115 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
10116 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
10117 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
10118 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
10119 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
10120 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
10121 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
10122 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
10123 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
10124 |
gezelter |
1490 |
|