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chrisfen |
3038 |
2006-10-10 10:08 chrisfen |
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* src/applications/utilities/: affineScale, affineScale.in, |
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solvator, solvator.in, waterBoxer, waterBoxer.in: who needs .in |
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files for perl? using env |
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2006-10-09 22:44 gezelter |
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* src/: applications/randomBuilder/randomBuilder.cpp, |
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applications/randomBuilder/randomBuilder.ggo, |
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applications/randomBuilder/randomBuilderCmd.c, |
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applications/randomBuilder/randomBuilderCmd.h, utils/MoLocator.cpp: |
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fixing bugs in randomBuilder |
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2006-10-09 18:16 gezelter |
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* samples/argon/lj.md, |
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src/applications/randomBuilder/randomBuilder.cpp, |
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src/applications/simpleBuilder/Makefile, |
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src/applications/simpleBuilder/randomBuilder.cpp, |
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src/applications/simpleBuilder/randomBuilder.ggo, |
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src/applications/simpleBuilder/randomBuilderCmd.c, |
| 23 |
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src/applications/simpleBuilder/randomBuilderCmd.h: Fixing the |
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builders to prepare for OOPSE-4 release |
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2006-10-06 17:29 chuckv |
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* src/applications/utilities/mdSplit: Added utility to split dump |
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file frames into md files. |
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2006-10-03 18:39 chrisfen |
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* src/applications/utilities/Makefile: forgot to adjust the |
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makefile |
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2006-10-03 18:38 chrisfen |
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* src/applications/utilities/: solvator.in, waterBoxer.in: added |
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solvator and adjusted waterBoxer |
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| 41 |
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2006-10-02 19:54 chrisfen |
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* src/applications/utilities/waterBoxer.in: improvements to |
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waterBoxer |
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2006-10-02 19:27 chrisfen |
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| 48 |
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* src/applications/utilities/waterBoxer.in: fixed a bug in |
| 49 |
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waterBoxer for invalid water names |
| 50 |
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| 51 |
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2006-09-26 17:55 gezelter |
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* AUTHORS, README: Starting cleanup for 4.0 release |
| 54 |
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| 55 |
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2006-09-26 12:08 gezelter |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 58 |
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BondOrderParameter.hpp: Cleaned up the code for BondOrderParameter |
| 59 |
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and added a bunch of comments. Fixed a memory leak or ten. |
| 60 |
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| 61 |
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2006-09-26 10:33 gezelter |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
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BondOrderParameter.hpp: Some efficiency fixes (now computes Wigner |
| 65 |
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3-j coefficients only once in the constructor). |
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| 67 |
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2006-09-25 21:30 gezelter |
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| 69 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 70 |
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BondOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
| 71 |
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StaticPropsCmd.c, StaticPropsCmd.h: Mostly done with |
| 72 |
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BondOrderParameter. Only a few performance tweaks remain |
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| 74 |
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2006-09-25 18:08 gezelter |
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* src/: applications/staticProps/BondOrderParameter.cpp, |
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applications/staticProps/BondOrderParameter.hpp, |
| 78 |
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applications/staticProps/StaticProps.cpp, brains/SimCreator.cpp, |
| 79 |
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math/SphericalHarmonic.cpp: fixing bond order parameter code |
| 80 |
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| 81 |
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2006-09-22 18:19 chrisfen |
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* src/: UseTheForce/DarkSide/simulation.F90, brains/SimInfo.cpp, |
| 84 |
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brains/fSimulation.h, io/ForceFieldOptions.cpp, |
| 85 |
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io/ForceFieldOptions.hpp, io/Globals.cpp, io/Globals.hpp: refined |
| 86 |
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the reaction field dielectric passing |
| 87 |
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| 88 |
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2006-09-21 21:41 gezelter |
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| 90 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 91 |
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BondOrderParameter.hpp: bug fixes (still broken, however) |
| 92 |
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| 93 |
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2006-09-21 21:36 gezelter |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 96 |
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BondOrderParameter.hpp: Following Rein ten Wolde article |
| 97 |
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| 98 |
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2006-09-21 17:47 gezelter |
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| 100 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 101 |
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BondOrderParameter.hpp: more bug fixes |
| 102 |
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| 103 |
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2006-09-21 16:43 gezelter |
| 104 |
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| 105 |
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* src/applications/staticProps/BondOrderParameter.cpp: more changes |
| 106 |
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to BOP and SH |
| 107 |
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| 108 |
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2006-09-21 14:25 chrisfen |
| 109 |
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| 110 |
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* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
| 111 |
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io/Globals.cpp: fixed the half self term for wolf electrostatics |
| 112 |
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and OOPSE now chooses a cutoff radius dependent alpha for damped |
| 113 |
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electrostatics |
| 114 |
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| 115 |
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2006-09-21 14:04 gezelter |
| 116 |
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| 117 |
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* src/applications/staticProps/BondOrderParameter.cpp: Fixed a bug |
| 118 |
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in Wl code in BondOrderParameter |
| 119 |
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| 120 |
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2006-09-21 10:45 gezelter |
| 121 |
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| 122 |
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* src/: applications/staticProps/BondOrderParameter.cpp, |
| 123 |
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math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: Bugfixes in |
| 124 |
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BondOrderParameter and SphericalHarmonic |
| 125 |
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| 126 |
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2006-09-20 18:16 gezelter |
| 127 |
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| 128 |
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* src/: applications/staticProps/BondOrderParameter.cpp, |
| 129 |
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math/Makefile, math/SphericalHarmonic.cpp, |
| 130 |
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math/SphericalHarmonic.hpp: added SphericalHarmonics, fixed a few |
| 131 |
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problems with BondOrderParameter |
| 132 |
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| 133 |
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2006-09-20 16:13 gezelter |
| 134 |
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| 135 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 136 |
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BondOrderParameter.hpp, GofAngle2.cpp, StaticProps.cpp, |
| 137 |
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StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed bugs |
| 138 |
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(mostly in BondOrderParameter) |
| 139 |
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| 140 |
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2006-09-19 17:20 gezelter |
| 141 |
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| 142 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 143 |
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BondOrderParameter.hpp: Adding BondOrderParameter to StaticProps |
| 144 |
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| 145 |
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2006-09-19 17:14 gezelter |
| 146 |
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| 147 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 148 |
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BondOrderParameter.hpp, Makefile, StaticProps.cpp, StaticProps.ggo, |
| 149 |
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StaticPropsCmd.c, StaticPropsCmd.h: Working on BondOrderParameter |
| 150 |
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| 151 |
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2006-09-18 17:31 chuckv |
| 152 |
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| 153 |
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* src/applications/staticProps/: BondOrderParameter.cpp, |
| 154 |
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BondOrderParameter.hpp: Latest Version |
| 155 |
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| 156 |
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2006-09-08 12:13 gezelter |
| 157 |
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| 158 |
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* src/: brains/BlockSnapshotManager.cpp, io/DumpReader.cpp, |
| 159 |
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utils/residentMem.c: fixed a DumpReader bug, took out extra |
| 160 |
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printing statements in residentMem and BlockSnapshotManager |
| 161 |
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| 162 |
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2006-09-04 09:37 gezelter |
| 163 |
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| 164 |
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* configure, ac-tools/configure.in, |
| 165 |
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src/applications/utilities/Makefile: changing configure script to |
| 166 |
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process the new utilities |
| 167 |
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| 168 |
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2006-09-01 18:58 chrisfen |
| 169 |
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| 170 |
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* src/applications/utilities/waterBoxer.in: added some features to |
| 171 |
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waterBoxer |
| 172 |
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| 173 |
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2006-09-01 17:08 chrisfen |
| 174 |
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| 175 |
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* src/applications/utilities/: Makefile, affineScale.in, |
| 176 |
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waterBoxer.in: added the waterBoxer script |
| 177 |
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| 178 |
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2006-09-01 15:22 chrisfen |
| 179 |
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| 180 |
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* src/applications/utilities/affineScale.in: added comment info |
| 181 |
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| 182 |
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2006-09-01 15:16 gezelter |
| 183 |
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| 184 |
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* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
| 185 |
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brains/Register.cpp, integrators/Makefile, integrators/NgammaT.cpp, |
| 186 |
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integrators/NgammaT.hpp, io/Globals.cpp: adding NgammaT integrator |
| 187 |
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| 188 |
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2006-09-01 14:29 chrisfen |
| 189 |
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| 190 |
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* src/applications/utilities/affineScale.in: modified affineScale |
| 191 |
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to work with the new OOPSE files |
| 192 |
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| 193 |
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2006-09-01 10:15 chrisfen |
| 194 |
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| 195 |
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* src/io/: RestReader.cpp, RestWriter.cpp: fixed TI MPI bug |
| 196 |
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| 197 |
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2006-08-31 18:34 chrisfen |
| 198 |
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| 199 |
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* src/: integrators/VelocityVerletIntegrator.cpp, |
| 200 |
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restraints/ThermoIntegrationForceManager.cpp: fixes to zang writing |
| 201 |
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| 202 |
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2006-08-31 16:12 chrisfen |
| 203 |
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| 204 |
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* samples/alkane/butane.in, samples/alkane/butane.md, |
| 205 |
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samples/argon/500.in, samples/argon/500.md, samples/argon/ar864.in, |
| 206 |
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samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 207 |
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samples/argon/argonNVT.md, samples/cutoff/GB-Ar-max.md, |
| 208 |
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samples/cutoff/GB-Ar-mix.md, samples/cutoff/GB-Ar-traditional.md, |
| 209 |
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samples/cutoff/cutoff_test.in, samples/cutoff/cutoff_test.md, |
| 210 |
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samples/cutoff/gb-ar.in, samples/cutoff/max.md, |
| 211 |
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samples/cutoff/mix.md, samples/cutoff/traditional.md, |
| 212 |
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samples/dipole/splitInWater.in, samples/dipole/splitInWater.md, |
| 213 |
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samples/dipole/split_SSD.in, samples/dipole/split_SSD.md, |
| 214 |
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samples/dipole/twoSplitDipole.in, samples/dipole/twoSplitDipole.md, |
| 215 |
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samples/gbljtest/2gb.in, samples/gbljtest/2gb.md, |
| 216 |
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samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
| 217 |
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samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
| 218 |
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samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
| 219 |
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samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
| 220 |
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samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 221 |
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samples/metals/EAM/Au_bulk.in, samples/metals/EAM/Au_bulk_FBD.md, |
| 222 |
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samples/metals/EAM/Au_bulk_voter.md, |
| 223 |
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samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.in, |
| 224 |
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samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.md, |
| 225 |
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samples/metals/EAM/nanoparticle/Au_nanoparticle.in, |
| 226 |
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samples/metals/EAM/nanoparticle/Au_nanoparticle.md, |
| 227 |
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samples/metals/EAM/nanorod/Au_nanoparticle.in, |
| 228 |
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samples/metals/EAM/nanorod/Au_nanoparticle_FCC.md, |
| 229 |
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samples/metals/Sutton-Chen/Au_bulk.in, |
| 230 |
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samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
| 231 |
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samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 232 |
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samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 233 |
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samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.md, |
| 234 |
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samples/thermoIntegration/liquid/ssde.in, |
| 235 |
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samples/thermoIntegration/liquid/ssde.md, |
| 236 |
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samples/thermoIntegration/solid/ssde.in, |
| 237 |
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samples/thermoIntegration/solid/ssde.md, samples/water/dimer/cl.in, |
| 238 |
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samples/water/dimer/cl.md, samples/water/dimer/mix.in, |
| 239 |
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samples/water/dimer/mix.md, samples/water/dimer/mix2.in, |
| 240 |
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samples/water/dimer/mix2.md, samples/water/dimer/ssd.in, |
| 241 |
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samples/water/dimer/ssd.md, samples/water/dimer/tap.in, |
| 242 |
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samples/water/dimer/tap.md, samples/water/dimer/two.in, |
| 243 |
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samples/water/dimer/two.md, samples/water/spce/spce.in, |
| 244 |
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samples/water/spce/spce.md, samples/water/ssd/ssd.in, |
| 245 |
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samples/water/ssd/ssd.md, samples/water/ssd-ion/ssd-ion.md, |
| 246 |
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samples/water/ssd-ion/ssdCl.in, samples/water/ssd-ion/ssdCl.md, |
| 247 |
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samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 248 |
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samples/water/ssdrf/ssdrf.in, samples/water/ssdrf/ssdrf.md, |
| 249 |
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samples/water/tap/tap.in, samples/water/tap/tap.md, |
| 250 |
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samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 251 |
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samples/water/tip4p/tp4.in, samples/water/tip4p/tp4.md, |
| 252 |
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samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 253 |
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samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 254 |
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src/restraints/ThermoIntegrationForceManager.cpp: converted samples |
| 255 |
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over to the OOPSE-4 file format |
| 256 |
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| 257 |
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Fixed an MPI bug in thermodynamic integration |
| 258 |
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| 259 |
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2006-08-30 17:13 gezelter |
| 260 |
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| 261 |
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* src/applications/hydrodynamics/Hydro.cpp: removed extra file in |
| 262 |
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Hydro.cpp |
| 263 |
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| 264 |
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2006-08-30 17:04 gezelter |
| 265 |
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| 266 |
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 267 |
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applications/dynamicProps/DynamicProps.cpp, |
| 268 |
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applications/staticProps/StaticProps.cpp, |
| 269 |
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applications/utilities/dumpConverter, openbabel/oopseformat.cpp: |
| 270 |
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Changing utility programs to use the new file format |
| 271 |
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| 272 |
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2006-08-30 16:33 gezelter |
| 273 |
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| 274 |
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* src/: brains/SimCreator.cpp, io/DumpReader.cpp, |
| 275 |
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io/DumpWriter.cpp: fixed some bugs in DumpWriter, eliminated some |
| 276 |
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extra printing of debugging information |
| 277 |
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| 278 |
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2006-08-30 14:42 tim |
| 279 |
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| 280 |
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* configure, ac-tools/OOPSE.m4, forceFields/Au.u3.funcfl, |
| 281 |
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forceFields/Ni.u3.funcfl, samples/argon/lj.md, |
| 282 |
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src/brains/Register.cpp, src/brains/SimCreator.cpp, |
| 283 |
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src/brains/SimCreator.hpp, src/brains/SimInfo.cpp, |
| 284 |
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src/brains/SimInfo.hpp, src/io/DumpReader.cpp, |
| 285 |
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src/io/DumpReader.hpp, src/io/DumpWriter.cpp, |
| 286 |
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src/io/DumpWriter.hpp, src/io/Globals.cpp, src/io/Globals.hpp, |
| 287 |
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src/mdParser/SimplePreprocessor.hpp, src/openbabel/Makefile, |
| 288 |
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src/openbabel/oopseformat.cpp, src/primitives/StuntDouble.cpp, |
| 289 |
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src/primitives/StuntDouble.hpp, src/utils/StringUtils.cpp, |
| 290 |
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src/utils/StringUtils.hpp: Massive changes preparing for release of |
| 291 |
|
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OOPSE-4: The main difference is that the new MD file format (.md, |
| 292 |
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.dump, .eor) now contains meta-data information along with the |
| 293 |
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configuration information. |
| 294 |
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| 295 |
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2006-08-24 13:42 xsun |
| 296 |
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| 297 |
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* src/io/Globals.cpp: change the globals.cpp to make sure we can |
| 298 |
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set targetPressure and surfaceTension to be negative. |
| 299 |
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| 300 |
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2006-08-14 16:32 chrisfen |
| 301 |
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| 302 |
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* src/UseTheForce/DarkSide/electrostatic.F90: fixed an ordering |
| 303 |
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issue in quadrupole-charge interactions |
| 304 |
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| 305 |
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2006-08-02 15:40 gezelter |
| 306 |
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| 307 |
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* make/Makefile.in, samples/water/ssde/ssde.md, src/config.h.in, |
| 308 |
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src/antlr/Makefile, src/applications/atom2md/atom2md.cpp, |
| 309 |
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src/brains/Snapshot.cpp, src/brains/Snapshot.hpp, |
| 310 |
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src/openbabel/Makefile, src/openbabel/oopseformat.cpp, |
| 311 |
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src/openbabel/oopseformat.hpp: starting change of file formats |
| 312 |
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| 313 |
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2006-08-02 14:06 gezelter |
| 314 |
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| 315 |
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* src/applications/: atom2md/Makefile, atom2md/atom2md.cpp, |
| 316 |
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atom2mdin/Makefile, atom2mdin/atom2mdin.cpp: Changing atom2mdin |
| 317 |
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into atom2md to reflect new unified file format |
| 318 |
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| 319 |
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2006-07-27 17:02 chrisfen |
| 320 |
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| 321 |
|
|
* src/applications/utilities/dumpConverter: fixed a pvf bug |
| 322 |
|
|
|
| 323 |
|
|
2006-07-27 16:36 tim |
| 324 |
|
|
|
| 325 |
|
|
* src/applications/utilities/dumpConverter: fixed dumpConverter |
| 326 |
|
|
problems |
| 327 |
|
|
|
| 328 |
|
|
2006-07-27 15:05 gezelter |
| 329 |
|
|
|
| 330 |
|
|
* src/applications/utilities/dumpConverter: added dumpConverter |
| 331 |
|
|
|
| 332 |
|
|
2006-07-26 17:45 gezelter |
| 333 |
|
|
|
| 334 |
|
|
* make/Makefile.in: removed shapes sample |
| 335 |
|
|
|
| 336 |
|
|
2006-07-26 17:45 gezelter |
| 337 |
|
|
|
| 338 |
|
|
* src/applications/utilities/affineScale.in: fixed a spelling bug |
| 339 |
|
|
|
| 340 |
|
|
2006-07-26 17:01 gezelter |
| 341 |
|
|
|
| 342 |
|
|
* configure: added perl interpreter to affineScale script |
| 343 |
|
|
|
| 344 |
|
|
2006-07-26 17:01 gezelter |
| 345 |
|
|
|
| 346 |
|
|
* ac-tools/configure.in: added perl substitution for affineScale |
| 347 |
|
|
script |
| 348 |
|
|
|
| 349 |
|
|
2006-07-26 17:00 gezelter |
| 350 |
|
|
|
| 351 |
|
|
* make/Makefile.in: added install target for scripts |
| 352 |
|
|
|
| 353 |
|
|
2006-07-26 17:00 gezelter |
| 354 |
|
|
|
| 355 |
|
|
* src/applications/utilities/: Makefile, affineScale.in: Adding a |
| 356 |
|
|
directory for scripts Adding affineScale script |
| 357 |
|
|
|
| 358 |
|
|
2006-07-24 10:51 xsun |
| 359 |
|
|
|
| 360 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed a getSigma bug |
| 361 |
|
|
|
| 362 |
|
|
2006-07-19 08:46 chrisfen |
| 363 |
|
|
|
| 364 |
|
|
* samples/: thermoIntegration/liquid/water.md, |
| 365 |
|
|
thermoIntegration/solid/water.md, water/dimer/water.md, |
| 366 |
|
|
water/spce/water.md, water/ssd/water.md, water/ssd-ion/water.md, |
| 367 |
|
|
water/ssde/water.md, water/ssdrf/water.md, water/tap/water.md, |
| 368 |
|
|
water/tip3p_ice/water.md, water/tip4p/water.md: Added tred to |
| 369 |
|
|
sample water.md files |
| 370 |
|
|
|
| 371 |
|
|
2006-07-19 08:35 chrisfen |
| 372 |
|
|
|
| 373 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp, |
| 374 |
|
|
RigidBodyVisitor.cpp, RigidBodyVisitor.hpp: Added TRED water |
| 375 |
|
|
visitor for Dump2XYZ visualization |
| 376 |
|
|
|
| 377 |
|
|
2006-07-19 08:33 chrisfen |
| 378 |
|
|
|
| 379 |
|
|
* forceFields/DUFF2.frc: Added TRED parameters to forcefield |
| 380 |
|
|
|
| 381 |
|
|
2006-07-17 14:13 xsun |
| 382 |
|
|
|
| 383 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed d / sigma0 confusion |
| 384 |
|
|
|
| 385 |
|
|
2006-07-15 22:48 gezelter |
| 386 |
|
|
|
| 387 |
|
|
* src/io/ForceFieldOptions.cpp: testing commit logger |
| 388 |
|
|
|
| 389 |
|
|
2006-07-15 22:46 gezelter |
| 390 |
|
|
|
| 391 |
|
|
* src/io/ForceFieldOptions.cpp: removed printing of GBN and GBM |
| 392 |
|
|
from previous debugging |
| 393 |
|
|
|
| 394 |
|
|
2006-07-14 10:47 xsun |
| 395 |
|
|
|
| 396 |
|
|
* configure, ac-tools/OOPSE.m4: Fixed a bug in the fftw part of the |
| 397 |
|
|
configure script. |
| 398 |
|
|
|
| 399 |
|
|
2006-07-07 15:44 gezelter |
| 400 |
|
|
|
| 401 |
|
|
* configure, ac-tools/configure.in, samples/gbljtest/2gb.md, |
| 402 |
|
|
src/UseTheForce/DarkSide/gb.F90: removed icc from C++ search lines, |
| 403 |
|
|
did some formatting work on GB module, mucked around with a GB |
| 404 |
|
|
example |
| 405 |
|
|
|
| 406 |
|
|
2006-07-07 10:18 chuckv |
| 407 |
|
|
|
| 408 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
| 409 |
|
|
BondOrderParameter.hpp: Adding more changes to orientational bond |
| 410 |
|
|
order parameter. |
| 411 |
|
|
|
| 412 |
|
|
2006-07-03 15:40 chuckv |
| 413 |
|
|
|
| 414 |
|
|
* src/math/Wigner3jm.F90: Added utility function to winger3jm from |
| 415 |
|
|
slatac. |
| 416 |
|
|
|
| 417 |
|
|
2006-07-03 10:06 chrisfen |
| 418 |
|
|
|
| 419 |
|
|
* src/UseTheForce/DarkSide/mpole.F90: Added the multipole |
| 420 |
|
|
interaction routine. It doesn't work yet, so it's not included in |
| 421 |
|
|
the build. |
| 422 |
|
|
|
| 423 |
|
|
2006-07-03 09:18 chrisfen |
| 424 |
|
|
|
| 425 |
|
|
* src/: UseTheForce/doForces.F90, |
| 426 |
|
|
UseTheForce/doForces_interface.F90, |
| 427 |
|
|
UseTheForce/doForces_interface.h, |
| 428 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 429 |
|
|
UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp, |
| 430 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
| 431 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 432 |
|
|
brains/fSimulation.h, integrators/VelocityVerletIntegrator.cpp, |
| 433 |
|
|
io/Globals.cpp, io/Globals.hpp, |
| 434 |
|
|
restraints/ThermoIntegrationForceManager.cpp: Added simulation box |
| 435 |
|
|
dipole moment accumulation for the purposes of calculating |
| 436 |
|
|
dielectric constants |
| 437 |
|
|
|
| 438 |
|
|
2006-07-01 18:27 kdaily |
| 439 |
|
|
|
| 440 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed forces and torques for GB |
| 441 |
|
|
|
| 442 |
|
|
2006-06-28 10:35 chrisfen |
| 443 |
|
|
|
| 444 |
|
|
* src/io/: DumpReader.cpp, RestReader.cpp, RestReader.hpp: more |
| 445 |
|
|
efficient file reading for thermodynamic integration, and fixed |
| 446 |
|
|
some formatting |
| 447 |
|
|
|
| 448 |
|
|
2006-06-27 12:36 chuckv |
| 449 |
|
|
|
| 450 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
| 451 |
|
|
BondOrderParameter.hpp: Beginnings of a order parameter. |
| 452 |
|
|
|
| 453 |
|
|
2006-06-27 12:19 chuckv |
| 454 |
|
|
|
| 455 |
|
|
* src/applications/staticProps/: BondOrderParameter.cpp, |
| 456 |
|
|
BondOrderParameter.hpp: Adding code for bond orientational |
| 457 |
|
|
parameters. |
| 458 |
|
|
|
| 459 |
|
|
2006-06-22 11:21 chrisfen |
| 460 |
|
|
|
| 461 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
| 462 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/RestWriter.cpp, |
| 463 |
|
|
io/RestWriter.hpp, restraints/ThermoIntegrationForceManager.cpp: |
| 464 |
|
|
MPI thermodynamic integration works now. |
| 465 |
|
|
|
| 466 |
|
|
2006-06-21 14:28 chrisfen |
| 467 |
|
|
|
| 468 |
|
|
* src/visitors/AtomVisitor.cpp: fixed a build problem... |
| 469 |
|
|
GB_12b_ratio no longer exists (replaced with BG_l). |
| 470 |
|
|
|
| 471 |
|
|
2006-06-19 13:55 chuckv |
| 472 |
|
|
|
| 473 |
|
|
* src/math/: Makefile, Wigner3jm.F90, Wigner3jm_interface.h: Added |
| 474 |
|
|
support for Winger3jm coefficients. |
| 475 |
|
|
|
| 476 |
|
|
2006-06-18 21:36 chrisfen |
| 477 |
|
|
|
| 478 |
|
|
* src/: io/RestReader.cpp, io/RestWriter.cpp, |
| 479 |
|
|
restraints/ThermoIntegrationForceManager.cpp: fixes for mpi |
| 480 |
|
|
thermodynamic integration, close to fully working... |
| 481 |
|
|
|
| 482 |
|
|
2006-06-17 13:02 tim |
| 483 |
|
|
|
| 484 |
|
|
* src/visitors/AtomVisitor.cpp: output the principle axis of GB |
| 485 |
|
|
|
| 486 |
|
|
2006-06-15 14:38 gezelter |
| 487 |
|
|
|
| 488 |
|
|
* configure, ac-tools/OOPSE.m4, ac-tools/configure.in, |
| 489 |
|
|
samples/water/tip4p/tp4.md: added mpi compilers, demoted pg |
| 490 |
|
|
compilers after pathscale |
| 491 |
|
|
|
| 492 |
|
|
2006-06-09 14:26 chrisfen |
| 493 |
|
|
|
| 494 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: reformulated some of |
| 495 |
|
|
the electrostatics |
| 496 |
|
|
|
| 497 |
|
|
2006-06-07 18:49 chrisfen |
| 498 |
|
|
|
| 499 |
|
|
* samples/water/ssd/ssd.md, |
| 500 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: damping now works for |
| 501 |
|
|
charge-quadrupole and dipole-dipole |
| 502 |
|
|
|
| 503 |
|
|
2006-06-07 14:05 chrisfen |
| 504 |
|
|
|
| 505 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, io/RestReader.cpp: |
| 506 |
|
|
Fixed a spelling error and a bug in MPI Thermodynamic Integration |
| 507 |
|
|
on file read-in |
| 508 |
|
|
|
| 509 |
|
|
2006-06-06 14:26 chrisfen |
| 510 |
|
|
|
| 511 |
|
|
* src/io/: DumpReader.cpp, MultipoleAtomTypesSectionParser.cpp: |
| 512 |
|
|
fixed some typos |
| 513 |
|
|
|
| 514 |
|
|
2006-06-06 13:43 gezelter |
| 515 |
|
|
|
| 516 |
|
|
* forceFields/DUFF2.frc, samples/gbljtest/2gb.in, |
| 517 |
|
|
samples/gbljtest/2gb.md, samples/gbljtest/gb.md, |
| 518 |
|
|
samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
| 519 |
|
|
samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
| 520 |
|
|
samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
| 521 |
|
|
samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
| 522 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
| 523 |
|
|
src/integrators/LDForceManager.cpp, |
| 524 |
|
|
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
| 525 |
|
|
src/utils/interpolation.F90, src/visitors/AtomVisitor.hpp: testing |
| 526 |
|
|
GB, removing CM drift in Langevin Dynamics, fixing a memory leak, |
| 527 |
|
|
adding a visitor |
| 528 |
|
|
|
| 529 |
|
|
2006-06-05 14:44 gezelter |
| 530 |
|
|
|
| 531 |
|
|
* src/UseTheForce/DarkSide/: fForceOptions.F90, gb.F90: Added |
| 532 |
|
|
methods to access GB_mu and GB_nu from the force field options |
| 533 |
|
|
|
| 534 |
|
|
2006-06-05 14:24 gezelter |
| 535 |
|
|
|
| 536 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
| 537 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/fForceOptions.h, |
| 538 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
| 539 |
|
|
src/UseTheForce/DarkSide/gb_interface.F90, |
| 540 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
| 541 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
| 542 |
|
|
src/applications/hydrodynamics/ApproximationModel.cpp, |
| 543 |
|
|
src/applications/hydrodynamics/ApproximationModel.hpp, |
| 544 |
|
|
src/applications/hydrodynamics/CompositeShape.cpp, |
| 545 |
|
|
src/applications/hydrodynamics/CompositeShape.hpp, |
| 546 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 547 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 548 |
|
|
src/applications/hydrodynamics/ShapeBuilder.cpp, |
| 549 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
| 550 |
|
|
src/hydrodynamics/HydroProp.cpp, src/hydrodynamics/HydroProp.hpp, |
| 551 |
|
|
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
| 552 |
|
|
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
| 553 |
|
|
src/integrators/LDForceManager.cpp, |
| 554 |
|
|
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
| 555 |
|
|
src/io/ForceFieldOptions.hpp, |
| 556 |
|
|
src/io/GayBerneAtomTypesSectionParser.cpp, |
| 557 |
|
|
src/io/GayBerneAtomTypesSectionParser.hpp, |
| 558 |
|
|
src/types/DirectionalAtomType.cpp, |
| 559 |
|
|
src/types/DirectionalAtomType.hpp, src/utils/HydroProps.hpp: |
| 560 |
|
|
Massive changes for GB code with multiple ellipsoid types (a la |
| 561 |
|
|
Cleaver's paper). |
| 562 |
|
|
|
| 563 |
|
|
Also, changes in hydrodynamics code to make HydroProp a somewhat |
| 564 |
|
|
smarter class (rather than just a struct). |
| 565 |
|
|
|
| 566 |
|
|
2006-06-01 14:06 xsun |
| 567 |
|
|
|
| 568 |
|
|
* src/applications/staticProps/: Makefile, RippleOP.cpp, |
| 569 |
|
|
RippleOP.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 570 |
|
|
StaticPropsCmd.h: Add the RippleOP to calculate the orderparameter |
| 571 |
|
|
of the ripples. |
| 572 |
|
|
|
| 573 |
|
|
2006-05-25 17:40 chrisfen |
| 574 |
|
|
|
| 575 |
|
|
* forceFields/DUFF2.frc, samples/thermoIntegration/liquid/water.md, |
| 576 |
|
|
samples/thermoIntegration/solid/water.md, |
| 577 |
|
|
samples/water/dimer/water.md, samples/water/spce/water.md, |
| 578 |
|
|
samples/water/ssd/water.md, samples/water/ssd-ion/water.md, |
| 579 |
|
|
samples/water/ssde/water.md, samples/water/ssdrf/water.md, |
| 580 |
|
|
samples/water/tap/water.md, samples/water/tip3p_ice/water.md, |
| 581 |
|
|
samples/water/tip4p/water.md, src/io/Globals.cpp: Added TIP5P-E and |
| 582 |
|
|
fixed a bug for Thermodynamic integration (you can now have a |
| 583 |
|
|
lambda of 0) |
| 584 |
|
|
|
| 585 |
|
|
2006-05-25 13:02 tim |
| 586 |
|
|
|
| 587 |
|
|
* src/applications/hydrodynamics/ApproximationModel.cpp: Fix a type |
| 588 |
|
|
promotion problem |
| 589 |
|
|
|
| 590 |
|
|
2006-05-25 12:27 tim |
| 591 |
|
|
|
| 592 |
|
|
* src/applications/hydrodynamics/: AnalyticalModel.hpp, |
| 593 |
|
|
ApproximationModel.cpp, Hydro.cpp, HydrodynamicsModel.hpp: replace |
| 594 |
|
|
double with RealType |
| 595 |
|
|
|
| 596 |
|
|
2006-05-25 11:27 gezelter |
| 597 |
|
|
|
| 598 |
|
|
* configure: What? |
| 599 |
|
|
|
| 600 |
|
|
2006-05-25 11:24 gezelter |
| 601 |
|
|
|
| 602 |
|
|
* ac-tools/OOPSE.m4: more changes |
| 603 |
|
|
|
| 604 |
|
|
2006-05-25 11:19 gezelter |
| 605 |
|
|
|
| 606 |
|
|
* configure, ac-tools/OOPSE.m4: more changes for MPICH with |
| 607 |
|
|
profiling libraries required |
| 608 |
|
|
|
| 609 |
|
|
2006-05-25 10:54 gezelter |
| 610 |
|
|
|
| 611 |
|
|
* configure, ac-tools/OOPSE.m4: MPI stuff |
| 612 |
|
|
|
| 613 |
|
|
2006-05-24 14:31 gezelter |
| 614 |
|
|
|
| 615 |
|
|
* configure, ac-tools/OOPSE.m4, src/config.h.in, |
| 616 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
| 617 |
|
|
src/applications/hydrodynamics/AnalyticalModel.hpp, |
| 618 |
|
|
src/applications/hydrodynamics/ApproximationModel.cpp, |
| 619 |
|
|
src/applications/hydrodynamics/ApproximationModel.hpp, |
| 620 |
|
|
src/applications/hydrodynamics/CompositeShape.cpp, |
| 621 |
|
|
src/applications/hydrodynamics/CompositeShape.hpp, |
| 622 |
|
|
src/applications/hydrodynamics/Ellipsoid.cpp, |
| 623 |
|
|
src/applications/hydrodynamics/Ellipsoid.hpp, |
| 624 |
|
|
src/applications/hydrodynamics/Hydro.cpp, |
| 625 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 626 |
|
|
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 627 |
|
|
src/applications/hydrodynamics/RoughShell.cpp, |
| 628 |
|
|
src/applications/hydrodynamics/RoughShell.hpp, |
| 629 |
|
|
src/applications/hydrodynamics/Shape.hpp, |
| 630 |
|
|
src/applications/hydrodynamics/ShapeBuilder.cpp, |
| 631 |
|
|
src/applications/hydrodynamics/ShapeBuilder.hpp, |
| 632 |
|
|
src/applications/hydrodynamics/Spheric.cpp, |
| 633 |
|
|
src/applications/hydrodynamics/Spheric.hpp: fixes for Hydrodynamics |
| 634 |
|
|
|
| 635 |
|
|
2006-05-24 12:18 tim |
| 636 |
|
|
|
| 637 |
|
|
* src/integrators/LDForceManager.cpp: fix a bug in parsing |
| 638 |
|
|
HydroProp file |
| 639 |
|
|
|
| 640 |
|
|
2006-05-24 11:24 gezelter |
| 641 |
|
|
|
| 642 |
|
|
* src/integrators/LDForceManager.cpp: Fixed a bug when spherical |
| 643 |
|
|
boundary conditions were off. |
| 644 |
|
|
|
| 645 |
|
|
2006-05-23 17:12 xsun |
| 646 |
|
|
|
| 647 |
|
|
* src/applications/staticProps/Hxy.cpp: fixed an initialization bug |
| 648 |
|
|
of Hxy.cpp. |
| 649 |
|
|
|
| 650 |
|
|
2006-05-23 14:46 tim |
| 651 |
|
|
|
| 652 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: wrapping back to PBC by |
| 653 |
|
|
molecule instead of by individual atom |
| 654 |
|
|
|
| 655 |
|
|
2006-05-22 11:30 xsun |
| 656 |
|
|
|
| 657 |
|
|
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, StaticProps.ggo, |
| 658 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: fixed the bugs of Hxy.cpp. |
| 659 |
|
|
|
| 660 |
|
|
2006-05-19 17:26 chrisfen |
| 661 |
|
|
|
| 662 |
|
|
* ChangeLog, src/io/DumpWriter.cpp: Last bug showed up in 2 places, |
| 663 |
|
|
fixed the other one. |
| 664 |
|
|
|
| 665 |
chrisfen |
2762 |
2006-05-19 16:45 tim |
| 666 |
chrisfen |
2727 |
|
| 667 |
chrisfen |
2762 |
* src/io/DumpWriter.cpp: Fix a bug of printing empty line in |
| 668 |
|
|
DumpWriter |
| 669 |
|
|
|
| 670 |
|
|
2006-05-19 11:11 tim |
| 671 |
|
|
|
| 672 |
|
|
* make/Makefile.in: change the order of include path and library |
| 673 |
|
|
path |
| 674 |
|
|
|
| 675 |
|
|
2006-05-17 17:51 tim |
| 676 |
|
|
|
| 677 |
|
|
* ChangeLog, samples/water/ssd/ssd.md, src/config.h.in, |
| 678 |
|
|
src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp, |
| 679 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
| 680 |
|
|
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
| 681 |
|
|
src/UseTheForce/doForces_interface.h, |
| 682 |
|
|
src/UseTheForce/fForceOptions.h, |
| 683 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
| 684 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 685 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
| 686 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
| 687 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
| 688 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
| 689 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
| 690 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.h, |
| 691 |
|
|
src/applications/dynamicProps/CrossTimeCorrFunc.cpp, |
| 692 |
|
|
src/applications/dynamicProps/CrossTimeCorrFunc.hpp, |
| 693 |
|
|
src/applications/dynamicProps/DipoleCorrFunc.cpp, |
| 694 |
|
|
src/applications/dynamicProps/DipoleCorrFunc.hpp, |
| 695 |
|
|
src/applications/dynamicProps/LegendreCorrFunc.cpp, |
| 696 |
|
|
src/applications/dynamicProps/LegendreCorrFunc.hpp, |
| 697 |
|
|
src/applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
| 698 |
|
|
src/applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
| 699 |
|
|
src/applications/dynamicProps/RCorrFunc.cpp, |
| 700 |
|
|
src/applications/dynamicProps/RCorrFunc.hpp, |
| 701 |
|
|
src/applications/dynamicProps/TimeCorrFunc.hpp, |
| 702 |
|
|
src/applications/dynamicProps/VCorrFunc.cpp, |
| 703 |
|
|
src/applications/dynamicProps/VCorrFunc.hpp, |
| 704 |
|
|
src/applications/hydrodynamics/Makefile, |
| 705 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 706 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 707 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 708 |
|
|
src/applications/randomBuilder/randomBuilder.cpp, |
| 709 |
|
|
src/applications/simpleBuilder/randomBuilder.cpp, |
| 710 |
|
|
src/applications/staticProps/DensityPlot.cpp, |
| 711 |
|
|
src/applications/staticProps/DensityPlot.hpp, |
| 712 |
|
|
src/applications/staticProps/GofAngle2.cpp, |
| 713 |
|
|
src/applications/staticProps/GofAngle2.hpp, |
| 714 |
|
|
src/applications/staticProps/GofR.cpp, |
| 715 |
|
|
src/applications/staticProps/GofR.hpp, |
| 716 |
|
|
src/applications/staticProps/GofRAngle.cpp, |
| 717 |
|
|
src/applications/staticProps/GofRAngle.hpp, |
| 718 |
|
|
src/applications/staticProps/GofXyz.cpp, |
| 719 |
|
|
src/applications/staticProps/GofXyz.hpp, |
| 720 |
|
|
src/applications/staticProps/Hxy.cpp, |
| 721 |
|
|
src/applications/staticProps/Hxy.hpp, |
| 722 |
|
|
src/applications/staticProps/P2OrderParameter.cpp, |
| 723 |
|
|
src/applications/staticProps/P2OrderParameter.hpp, |
| 724 |
|
|
src/applications/staticProps/RhoZ.cpp, |
| 725 |
|
|
src/applications/staticProps/RhoZ.hpp, |
| 726 |
|
|
src/applications/staticProps/SCDOrderParameter.cpp, |
| 727 |
|
|
src/applications/staticProps/SCDOrderParameter.hpp, |
| 728 |
|
|
src/applications/staticProps/StaticProps.cpp, |
| 729 |
|
|
src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp, |
| 730 |
|
|
src/brains/DataStorage.hpp, src/brains/ForceManager.cpp, |
| 731 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
| 732 |
|
|
src/brains/SimInfo.hpp, src/brains/Snapshot.cpp, |
| 733 |
|
|
src/brains/Snapshot.hpp, src/brains/Stats.hpp, |
| 734 |
|
|
src/brains/Thermo.cpp, src/brains/Thermo.hpp, |
| 735 |
|
|
src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp, |
| 736 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp, |
| 737 |
|
|
src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp, |
| 738 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
| 739 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
| 740 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
| 741 |
|
|
src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp, |
| 742 |
|
|
src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp, |
| 743 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.hpp, |
| 744 |
|
|
src/integrators/LDForceManager.cpp, |
| 745 |
|
|
src/integrators/LDForceManager.hpp, |
| 746 |
|
|
src/integrators/LangevinDynamics.cpp, |
| 747 |
|
|
src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp, |
| 748 |
|
|
src/integrators/NPAT.hpp, src/integrators/NPT.cpp, |
| 749 |
|
|
src/integrators/NPT.hpp, src/integrators/NPTf.cpp, |
| 750 |
|
|
src/integrators/NPTf.hpp, src/integrators/NPTi.cpp, |
| 751 |
|
|
src/integrators/NPTi.hpp, src/integrators/NPTxyz.cpp, |
| 752 |
|
|
src/integrators/NPTxyz.hpp, src/integrators/NPrT.cpp, |
| 753 |
|
|
src/integrators/NPrT.hpp, src/integrators/NVE.cpp, |
| 754 |
|
|
src/integrators/NVE.hpp, src/integrators/NVT.cpp, |
| 755 |
|
|
src/integrators/NVT.hpp, src/integrators/RotationAlgorithm.hpp, |
| 756 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
| 757 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
| 758 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
| 759 |
|
|
src/io/AtomTypesSectionParser.cpp, |
| 760 |
|
|
src/io/BendTypesSectionParser.cpp, |
| 761 |
|
|
src/io/BondTypesSectionParser.cpp, |
| 762 |
|
|
src/io/ChargeAtomTypesSectionParser.cpp, |
| 763 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
| 764 |
|
|
src/io/DumpReader.cpp, src/io/DumpWriter.cpp, |
| 765 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
| 766 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp, |
| 767 |
|
|
src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp, |
| 768 |
|
|
src/io/RestReader.cpp, src/io/RestReader.hpp, |
| 769 |
|
|
src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp, |
| 770 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 771 |
|
|
src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp, |
| 772 |
|
|
src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp, |
| 773 |
|
|
src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp, |
| 774 |
|
|
src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp, |
| 775 |
|
|
src/math/CholeskyDecomposition.hpp, |
| 776 |
|
|
src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp, |
| 777 |
|
|
src/math/MatVec3.c, src/math/MatVec3.h, |
| 778 |
|
|
src/math/MersenneTwister.hpp, src/math/Polynomial.hpp, |
| 779 |
|
|
src/math/Quaternion.hpp, src/math/RandNumGen.hpp, |
| 780 |
|
|
src/math/RealSphericalHarmonic.cpp, |
| 781 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp, |
| 782 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 783 |
|
|
src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp, |
| 784 |
|
|
src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp, |
| 785 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
| 786 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp, |
| 787 |
|
|
src/minimizers/Minimizer.hpp, |
| 788 |
|
|
src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp, |
| 789 |
|
|
src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp, |
| 790 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 791 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
| 792 |
|
|
src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp, |
| 793 |
|
|
src/primitives/DirectionalAtom.cpp, |
| 794 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 795 |
|
|
src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp, |
| 796 |
|
|
src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp, |
| 797 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 798 |
|
|
src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp, |
| 799 |
|
|
src/primitives/Torsion.cpp, src/primitives/Torsion.hpp, |
| 800 |
|
|
src/primitives/UreyBradleyBend.cpp, |
| 801 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
| 802 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
| 803 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp, |
| 804 |
|
|
src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp, |
| 805 |
|
|
src/selection/SelectionEvaluator.cpp, |
| 806 |
|
|
src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp, |
| 807 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
| 808 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
| 809 |
|
|
src/types/BendType.hpp, src/types/BondType.hpp, |
| 810 |
|
|
src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp, |
| 811 |
|
|
src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp, |
| 812 |
|
|
src/types/DirectionalAtomType.cpp, |
| 813 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
| 814 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
| 815 |
|
|
src/types/MorseBondType.hpp, src/types/OplsTorsionType.hpp, |
| 816 |
|
|
src/types/PolynomialBendType.hpp, src/types/PolynomialBondType.hpp, |
| 817 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
| 818 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
| 819 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
| 820 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
| 821 |
|
|
src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp, |
| 822 |
|
|
src/utils/GenericData.hpp, src/utils/MoLocator.cpp, |
| 823 |
|
|
src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp, |
| 824 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp, |
| 825 |
|
|
src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp, |
| 826 |
|
|
src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h, |
| 827 |
|
|
src/utils/residentMem.c, src/utils/residentMem.h, |
| 828 |
|
|
src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp: |
| 829 |
|
|
Adding single precision capabilities to c++ side |
| 830 |
|
|
|
| 831 |
|
|
2006-05-17 15:54 gezelter |
| 832 |
|
|
|
| 833 |
tim |
2759 |
* configure, ac-tools/configure.in, make/Makefile.in, |
| 834 |
|
|
src/UseTheForce/doForces.F90, |
| 835 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 836 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
| 837 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
| 838 |
|
|
src/UseTheForce/DarkSide/simulation_interface.F90, |
| 839 |
|
|
src/utils/definitions.F90: Adding single precision capabilities to |
| 840 |
|
|
the fortran side |
| 841 |
|
|
|
| 842 |
chrisfen |
2762 |
2006-05-17 12:10 gezelter |
| 843 |
tim |
2759 |
|
| 844 |
|
|
* configure, ac-tools/configure.in, src/config.h.in: adding |
| 845 |
|
|
--enable-single to configure script |
| 846 |
|
|
|
| 847 |
chrisfen |
2762 |
2006-05-17 11:37 gezelter |
| 848 |
tim |
2759 |
|
| 849 |
|
|
* ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, |
| 850 |
|
|
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
| 851 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 852 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 853 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
| 854 |
|
|
src/UseTheForce/DarkSide/lj_interface.F90, |
| 855 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
| 856 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
| 857 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
| 858 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.F90, |
| 859 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, src/math/derfc.F90, |
| 860 |
|
|
src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran |
| 861 |
|
|
side prepped for single precision... |
| 862 |
|
|
|
| 863 |
chrisfen |
2762 |
2006-05-17 10:03 chrisfen |
| 864 |
tim |
2759 |
|
| 865 |
|
|
* samples/water/ssd-ion/ssdCl.md, |
| 866 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: electrostatic |
| 867 |
|
|
refinement |
| 868 |
|
|
|
| 869 |
chrisfen |
2762 |
2006-05-16 23:03 gezelter |
| 870 |
tim |
2759 |
|
| 871 |
|
|
* configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes |
| 872 |
|
|
|
| 873 |
chrisfen |
2762 |
2006-05-16 16:38 gezelter |
| 874 |
tim |
2759 |
|
| 875 |
|
|
* configure, ac-tools/OOPSE.m4, ac-tools/config.guess, |
| 876 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, |
| 877 |
|
|
ac-tools/missing, ac-tools/mkinstalldirs, make/Makefile.in, |
| 878 |
|
|
src/config.h.in, src/applications/staticProps/Hxy.cpp, |
| 879 |
|
|
src/applications/staticProps/Hxy.hpp, |
| 880 |
|
|
src/applications/staticProps/StaticProps.cpp: Autoconf fixes for |
| 881 |
|
|
FFTW. Multiple FFTW version support. |
| 882 |
|
|
|
| 883 |
chrisfen |
2762 |
2006-05-15 22:06 gezelter |
| 884 |
tim |
2759 |
|
| 885 |
|
|
* README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 886 |
|
|
make/Makefile.in, src/config.h.in, |
| 887 |
|
|
src/applications/hydrodynamics/AnalyticalModel.cpp, |
| 888 |
|
|
src/applications/hydrodynamics/AnalyticalModel.hpp, |
| 889 |
|
|
src/applications/staticProps/Hxy.cpp, |
| 890 |
|
|
src/applications/staticProps/Hxy.hpp, |
| 891 |
|
|
src/applications/staticProps/StaticProps.cpp, |
| 892 |
|
|
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
| 893 |
|
|
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
| 894 |
|
|
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
| 895 |
|
|
src/integrators/LDForceManager.cpp, |
| 896 |
|
|
src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, |
| 897 |
|
|
src/utils/HydroProps.hpp: [no log message] |
| 898 |
|
|
|
| 899 |
chrisfen |
2762 |
2006-05-12 17:34 xsun |
| 900 |
tim |
2759 |
|
| 901 |
|
|
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, |
| 902 |
|
|
StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to |
| 903 |
|
|
calculate undulation spectrum |
| 904 |
|
|
|
| 905 |
chrisfen |
2762 |
2006-05-09 21:44 tim |
| 906 |
tim |
2759 |
|
| 907 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 908 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
| 909 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 910 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
| 911 |
|
|
applications/hydrodynamics/ApproximationModel.cpp, |
| 912 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a |
| 913 |
|
|
gay-berne switch to Dump2XYZ |
| 914 |
|
|
|
| 915 |
chrisfen |
2762 |
2006-05-05 13:58 gezelter |
| 916 |
tim |
2759 |
|
| 917 |
|
|
* src/UseTheForce/DarkSide/qpole.F90: Adding qpole |
| 918 |
|
|
|
| 919 |
chrisfen |
2762 |
2006-05-05 10:34 tim |
| 920 |
tim |
2759 |
|
| 921 |
|
|
* ac-tools/aclocal.m4: finding ifort arguments that won't die under |
| 922 |
|
|
two different versions of the intel fortran compiler |
| 923 |
|
|
|
| 924 |
chrisfen |
2762 |
2006-05-03 09:15 chrisfen |
| 925 |
tim |
2759 |
|
| 926 |
|
|
* src/applications/randomBuilder/Makefile: missing makefile was |
| 927 |
|
|
hanging up 'make clean' |
| 928 |
|
|
|
| 929 |
chrisfen |
2762 |
2006-04-25 18:59 chuckv |
| 930 |
tim |
2759 |
|
| 931 |
|
|
* src/applications/randomBuilder/: randomBuilder.cpp, |
| 932 |
|
|
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added |
| 933 |
|
|
random builder to cvs. |
| 934 |
|
|
|
| 935 |
chrisfen |
2762 |
2006-04-25 18:54 chuckv |
| 936 |
tim |
2759 |
|
| 937 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 938 |
|
|
Change in siminfo used in nanoparticleBuilder. |
| 939 |
|
|
|
| 940 |
chrisfen |
2762 |
2006-04-25 18:30 chuckv |
| 941 |
tim |
2759 |
|
| 942 |
|
|
* make/Makefile.in: Added random builder |
| 943 |
|
|
|
| 944 |
chrisfen |
2762 |
2006-04-25 18:29 chuckv |
| 945 |
tim |
2759 |
|
| 946 |
|
|
* src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, |
| 947 |
|
|
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a |
| 948 |
|
|
random builder to oopse. |
| 949 |
|
|
|
| 950 |
chrisfen |
2762 |
2006-04-25 09:35 gezelter |
| 951 |
tim |
2759 |
|
| 952 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
| 953 |
|
|
ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table |
| 954 |
|
|
to pick vdw radii for hydrodynamics if the LJ sigma can't be found. |
| 955 |
|
|
|
| 956 |
chrisfen |
2762 |
2006-04-24 22:09 gezelter |
| 957 |
tim |
2759 |
|
| 958 |
|
|
* configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, |
| 959 |
|
|
src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, |
| 960 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
| 961 |
|
|
src/brains/SimInfo.hpp, src/brains/Thermo.cpp, |
| 962 |
|
|
src/brains/Thermo.hpp, src/integrators/LDForceManager.cpp, |
| 963 |
|
|
src/integrators/LDForceManager.hpp, |
| 964 |
|
|
src/integrators/LangevinDynamics.cpp, src/io/Globals.cpp, |
| 965 |
|
|
src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding |
| 966 |
|
|
spherical boundary conditions to LD integrator |
| 967 |
|
|
|
| 968 |
chrisfen |
2762 |
2006-04-24 22:06 gezelter |
| 969 |
tim |
2759 |
|
| 970 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: |
| 971 |
|
|
Added EAM atom types to Hydro models |
| 972 |
|
|
|
| 973 |
chrisfen |
2762 |
2006-04-21 16:02 chrisfen |
| 974 |
tim |
2759 |
|
| 975 |
|
|
* src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the |
| 976 |
|
|
EAM module |
| 977 |
|
|
|
| 978 |
chrisfen |
2762 |
2006-04-21 15:32 chrisfen |
| 979 |
tim |
2759 |
|
| 980 |
|
|
* ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, |
| 981 |
|
|
samples/shape/C60.shape, samples/shape/C70.shape, |
| 982 |
|
|
samples/shape/Makefile, samples/shape/Shapes.frc, |
| 983 |
|
|
samples/shape/cholesterol.shape, samples/shape/ethylBenzene.shape, |
| 984 |
|
|
samples/shape/linear.in, samples/shape/linear.md, |
| 985 |
|
|
samples/shape/linear.shape, samples/shape/toluene.shape, |
| 986 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
| 987 |
|
|
samples/thermoIntegration/solid/ssde.md, |
| 988 |
|
|
samples/water/spce/spce.md, samples/water/ssd/ssd.md, |
| 989 |
|
|
samples/water/ssd-ion/ssdCl.md, samples/water/ssde/ssde.md, |
| 990 |
|
|
samples/water/ssdrf/ssdrf.md, samples/water/tip3p_ice/tp3.md, |
| 991 |
|
|
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90, |
| 992 |
|
|
src/UseTheForce/DarkSide/LJ.F90: Removed sqrt splines and shape |
| 993 |
|
|
stuff (doesn't work, so why was it in there?). Changed some of the |
| 994 |
|
|
water samples to use shifted_force. Probably should set the |
| 995 |
|
|
defaults to use the damped version now that we sped it up. |
| 996 |
|
|
|
| 997 |
chrisfen |
2762 |
2006-04-20 23:19 chrisfen |
| 998 |
tim |
2759 |
|
| 999 |
chrisfen |
2727 |
* samples/water/spce/spce.md, |
| 1000 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
| 1001 |
|
|
|
| 1002 |
chrisfen |
2762 |
2006-04-20 17:02 chrisfen |
| 1003 |
chrisfen |
2727 |
|
| 1004 |
|
|
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
| 1005 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
| 1006 |
|
|
|
| 1007 |
chrisfen |
2762 |
2006-04-20 14:24 gezelter |
| 1008 |
chrisfen |
2727 |
|
| 1009 |
|
|
* samples/metals/EAM/Au_bulk_voter.md, |
| 1010 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 1011 |
|
|
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
| 1012 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
| 1013 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
| 1014 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 1015 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
| 1016 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
| 1017 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
| 1018 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.h, |
| 1019 |
|
|
src/utils/interpolation.F90: Complete rewrite of spline code and |
| 1020 |
|
|
everything that uses it. |
| 1021 |
|
|
|
| 1022 |
chrisfen |
2762 |
2006-04-17 17:49 gezelter |
| 1023 |
chrisfen |
2727 |
|
| 1024 |
|
|
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
| 1025 |
|
|
samples/metals/EAM/Au_bulk_voter.md, |
| 1026 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 1027 |
|
|
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
| 1028 |
|
|
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
| 1029 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 1030 |
|
|
src/UseTheForce/DarkSide/interpolation.F90, |
| 1031 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
| 1032 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, |
| 1033 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
| 1034 |
|
|
src/applications/hydrodynamics/Hydro.ggo, |
| 1035 |
|
|
src/applications/hydrodynamics/HydroCmd.c, |
| 1036 |
|
|
src/applications/hydrodynamics/HydroCmd.h, |
| 1037 |
|
|
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
| 1038 |
|
|
src/utils/interpolation.F90: Many performance improvements |
| 1039 |
|
|
|
| 1040 |
chrisfen |
2762 |
2006-04-15 22:51 chrisfen |
| 1041 |
chrisfen |
2727 |
|
| 1042 |
|
|
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
| 1043 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 1044 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 1045 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
| 1046 |
|
|
switcheroo |
| 1047 |
|
|
|
| 1048 |
chrisfen |
2762 |
2006-04-15 17:58 chrisfen |
| 1049 |
chrisfen |
2727 |
|
| 1050 |
|
|
* src/utils/Makefile.in: Since status.F90 is used by |
| 1051 |
|
|
interpolation.F90, the former needs to be listed above the later in |
| 1052 |
|
|
the Makefile. |
| 1053 |
|
|
|
| 1054 |
chrisfen |
2762 |
2006-04-14 17:59 gezelter |
| 1055 |
chrisfen |
2727 |
|
| 1056 |
|
|
* src/utils/interpolation.F90: changed the interface a bit |
| 1057 |
|
|
|
| 1058 |
chrisfen |
2762 |
2006-04-14 17:49 gezelter |
| 1059 |
chrisfen |
2727 |
|
| 1060 |
|
|
* src/utils/interpolation.F90: added some logical flags |
| 1061 |
|
|
|
| 1062 |
chrisfen |
2762 |
2006-04-14 17:06 chrisfen |
| 1063 |
chrisfen |
2727 |
|
| 1064 |
|
|
* src/utils/interpolation.F90: Wiped the spline with derivatives |
| 1065 |
|
|
and corrected a boundary comparision error by eliminating the |
| 1066 |
|
|
check. This algorithm REQUIRES known first derivatives at the |
| 1067 |
|
|
endpoints. |
| 1068 |
|
|
|
| 1069 |
chrisfen |
2762 |
2006-04-14 16:04 gezelter |
| 1070 |
chrisfen |
2727 |
|
| 1071 |
|
|
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
| 1072 |
|
|
interpolation module |
| 1073 |
|
|
|
| 1074 |
chrisfen |
2762 |
2006-04-14 15:57 gezelter |
| 1075 |
chrisfen |
2727 |
|
| 1076 |
|
|
* src/utils/interpolation.F90: Heavily modified interpolation |
| 1077 |
|
|
module, also moved to "utils" |
| 1078 |
|
|
|
| 1079 |
chrisfen |
2762 |
2006-04-12 17:15 chuckv |
| 1080 |
chrisfen |
2727 |
|
| 1081 |
|
|
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
| 1082 |
|
|
module. |
| 1083 |
|
|
|
| 1084 |
chrisfen |
2762 |
2006-04-11 11:33 gezelter |
| 1085 |
chrisfen |
2727 |
|
| 1086 |
|
|
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
| 1087 |
|
|
StaticPropsCmd.h: [no log message] |
| 1088 |
|
|
|
| 1089 |
chrisfen |
2762 |
2006-04-03 11:37 chuckv |
| 1090 |
chrisfen |
2727 |
|
| 1091 |
|
|
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
| 1092 |
|
|
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
| 1093 |
|
|
simParallel for error reporting. |
| 1094 |
|
|
|
| 1095 |
|
|
2006-03-31 13:09 tim |
| 1096 |
|
|
|
| 1097 |
|
|
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
| 1098 |
|
|
|
| 1099 |
|
|
2006-03-30 16:08 chuckv |
| 1100 |
|
|
|
| 1101 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
| 1102 |
|
|
where SCList capacity was not reset to zero on destruction. |
| 1103 |
|
|
|
| 1104 |
|
|
2006-03-30 14:37 chuckv |
| 1105 |
|
|
|
| 1106 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 1107 |
|
|
More testing of nanoparticleBuilder. |
| 1108 |
|
|
|
| 1109 |
|
|
2006-03-29 17:24 chuckv |
| 1110 |
|
|
|
| 1111 |
|
|
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
| 1112 |
|
|
file exists. |
| 1113 |
|
|
|
| 1114 |
|
|
2006-03-29 14:17 chuckv |
| 1115 |
|
|
|
| 1116 |
|
|
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
| 1117 |
|
|
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
| 1118 |
|
|
latticeOrt in shapedlatice and latticebuilder. |
| 1119 |
|
|
|
| 1120 |
|
|
2006-03-29 13:11 tim |
| 1121 |
|
|
|
| 1122 |
|
|
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 1123 |
|
|
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
| 1124 |
|
|
in calculating correlation functions |
| 1125 |
|
|
|
| 1126 |
|
|
2006-03-29 13:09 tim |
| 1127 |
|
|
|
| 1128 |
|
|
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
| 1129 |
|
|
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
| 1130 |
|
|
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
| 1131 |
|
|
RoughShell Model is working; (20)Adding a new option into Hydro |
| 1132 |
|
|
which allows user to generate the beads only |
| 1133 |
|
|
|
| 1134 |
|
|
2006-03-27 11:21 chuckv |
| 1135 |
|
|
|
| 1136 |
|
|
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
| 1137 |
|
|
nanoparticle builder. |
| 1138 |
|
|
|
| 1139 |
|
|
2006-03-27 11:03 chuckv |
| 1140 |
|
|
|
| 1141 |
|
|
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
| 1142 |
|
|
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
| 1143 |
|
|
makefile |
| 1144 |
|
|
|
| 1145 |
|
|
2006-03-24 15:46 chuckv |
| 1146 |
|
|
|
| 1147 |
|
|
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 1148 |
|
|
Debugging changes to nanoparticle builder. |
| 1149 |
|
|
|
| 1150 |
|
|
2006-03-24 12:29 tim |
| 1151 |
|
|
|
| 1152 |
|
|
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 1153 |
|
|
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 1154 |
|
|
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
| 1155 |
|
|
|
| 1156 |
|
|
2006-03-24 11:49 tim |
| 1157 |
|
|
|
| 1158 |
|
|
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 1159 |
|
|
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 1160 |
|
|
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
| 1161 |
|
|
function. The command line option for DynamicProps is now changed. |
| 1162 |
|
|
--rcorr is for position correlation and --rmsd is for mean square |
| 1163 |
|
|
displacement. |
| 1164 |
|
|
|
| 1165 |
|
|
2006-03-23 10:03 tim |
| 1166 |
|
|
|
| 1167 |
|
|
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
| 1168 |
|
|
AnalyticalModel.hpp, ApproximationModel.cpp, |
| 1169 |
|
|
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
| 1170 |
|
|
method |
| 1171 |
|
|
|
| 1172 |
|
|
2006-03-23 10:02 tim |
| 1173 |
|
|
|
| 1174 |
|
|
* src/io/Globals.hpp: remove a unknown method |
| 1175 |
|
|
|
| 1176 |
|
|
2006-03-23 10:00 tim |
| 1177 |
|
|
|
| 1178 |
|
|
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
| 1179 |
|
|
|
| 1180 |
|
|
2006-03-23 09:59 tim |
| 1181 |
|
|
|
| 1182 |
|
|
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
| 1183 |
|
|
can not be opened for preprocessing |
| 1184 |
|
|
|
| 1185 |
|
|
2006-03-22 15:57 chuckv |
| 1186 |
|
|
|
| 1187 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
| 1188 |
|
|
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
| 1189 |
|
|
shaped lattice. |
| 1190 |
|
|
|
| 1191 |
|
|
2006-03-21 10:33 tim |
| 1192 |
|
|
|
| 1193 |
|
|
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
| 1194 |
|
|
in calculating hydrodynamics tensor when the radius of beads are |
| 1195 |
|
|
not the same |
| 1196 |
|
|
|
| 1197 |
|
|
2006-03-20 19:26 tim |
| 1198 |
|
|
|
| 1199 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 1200 |
|
|
applications/hydrodynamics/BeadModel.cpp, |
| 1201 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
| 1202 |
|
|
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
| 1203 |
|
|
for ellipsoid |
| 1204 |
|
|
|
| 1205 |
|
|
2006-03-20 14:12 tim |
| 1206 |
|
|
|
| 1207 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 1208 |
|
|
applications/hydrodynamics/Ellipsoid.cpp, |
| 1209 |
|
|
applications/hydrodynamics/Ellipsoid.hpp, |
| 1210 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
| 1211 |
|
|
integrators/LDForceManager.cpp: Verify the correctness of |
| 1212 |
|
|
Ellipsoid's hydrodynamics properties |
| 1213 |
|
|
|
| 1214 |
|
|
2006-03-17 18:51 tim |
| 1215 |
|
|
|
| 1216 |
|
|
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
| 1217 |
|
|
version of Hydro is working now. |
| 1218 |
|
|
|
| 1219 |
|
|
2006-03-17 18:20 tim |
| 1220 |
|
|
|
| 1221 |
|
|
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 1222 |
|
|
applications/hydrodynamics/AnalyticalModel.hpp, |
| 1223 |
|
|
applications/hydrodynamics/ApproximationModel.cpp, |
| 1224 |
|
|
applications/hydrodynamics/ApproximationModel.hpp, |
| 1225 |
|
|
applications/hydrodynamics/BeadModel.hpp, |
| 1226 |
|
|
applications/hydrodynamics/CompositeShape.cpp, |
| 1227 |
|
|
applications/hydrodynamics/CompositeShape.hpp, |
| 1228 |
|
|
applications/hydrodynamics/Ellipsoid.cpp, |
| 1229 |
|
|
applications/hydrodynamics/Ellipsoid.hpp, |
| 1230 |
|
|
applications/hydrodynamics/Hydro.cpp, |
| 1231 |
|
|
applications/hydrodynamics/Hydro.ggo, |
| 1232 |
|
|
applications/hydrodynamics/HydroCmd.c, |
| 1233 |
|
|
applications/hydrodynamics/HydroCmd.h, |
| 1234 |
|
|
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 1235 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 1236 |
|
|
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 1237 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 1238 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 1239 |
|
|
applications/hydrodynamics/Makefile, |
| 1240 |
|
|
applications/hydrodynamics/RoughShell.cpp, |
| 1241 |
|
|
applications/hydrodynamics/RoughShell.hpp, |
| 1242 |
|
|
applications/hydrodynamics/Shape.hpp, |
| 1243 |
|
|
applications/hydrodynamics/ShapeBuilder.cpp, |
| 1244 |
|
|
applications/hydrodynamics/ShapeBuilder.hpp, |
| 1245 |
|
|
applications/hydrodynamics/Spheric.cpp, |
| 1246 |
|
|
applications/hydrodynamics/Spheric.hpp, |
| 1247 |
|
|
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 1248 |
|
|
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 1249 |
|
|
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
| 1250 |
|
|
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
| 1251 |
|
|
utils/HydroProps.hpp: refactor Hydrodynamics module. |
| 1252 |
|
|
|
| 1253 |
|
|
2006-03-17 11:10 chuckv |
| 1254 |
|
|
|
| 1255 |
|
|
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
| 1256 |
|
|
Generic Shaped Lattice for oopse. Can overload to get spherical or |
| 1257 |
|
|
nanorod. |
| 1258 |
|
|
|
| 1259 |
|
|
2006-03-16 17:50 tim |
| 1260 |
|
|
|
| 1261 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 1262 |
|
|
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
| 1263 |
|
|
LagevinDynamics is working? |
| 1264 |
|
|
|
| 1265 |
|
|
2006-03-16 16:52 gezelter |
| 1266 |
|
|
|
| 1267 |
|
|
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
| 1268 |
|
|
problem |
| 1269 |
|
|
|
| 1270 |
|
|
2006-03-15 17:08 tim |
| 1271 |
|
|
|
| 1272 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
| 1273 |
|
|
conversion for diffusion tensor is wrong |
| 1274 |
|
|
|
| 1275 |
|
|
2006-03-15 16:28 tim |
| 1276 |
|
|
|
| 1277 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 1278 |
|
|
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
| 1279 |
|
|
|
| 1280 |
|
|
2006-03-15 15:58 tim |
| 1281 |
|
|
|
| 1282 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
| 1283 |
|
|
the unit in HydrodynamicsModel |
| 1284 |
|
|
|
| 1285 |
|
|
2006-03-15 12:35 tim |
| 1286 |
|
|
|
| 1287 |
|
|
* src/primitives/RigidBody.cpp: using setFrc in |
| 1288 |
|
|
RigidBody::calcForcesAndTorques will discard if there are force and |
| 1289 |
|
|
torque applied in rigid body itself. use addFrc instead. |
| 1290 |
|
|
|
| 1291 |
|
|
2006-03-15 10:51 tim |
| 1292 |
|
|
|
| 1293 |
|
|
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
| 1294 |
|
|
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
| 1295 |
|
|
|
| 1296 |
|
|
2006-03-15 10:50 tim |
| 1297 |
|
|
|
| 1298 |
|
|
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
| 1299 |
|
|
hydrodynamics module into build system |
| 1300 |
|
|
|
| 1301 |
|
|
2006-03-14 18:46 tim |
| 1302 |
|
|
|
| 1303 |
|
|
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
| 1304 |
|
|
|
| 1305 |
|
|
2006-03-13 17:42 tim |
| 1306 |
|
|
|
| 1307 |
|
|
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 1308 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 1309 |
|
|
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 1310 |
|
|
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 1311 |
|
|
brains/Register.cpp, integrators/LDForceManager.cpp, |
| 1312 |
|
|
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
| 1313 |
|
|
integrators/LangevinDynamics.hpp, integrators/Makefile, |
| 1314 |
|
|
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
| 1315 |
|
|
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
| 1316 |
|
|
progress |
| 1317 |
|
|
|
| 1318 |
|
|
2006-03-07 11:43 gezelter |
| 1319 |
|
|
|
| 1320 |
|
|
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
| 1321 |
|
|
double/int bug. Surprised no one ever noticed before... |
| 1322 |
|
|
|
| 1323 |
|
|
2006-02-24 16:17 tim |
| 1324 |
|
|
|
| 1325 |
|
|
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
| 1326 |
|
|
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
| 1327 |
|
|
product of Rij |
| 1328 |
|
|
|
| 1329 |
|
|
2006-02-23 18:16 tim |
| 1330 |
|
|
|
| 1331 |
|
|
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
| 1332 |
|
|
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
| 1333 |
|
|
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
| 1334 |
|
|
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
| 1335 |
|
|
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
| 1336 |
|
|
StuntDoubleShape.hpp: Bead Model is working |
| 1337 |
|
|
|
| 1338 |
|
|
2006-02-22 15:35 tim |
| 1339 |
|
|
|
| 1340 |
|
|
* src/: applications/hydrodynamics/Hydro.cpp, |
| 1341 |
|
|
applications/hydrodynamics/Hydro.ggo, |
| 1342 |
|
|
applications/hydrodynamics/HydroCmd.c, |
| 1343 |
|
|
applications/hydrodynamics/HydroCmd.h, |
| 1344 |
|
|
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 1345 |
|
|
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 1346 |
|
|
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 1347 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 1348 |
|
|
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 1349 |
|
|
applications/hydrodynamics/MoleculeShape.cpp, |
| 1350 |
|
|
applications/hydrodynamics/MoleculeShape.hpp, |
| 1351 |
|
|
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
| 1352 |
|
|
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
| 1353 |
|
|
Module |
| 1354 |
|
|
|
| 1355 |
|
|
2006-02-16 17:05 gezelter |
| 1356 |
|
|
|
| 1357 |
|
|
* src/brains/Snapshot.cpp: fixed a spelling error |
| 1358 |
|
|
|
| 1359 |
|
|
2006-02-16 16:40 gezelter |
| 1360 |
|
|
|
| 1361 |
|
|
* src/: UseTheForce/doForces.F90, |
| 1362 |
|
|
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
| 1363 |
|
|
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
| 1364 |
|
|
larger than 1/2 the length of the shortest box dimension. added a |
| 1365 |
|
|
few fortran utility routines |
| 1366 |
|
|
|
| 1367 |
|
|
2006-02-15 15:46 chuckv |
| 1368 |
|
|
|
| 1369 |
|
|
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
| 1370 |
|
|
sphericalNanoparticle.hpp: Changed Names of class files. |
| 1371 |
|
|
|
| 1372 |
|
|
2006-02-10 10:45 kdaily |
| 1373 |
|
|
|
| 1374 |
|
|
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
| 1375 |
|
|
message] |
| 1376 |
|
|
|
| 1377 |
|
|
2006-02-10 10:12 tim |
| 1378 |
|
|
|
| 1379 |
|
|
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
| 1380 |
|
|
converting integer to double |
| 1381 |
|
|
|
| 1382 |
|
|
2006-02-08 13:21 chrisfen |
| 1383 |
|
|
|
| 1384 |
|
|
* forceFields/DUFF2.frc: added DPD molecule type parameters |
| 1385 |
|
|
|
| 1386 |
|
|
2006-02-07 11:39 tim |
| 1387 |
|
|
|
| 1388 |
|
|
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 1389 |
|
|
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
| 1390 |
|
|
trajectory file during analysis |
| 1391 |
|
|
|
| 1392 |
|
|
2006-02-02 12:14 tim |
| 1393 |
|
|
|
| 1394 |
|
|
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
| 1395 |
|
|
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
| 1396 |
|
|
in AtomStamp where orientation is not set correctly. |
| 1397 |
|
|
|
| 1398 |
|
|
2006-02-02 11:49 gezelter |
| 1399 |
|
|
|
| 1400 |
|
|
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
| 1401 |
|
|
contain directional atoms |
| 1402 |
|
|
|
| 1403 |
|
|
2006-02-02 10:49 xsun |
| 1404 |
|
|
|
| 1405 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 1406 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
| 1407 |
|
|
for GBlipid atom type |
| 1408 |
|
|
|
| 1409 |
|
|
2006-02-01 21:57 gezelter |
| 1410 |
|
|
|
| 1411 |
|
|
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
| 1412 |
|
|
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
| 1413 |
|
|
|
| 1414 |
|
|
2006-02-01 16:06 chrisfen |
| 1415 |
|
|
|
| 1416 |
|
|
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
| 1417 |
|
|
to build |
| 1418 |
|
|
|
| 1419 |
|
|
2006-02-01 15:54 chrisfen |
| 1420 |
|
|
|
| 1421 |
|
|
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
| 1422 |
|
|
cutoff radius setting to a more logical procedure - still may |
| 1423 |
|
|
change... |
| 1424 |
|
|
|
| 1425 |
|
|
2006-02-01 12:26 gezelter |
| 1426 |
|
|
|
| 1427 |
|
|
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
| 1428 |
|
|
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
| 1429 |
|
|
|
| 1430 |
|
|
2006-01-30 17:25 tim |
| 1431 |
|
|
|
| 1432 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
| 1433 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
| 1434 |
|
|
applications/dynamicProps/DynamicProps.ggo, |
| 1435 |
|
|
applications/dynamicProps/DynamicPropsCmd.c, |
| 1436 |
|
|
applications/dynamicProps/DynamicPropsCmd.h, |
| 1437 |
|
|
applications/dynamicProps/LegendreCorrFunc.cpp, |
| 1438 |
|
|
applications/dynamicProps/LegendreCorrFunc.hpp, |
| 1439 |
|
|
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
| 1440 |
|
|
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
| 1441 |
|
|
Adding :LegendrePolynomial |
| 1442 |
|
|
|
| 1443 |
|
|
2006-01-19 17:54 chuckv |
| 1444 |
|
|
|
| 1445 |
|
|
* src/applications/nanoparticleBuilder/: Makefile, |
| 1446 |
|
|
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
| 1447 |
|
|
nanoparticle builder |
| 1448 |
|
|
|
| 1449 |
|
|
2006-01-18 16:08 chuckv |
| 1450 |
|
|
|
| 1451 |
|
|
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
| 1452 |
|
|
nanoparticle builder. |
| 1453 |
|
|
|
| 1454 |
|
|
2006-01-17 11:16 gezelter |
| 1455 |
|
|
|
| 1456 |
|
|
* AUTHORS, README: Cleaning up for 3.0.1 release |
| 1457 |
|
|
|
| 1458 |
|
|
2006-01-17 10:50 gezelter |
| 1459 |
|
|
|
| 1460 |
|
|
* ChangeLog: Prepping 3.0.1 release |
| 1461 |
|
|
|
| 1462 |
gezelter |
2571 |
2006-01-17 10:32 gezelter |
| 1463 |
|
|
|
| 1464 |
|
|
* src/config.h.in: new version number |
| 1465 |
|
|
|
| 1466 |
|
|
2006-01-17 10:32 gezelter |
| 1467 |
|
|
|
| 1468 |
|
|
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
| 1469 |
|
|
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
| 1470 |
|
|
oopseManual.pdf: Updated Documentation |
| 1471 |
|
|
|
| 1472 |
|
|
2006-01-16 18:10 gezelter |
| 1473 |
|
|
|
| 1474 |
|
|
* ChangeLog, README: Getting ready for release! |
| 1475 |
|
|
|
| 1476 |
gezelter |
2568 |
2006-01-16 10:26 gezelter |
| 1477 |
|
|
|
| 1478 |
|
|
* configure: Testing commit |
| 1479 |
|
|
|
| 1480 |
|
|
2006-01-13 16:57 chuckv |
| 1481 |
|
|
|
| 1482 |
|
|
* src/: UseTheForce/SC_FF.cpp, |
| 1483 |
|
|
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
| 1484 |
|
|
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
| 1485 |
|
|
Handled by forceField now. |
| 1486 |
|
|
|
| 1487 |
|
|
2006-01-13 14:17 chuckv |
| 1488 |
|
|
|
| 1489 |
|
|
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
| 1490 |
|
|
|
| 1491 |
|
|
2006-01-13 11:33 gezelter |
| 1492 |
|
|
|
| 1493 |
|
|
* Makefile: [no log message] |
| 1494 |
|
|
|
| 1495 |
|
|
2006-01-13 11:26 gezelter |
| 1496 |
|
|
|
| 1497 |
|
|
* Makefile: testing to make sure GNU make is the make that was used |
| 1498 |
|
|
to build OOPSE |
| 1499 |
|
|
|
| 1500 |
|
|
2006-01-13 10:48 gezelter |
| 1501 |
|
|
|
| 1502 |
|
|
* configure, ac-tools/configure.in: changed compiler search order |
| 1503 |
|
|
|
| 1504 |
|
|
2006-01-12 19:09 chuckv |
| 1505 |
|
|
|
| 1506 |
|
|
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
| 1507 |
|
|
samples/metals/Sutton-Chen/Au_bulk.in, |
| 1508 |
|
|
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
| 1509 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
| 1510 |
|
|
units |
| 1511 |
|
|
|
| 1512 |
|
|
2006-01-12 16:16 gezelter |
| 1513 |
|
|
|
| 1514 |
|
|
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
| 1515 |
|
|
version info and the copyright date |
| 1516 |
|
|
|
| 1517 |
|
|
2006-01-12 15:52 gezelter |
| 1518 |
|
|
|
| 1519 |
|
|
* src/config.h.in: added some missing checks for header files |
| 1520 |
|
|
(particularly zlib.h), used autoheader to help generate config.h.in |
| 1521 |
|
|
|
| 1522 |
|
|
2006-01-12 15:51 gezelter |
| 1523 |
|
|
|
| 1524 |
|
|
* configure, ac-tools/configure.in: added some missing checks for |
| 1525 |
|
|
header files (particularly zlib.h) |
| 1526 |
|
|
|
| 1527 |
|
|
2006-01-12 15:19 gezelter |
| 1528 |
|
|
|
| 1529 |
|
|
* make/Makefile.in: fixed a dependency problem for the Executable |
| 1530 |
|
|
builds |
| 1531 |
|
|
|
| 1532 |
|
|
2006-01-12 15:02 gezelter |
| 1533 |
|
|
|
| 1534 |
|
|
* samples/gbljtest/Makefile: Missing Makefile in this sample |
| 1535 |
|
|
directory |
| 1536 |
|
|
|
| 1537 |
|
|
2006-01-12 15:01 gezelter |
| 1538 |
|
|
|
| 1539 |
|
|
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
| 1540 |
|
|
Old makefile.in no longer required |
| 1541 |
|
|
|
| 1542 |
|
|
2006-01-12 15:01 gezelter |
| 1543 |
|
|
|
| 1544 |
|
|
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
| 1545 |
|
|
needs to be installed |
| 1546 |
|
|
|
| 1547 |
|
|
2006-01-12 14:56 chuckv |
| 1548 |
|
|
|
| 1549 |
|
|
* src/io/DumpWriter.cpp: Changed formating. |
| 1550 |
|
|
|
| 1551 |
|
|
2006-01-12 11:47 chrisfen |
| 1552 |
|
|
|
| 1553 |
|
|
* samples/water/tip4p/tp4.md, |
| 1554 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 1555 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 1556 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 1557 |
|
|
src/brains/SimInfo.cpp: unifying function name in electrostatics |
| 1558 |
|
|
|
| 1559 |
|
|
2006-01-12 11:04 tim |
| 1560 |
|
|
|
| 1561 |
|
|
* samples/metals/: EAM/nanoparticle/Makefile, |
| 1562 |
|
|
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
| 1563 |
|
|
Sutton-Chen/Makefile: fix make install problem for metals samples |
| 1564 |
|
|
|
| 1565 |
|
|
2006-01-12 10:22 tim |
| 1566 |
|
|
|
| 1567 |
|
|
* make/Makefile.in: remove samples/metals from install list. |
| 1568 |
|
|
|
| 1569 |
|
|
2006-01-12 09:31 tim |
| 1570 |
|
|
|
| 1571 |
|
|
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
| 1572 |
|
|
handle multiple line macro, just convert multiple line macro into |
| 1573 |
|
|
single line macro. |
| 1574 |
|
|
|
| 1575 |
|
|
2006-01-11 23:13 chrisfen |
| 1576 |
|
|
|
| 1577 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 1578 |
|
|
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
| 1579 |
|
|
changes to electrostatics for shifted-potential and shifted-force |
| 1580 |
|
|
with mono and multipoles |
| 1581 |
|
|
|
| 1582 |
|
|
2006-01-11 18:04 gezelter |
| 1583 |
|
|
|
| 1584 |
|
|
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
| 1585 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
| 1586 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
| 1587 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 1588 |
|
|
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
| 1589 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
| 1590 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
| 1591 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
| 1592 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 1593 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
| 1594 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
| 1595 |
|
|
src/UseTheForce/DarkSide/suttonchen_interface.h, |
| 1596 |
|
|
src/UseTheForce/DarkSide/switcheroo_interface.h, |
| 1597 |
|
|
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
| 1598 |
|
|
src/utils/fError.c, configure, make/Makefile.in: autoconf |
| 1599 |
|
|
modernization and cruft removal |
| 1600 |
|
|
|
| 1601 |
|
|
2006-01-11 18:04 gezelter |
| 1602 |
|
|
|
| 1603 |
|
|
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
| 1604 |
|
|
modernization and cruft-removal |
| 1605 |
|
|
|
| 1606 |
|
|
2006-01-11 17:50 tim |
| 1607 |
|
|
|
| 1608 |
|
|
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
| 1609 |
|
|
some error messages |
| 1610 |
|
|
|
| 1611 |
|
|
2006-01-11 14:01 tim |
| 1612 |
|
|
|
| 1613 |
|
|
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
| 1614 |
|
|
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
| 1615 |
|
|
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
| 1616 |
|
|
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
| 1617 |
|
|
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
| 1618 |
|
|
an exception when error is found. |
| 1619 |
|
|
|
| 1620 |
|
|
2006-01-11 13:41 gezelter |
| 1621 |
|
|
|
| 1622 |
|
|
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
| 1623 |
|
|
error |
| 1624 |
|
|
|
| 1625 |
|
|
2006-01-10 17:55 chuckv |
| 1626 |
|
|
|
| 1627 |
|
|
* forceFields/SuttonChen.frc: Changed conversion factor. |
| 1628 |
|
|
|
| 1629 |
|
|
2006-01-10 16:14 chuckv |
| 1630 |
|
|
|
| 1631 |
|
|
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 1632 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
| 1633 |
|
|
working now. |
| 1634 |
|
|
|
| 1635 |
|
|
2006-01-09 17:22 chuckv |
| 1636 |
|
|
|
| 1637 |
|
|
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
| 1638 |
|
|
|
| 1639 |
|
|
2006-01-09 17:14 tim |
| 1640 |
|
|
|
| 1641 |
|
|
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
| 1642 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 1643 |
|
|
StaticPropsCmd.h: fixing RhoZ |
| 1644 |
|
|
|
| 1645 |
|
|
2006-01-09 14:26 chuckv |
| 1646 |
|
|
|
| 1647 |
|
|
* forceFields/SuttonChen.frc, |
| 1648 |
|
|
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 1649 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
| 1650 |
|
|
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
| 1651 |
|
|
section parsers. |
| 1652 |
|
|
|
| 1653 |
|
|
2006-01-09 14:11 tim |
| 1654 |
|
|
|
| 1655 |
|
|
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
| 1656 |
|
|
utils/StringUtils.hpp: replace isType<int> with isInteger |
| 1657 |
|
|
|
| 1658 |
|
|
2006-01-06 16:15 tim |
| 1659 |
|
|
|
| 1660 |
|
|
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
| 1661 |
|
|
forceFieldOptions from SC_FF |
| 1662 |
|
|
|
| 1663 |
|
|
2006-01-06 15:27 chuckv |
| 1664 |
|
|
|
| 1665 |
|
|
* forceFields/SuttonChen.frc: Add force file. |
| 1666 |
|
|
|
| 1667 |
|
|
2005-12-31 17:42 chuckv |
| 1668 |
|
|
|
| 1669 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
| 1670 |
|
|
segfaults or produces 0 potential, but rather produces Inf for the |
| 1671 |
|
|
potential. Progress.... |
| 1672 |
|
|
|
| 1673 |
|
|
2005-12-30 18:15 chuckv |
| 1674 |
|
|
|
| 1675 |
|
|
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 1676 |
|
|
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
| 1677 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
| 1678 |
|
|
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
| 1679 |
|
|
Sutton-Chen bug fixes. |
| 1680 |
|
|
|
| 1681 |
|
|
2005-12-30 16:25 tim |
| 1682 |
|
|
|
| 1683 |
|
|
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
| 1684 |
|
|
potential return from fortran is already accumulated, it should not |
| 1685 |
|
|
be accumulated again; nGroupTypesCol is not initialized; |
| 1686 |
|
|
GroupMaxCutoffCol is not allocated; |
| 1687 |
|
|
|
| 1688 |
|
|
2005-12-30 10:32 tim |
| 1689 |
|
|
|
| 1690 |
|
|
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
| 1691 |
|
|
MPI version, we need to cast const char* to void* for |
| 1692 |
|
|
stringstream.str(); Previous Makefile use bjects of single version |
| 1693 |
|
|
to make the MPI library; |
| 1694 |
|
|
|
| 1695 |
|
|
2005-12-29 19:18 chuckv |
| 1696 |
|
|
|
| 1697 |
|
|
* make/Makefile.in, samples/metals/Makefile, |
| 1698 |
|
|
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
| 1699 |
|
|
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
| 1700 |
|
|
Almost there... |
| 1701 |
|
|
|
| 1702 |
|
|
2005-12-29 15:19 chuckv |
| 1703 |
|
|
|
| 1704 |
|
|
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
| 1705 |
|
|
forcefield. |
| 1706 |
|
|
|
| 1707 |
|
|
2005-12-29 15:07 chuckv |
| 1708 |
|
|
|
| 1709 |
|
|
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
| 1710 |
|
|
metals.md: added files for sutton-chen |
| 1711 |
|
|
|
| 1712 |
|
|
2005-12-29 11:37 chuckv |
| 1713 |
|
|
|
| 1714 |
|
|
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
| 1715 |
|
|
metals.md: More cvs changing. |
| 1716 |
|
|
|
| 1717 |
|
|
2005-12-29 11:34 chuckv |
| 1718 |
|
|
|
| 1719 |
|
|
* samples/metals/Au_nanoparticle.in: More moving... |
| 1720 |
|
|
|
| 1721 |
|
|
2005-12-29 11:33 chuckv |
| 1722 |
|
|
|
| 1723 |
|
|
* samples/metals/EAM/nanoparticle/: |
| 1724 |
|
|
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
| 1725 |
|
|
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
| 1726 |
|
|
changes to directory structure. |
| 1727 |
|
|
|
| 1728 |
|
|
2005-12-29 11:21 chuckv |
| 1729 |
|
|
|
| 1730 |
|
|
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
| 1731 |
|
|
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
| 1732 |
|
|
|
| 1733 |
|
|
2005-12-29 11:17 chuckv |
| 1734 |
|
|
|
| 1735 |
|
|
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
| 1736 |
|
|
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
| 1737 |
|
|
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
| 1738 |
|
|
directory structure |
| 1739 |
|
|
|
| 1740 |
|
|
2005-12-29 11:03 chuckv |
| 1741 |
|
|
|
| 1742 |
|
|
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
| 1743 |
|
|
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
| 1744 |
|
|
call to set force options in SimCreator. |
| 1745 |
|
|
|
| 1746 |
|
|
2005-12-28 16:44 chuckv |
| 1747 |
|
|
|
| 1748 |
|
|
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
| 1749 |
|
|
changes to forcefield options. |
| 1750 |
|
|
|
| 1751 |
|
|
2005-12-28 16:42 chuckv |
| 1752 |
|
|
|
| 1753 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
| 1754 |
|
|
passed to fortran. |
| 1755 |
|
|
|
| 1756 |
|
|
2005-12-23 18:04 chuckv |
| 1757 |
|
|
|
| 1758 |
|
|
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
| 1759 |
|
|
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
| 1760 |
|
|
changes. |
| 1761 |
|
|
|
| 1762 |
|
|
2005-12-16 16:52 tim |
| 1763 |
|
|
|
| 1764 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1765 |
|
|
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
| 1766 |
|
|
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
| 1767 |
|
|
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
| 1768 |
|
|
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
| 1769 |
|
|
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
| 1770 |
|
|
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
| 1771 |
|
|
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
| 1772 |
|
|
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
| 1773 |
|
|
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
| 1774 |
|
|
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
| 1775 |
|
|
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
| 1776 |
|
|
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
| 1777 |
|
|
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
| 1778 |
|
|
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
| 1779 |
|
|
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
| 1780 |
|
|
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
| 1781 |
|
|
__FUNCTION__ to __func__ to match C99 standard, and then added an |
| 1782 |
|
|
autoconf test to check for __func__ usability. Changed some |
| 1783 |
|
|
default compile flags for the Sun architecture |
| 1784 |
|
|
|
| 1785 |
|
|
2005-12-16 14:01 gezelter |
| 1786 |
|
|
|
| 1787 |
|
|
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
| 1788 |
|
|
|
| 1789 |
|
|
2005-12-16 13:55 tim |
| 1790 |
|
|
|
| 1791 |
|
|
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
| 1792 |
|
|
change to build oopse under solaris |
| 1793 |
|
|
|
| 1794 |
|
|
2005-12-16 13:26 tim |
| 1795 |
|
|
|
| 1796 |
|
|
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
| 1797 |
|
|
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
| 1798 |
|
|
came with SUN compiler does not have a conforming std::use_facet, |
| 1799 |
|
|
define a macro to handle it. Adding exception handling to |
| 1800 |
|
|
SimCreator. |
| 1801 |
|
|
|
| 1802 |
|
|
2005-12-16 10:53 gezelter |
| 1803 |
|
|
|
| 1804 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 1805 |
|
|
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
| 1806 |
|
|
which was living inside the GB particle. No alien-like ripping out |
| 1807 |
|
|
of the stomach was required. |
| 1808 |
|
|
|
| 1809 |
|
|
2005-12-15 21:57 tim |
| 1810 |
|
|
|
| 1811 |
|
|
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
| 1812 |
|
|
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
| 1813 |
|
|
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
| 1814 |
|
|
replace grammar for numerical parsing |
| 1815 |
|
|
|
| 1816 |
|
|
2005-12-15 16:43 gezelter |
| 1817 |
|
|
|
| 1818 |
|
|
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
| 1819 |
|
|
|
| 1820 |
|
|
2005-12-15 09:48 gezelter |
| 1821 |
|
|
|
| 1822 |
|
|
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
| 1823 |
|
|
dependencies and replacing them with real autoconf checks |
| 1824 |
|
|
|
| 1825 |
|
|
2005-12-15 09:47 gezelter |
| 1826 |
|
|
|
| 1827 |
|
|
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
| 1828 |
|
|
ac-tools/configure.in, src/config.h.in: Adding checks for various |
| 1829 |
|
|
features used by ANTLR |
| 1830 |
|
|
|
| 1831 |
|
|
2005-12-14 13:02 tim |
| 1832 |
|
|
|
| 1833 |
|
|
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
| 1834 |
|
|
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
| 1835 |
|
|
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
| 1836 |
|
|
nasty negative integer parsing problem by refining the grammar |
| 1837 |
|
|
|
| 1838 |
|
|
2005-12-12 14:32 gezelter |
| 1839 |
|
|
|
| 1840 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
| 1841 |
|
|
UseTheForce/doForces_interface.h, |
| 1842 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 1843 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 1844 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
| 1845 |
|
|
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
| 1846 |
|
|
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
| 1847 |
|
|
some minor changes to allow compilation with the portland group |
| 1848 |
|
|
compilers |
| 1849 |
|
|
|
| 1850 |
|
|
2005-12-10 11:54 tim |
| 1851 |
|
|
|
| 1852 |
|
|
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
| 1853 |
|
|
problem for icc7 |
| 1854 |
|
|
|
| 1855 |
|
|
2005-12-09 16:18 gezelter |
| 1856 |
|
|
|
| 1857 |
|
|
* src/utils/CaseConversion.hpp: added missing include |
| 1858 |
|
|
|
| 1859 |
|
|
2005-12-09 12:11 gezelter |
| 1860 |
|
|
|
| 1861 |
|
|
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
| 1862 |
|
|
compiler |
| 1863 |
|
|
|
| 1864 |
|
|
2005-12-08 17:05 gezelter |
| 1865 |
|
|
|
| 1866 |
|
|
* src/io/ForceFieldOptions.cpp: added copyright |
| 1867 |
|
|
|
| 1868 |
|
|
2005-12-08 17:04 gezelter |
| 1869 |
|
|
|
| 1870 |
|
|
* src/UseTheForce/doForces.F90: added info printout |
| 1871 |
|
|
|
| 1872 |
|
|
2005-12-08 17:04 gezelter |
| 1873 |
|
|
|
| 1874 |
|
|
* configure, ac-tools/configure.in: added pathscale |
| 1875 |
|
|
|
| 1876 |
|
|
2005-12-08 10:38 chuckv |
| 1877 |
|
|
|
| 1878 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
| 1879 |
|
|
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
| 1880 |
|
|
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
| 1881 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 1882 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 1883 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
| 1884 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 1885 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
| 1886 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 1887 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
| 1888 |
|
|
io/GayBerneAtomTypesSectionParser.hpp, |
| 1889 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
| 1890 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
| 1891 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
| 1892 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
| 1893 |
|
|
io/ShapeAtomTypesSectionParser.hpp, |
| 1894 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
| 1895 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
| 1896 |
|
|
io/StickyPowerAtomTypesSectionParser.cpp, |
| 1897 |
|
|
io/StickyPowerAtomTypesSectionParser.hpp, |
| 1898 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
| 1899 |
|
|
Wow thats alot o' files. Now passing forceFieldOptions to all of |
| 1900 |
|
|
the parsers. |
| 1901 |
|
|
|
| 1902 |
|
|
2005-12-07 18:10 chuckv |
| 1903 |
|
|
|
| 1904 |
|
|
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
| 1905 |
|
|
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
| 1906 |
|
|
Started adding support for ForceOptions to section parsers. |
| 1907 |
|
|
|
| 1908 |
|
|
2005-12-07 18:01 gezelter |
| 1909 |
|
|
|
| 1910 |
|
|
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
| 1911 |
|
|
|
| 1912 |
|
|
2005-12-07 18:00 chuckv |
| 1913 |
|
|
|
| 1914 |
|
|
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
| 1915 |
|
|
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
| 1916 |
|
|
section parser |
| 1917 |
|
|
|
| 1918 |
|
|
2005-12-07 14:58 chuckv |
| 1919 |
|
|
|
| 1920 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
| 1921 |
|
|
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
| 1922 |
|
|
suttonchen_interface.h: Removed geometric distance mixing from |
| 1923 |
|
|
individual modules and now use force options to detemine what the |
| 1924 |
|
|
deal is. |
| 1925 |
|
|
|
| 1926 |
|
|
2005-12-07 14:46 chuckv |
| 1927 |
|
|
|
| 1928 |
|
|
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
| 1929 |
|
|
Further fixes for compiler issues. |
| 1930 |
|
|
|
| 1931 |
|
|
2005-12-07 14:44 chuckv |
| 1932 |
|
|
|
| 1933 |
|
|
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
| 1934 |
|
|
|
| 1935 |
|
|
2005-12-07 14:38 chuckv |
| 1936 |
|
|
|
| 1937 |
|
|
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
| 1938 |
|
|
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
| 1939 |
|
|
support for fortran force options. |
| 1940 |
|
|
|
| 1941 |
|
|
2005-12-06 16:01 tim |
| 1942 |
|
|
|
| 1943 |
|
|
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
| 1944 |
|
|
|
| 1945 |
|
|
2005-12-06 14:26 chuckv |
| 1946 |
|
|
|
| 1947 |
|
|
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
| 1948 |
|
|
|
| 1949 |
|
|
2005-12-06 12:53 chuckv |
| 1950 |
|
|
|
| 1951 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 1952 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
| 1953 |
|
|
crystal |
| 1954 |
|
|
|
| 1955 |
|
|
2005-12-06 12:52 chuckv |
| 1956 |
|
|
|
| 1957 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
| 1958 |
|
|
dumpwriter. |
| 1959 |
|
|
|
| 1960 |
|
|
2005-12-06 11:49 tim |
| 1961 |
|
|
|
| 1962 |
|
|
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
| 1963 |
|
|
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
| 1964 |
|
|
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
| 1965 |
|
|
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
| 1966 |
|
|
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
| 1967 |
|
|
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
| 1968 |
|
|
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
| 1969 |
|
|
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
| 1970 |
|
|
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
| 1971 |
|
|
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
| 1972 |
|
|
minimizer/water.md, shape/linear.md, |
| 1973 |
|
|
thermoIntegration/liquid/ssde.md, |
| 1974 |
|
|
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
| 1975 |
|
|
thermoIntegration/solid/water.md, water/dimer/cl.md, |
| 1976 |
|
|
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
| 1977 |
|
|
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
| 1978 |
|
|
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
| 1979 |
|
|
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
| 1980 |
|
|
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
| 1981 |
|
|
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
| 1982 |
|
|
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
| 1983 |
|
|
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
| 1984 |
|
|
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
| 1985 |
|
|
keywords from samples |
| 1986 |
|
|
|
| 1987 |
|
|
2005-12-05 18:37 tim |
| 1988 |
|
|
|
| 1989 |
|
|
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
| 1990 |
|
|
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
| 1991 |
|
|
|
| 1992 |
|
|
2005-12-05 17:23 gezelter |
| 1993 |
|
|
|
| 1994 |
|
|
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
| 1995 |
|
|
UseTheForce/Makefile, brains/Register.cpp, |
| 1996 |
|
|
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
| 1997 |
|
|
handler for CLAY force field |
| 1998 |
|
|
|
| 1999 |
|
|
2005-12-05 16:45 chuckv |
| 2000 |
|
|
|
| 2001 |
|
|
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
| 2002 |
|
|
in openbabel. |
| 2003 |
|
|
|
| 2004 |
|
|
2005-12-05 14:10 tim |
| 2005 |
|
|
|
| 2006 |
|
|
* src/types/MoleculeStamp.cpp: reformat error message |
| 2007 |
|
|
|
| 2008 |
|
|
2005-12-05 14:07 gezelter |
| 2009 |
|
|
|
| 2010 |
|
|
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
| 2011 |
|
|
|
| 2012 |
|
|
2005-12-05 13:23 tim |
| 2013 |
|
|
|
| 2014 |
|
|
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 2015 |
|
|
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
| 2016 |
|
|
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
| 2017 |
|
|
adding more checking for topology |
| 2018 |
|
|
|
| 2019 |
|
|
2005-12-02 17:37 gezelter |
| 2020 |
|
|
|
| 2021 |
|
|
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
| 2022 |
|
|
removal |
| 2023 |
|
|
|
| 2024 |
|
|
2005-12-02 17:37 gezelter |
| 2025 |
|
|
|
| 2026 |
|
|
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
| 2027 |
|
|
|
| 2028 |
|
|
2005-12-02 17:37 gezelter |
| 2029 |
|
|
|
| 2030 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 2031 |
|
|
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
| 2032 |
|
|
traditional.md: removing deprecated nAtoms and nComponents lines |
| 2033 |
|
|
|
| 2034 |
|
|
2005-12-02 15:34 tim |
| 2035 |
|
|
|
| 2036 |
|
|
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
| 2037 |
|
|
|
| 2038 |
|
|
2005-12-02 15:18 tim |
| 2039 |
|
|
|
| 2040 |
|
|
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
| 2041 |
|
|
FragmentStamp |
| 2042 |
|
|
|
| 2043 |
|
|
2005-12-02 15:11 gezelter |
| 2044 |
|
|
|
| 2045 |
|
|
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
| 2046 |
|
|
longer thrown with consts (fixes compilation bug on the Mac). |
| 2047 |
|
|
|
| 2048 |
|
|
2005-12-02 15:10 gezelter |
| 2049 |
|
|
|
| 2050 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
| 2051 |
|
|
printing out of timestep |
| 2052 |
|
|
|
| 2053 |
|
|
2005-12-02 15:10 gezelter |
| 2054 |
|
|
|
| 2055 |
|
|
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
| 2056 |
|
|
junk |
| 2057 |
|
|
|
| 2058 |
|
|
2005-12-02 15:10 gezelter |
| 2059 |
|
|
|
| 2060 |
|
|
* make/Makefile.in: Change build process for libOOPSE.a so that the |
| 2061 |
|
|
libraries aren't unpacked. libOOPSE.a is now made directly from |
| 2062 |
|
|
the object files |
| 2063 |
|
|
|
| 2064 |
|
|
2005-12-02 15:09 gezelter |
| 2065 |
|
|
|
| 2066 |
|
|
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
| 2067 |
|
|
needed for new build of libOOPSE.a |
| 2068 |
|
|
|
| 2069 |
|
|
2005-12-02 13:43 tim |
| 2070 |
|
|
|
| 2071 |
|
|
* src/types/DataHolder.hpp: adding DataHolder |
| 2072 |
|
|
|
| 2073 |
|
|
2005-12-02 12:01 gezelter |
| 2074 |
|
|
|
| 2075 |
|
|
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 2076 |
|
|
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
| 2077 |
|
|
case for the cutoff policies |
| 2078 |
|
|
|
| 2079 |
|
|
2005-12-02 10:38 tim |
| 2080 |
|
|
|
| 2081 |
|
|
* make/Makefile.in: update Makefile |
| 2082 |
|
|
|
| 2083 |
|
|
2005-12-02 10:38 tim |
| 2084 |
|
|
|
| 2085 |
|
|
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
| 2086 |
|
|
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
| 2087 |
|
|
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
| 2088 |
|
|
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
| 2089 |
|
|
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
| 2090 |
|
|
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
| 2091 |
|
|
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
| 2092 |
|
|
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
| 2093 |
|
|
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
| 2094 |
|
|
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
| 2095 |
|
|
antlr/CommonASTWithHiddenTokens.cpp, |
| 2096 |
|
|
antlr/CommonASTWithHiddenTokens.hpp, |
| 2097 |
|
|
antlr/CommonHiddenStreamToken.cpp, |
| 2098 |
|
|
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
| 2099 |
|
|
antlr/CommonToken.hpp, antlr/IOException.hpp, |
| 2100 |
|
|
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
| 2101 |
|
|
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
| 2102 |
|
|
antlr/Makefile, antlr/MismatchedCharException.cpp, |
| 2103 |
|
|
antlr/MismatchedCharException.hpp, |
| 2104 |
|
|
antlr/MismatchedTokenException.cpp, |
| 2105 |
|
|
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
| 2106 |
|
|
antlr/NoViableAltException.hpp, |
| 2107 |
|
|
antlr/NoViableAltForCharException.cpp, |
| 2108 |
|
|
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
| 2109 |
|
|
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
| 2110 |
|
|
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
| 2111 |
|
|
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
| 2112 |
|
|
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
| 2113 |
|
|
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
| 2114 |
|
|
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
| 2115 |
|
|
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
| 2116 |
|
|
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
| 2117 |
|
|
antlr/TokenStreamHiddenTokenFilter.cpp, |
| 2118 |
|
|
antlr/TokenStreamHiddenTokenFilter.hpp, |
| 2119 |
|
|
antlr/TokenStreamIOException.hpp, |
| 2120 |
|
|
antlr/TokenStreamRecognitionException.hpp, |
| 2121 |
|
|
antlr/TokenStreamRetryException.hpp, |
| 2122 |
|
|
antlr/TokenStreamRewriteEngine.cpp, |
| 2123 |
|
|
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
| 2124 |
|
|
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
| 2125 |
|
|
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
| 2126 |
|
|
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
| 2127 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
| 2128 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 2129 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 2130 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 2131 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
| 2132 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
| 2133 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
| 2134 |
|
|
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
| 2135 |
|
|
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
| 2136 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
| 2137 |
|
|
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
| 2138 |
|
|
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
| 2139 |
|
|
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
| 2140 |
|
|
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
| 2141 |
|
|
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
| 2142 |
|
|
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
| 2143 |
|
|
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
| 2144 |
|
|
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
| 2145 |
|
|
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
| 2146 |
|
|
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
| 2147 |
|
|
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 2148 |
|
|
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 2149 |
|
|
selection/Makefile, selection/NameFinder.cpp, |
| 2150 |
|
|
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
| 2151 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 2152 |
|
|
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
| 2153 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
| 2154 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
| 2155 |
|
|
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
| 2156 |
|
|
types/Component.cpp, types/Component.hpp, |
| 2157 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 2158 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
| 2159 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 2160 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 2161 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 2162 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
| 2163 |
|
|
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
| 2164 |
|
|
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
| 2165 |
|
|
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
| 2166 |
|
|
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
| 2167 |
|
|
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
| 2168 |
|
|
with antlr parser |
| 2169 |
|
|
|
| 2170 |
|
|
2005-11-30 16:00 chuckv |
| 2171 |
|
|
|
| 2172 |
|
|
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
| 2173 |
|
|
calculate rho(Z) to calculate density profiles for water slabs. |
| 2174 |
|
|
|
| 2175 |
|
|
2005-11-29 17:54 chuckv |
| 2176 |
|
|
|
| 2177 |
|
|
* configure, ac-tools/configure.in: added checks for some functions |
| 2178 |
|
|
to configure script |
| 2179 |
|
|
|
| 2180 |
|
|
2005-11-22 20:05 chuckv |
| 2181 |
|
|
|
| 2182 |
|
|
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
| 2183 |
|
|
obbond.cpp: Changed file names that conflict w/ oopse file name |
| 2184 |
|
|
object files. |
| 2185 |
|
|
|
| 2186 |
|
|
2005-11-21 17:59 gezelter |
| 2187 |
|
|
|
| 2188 |
|
|
* src/utils/residentMem.c: compilation bug |
| 2189 |
|
|
|
| 2190 |
|
|
2005-11-21 17:59 gezelter |
| 2191 |
|
|
|
| 2192 |
|
|
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
| 2193 |
|
|
|
| 2194 |
|
|
2005-11-21 17:59 gezelter |
| 2195 |
|
|
|
| 2196 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
| 2197 |
|
|
|
| 2198 |
|
|
2005-11-21 17:59 gezelter |
| 2199 |
|
|
|
| 2200 |
|
|
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
| 2201 |
|
|
issue |
| 2202 |
|
|
|
| 2203 |
|
|
2005-11-21 17:58 gezelter |
| 2204 |
|
|
|
| 2205 |
|
|
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
| 2206 |
|
|
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
| 2207 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
| 2208 |
|
|
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
| 2209 |
|
|
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
| 2210 |
|
|
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
| 2211 |
|
|
|
| 2212 |
|
|
2005-11-21 11:22 tim |
| 2213 |
|
|
|
| 2214 |
|
|
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
| 2215 |
|
|
|
| 2216 |
|
|
2005-11-21 09:59 tim |
| 2217 |
|
|
|
| 2218 |
|
|
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
| 2219 |
|
|
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
| 2220 |
|
|
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
| 2221 |
|
|
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
| 2222 |
|
|
|
| 2223 |
|
|
2005-11-18 15:17 tim |
| 2224 |
|
|
|
| 2225 |
|
|
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
| 2226 |
|
|
adding support for soft linking |
| 2227 |
|
|
|
| 2228 |
|
|
2005-11-18 15:17 tim |
| 2229 |
|
|
|
| 2230 |
|
|
* make/Makefile.in: Adding support for soft linking |
| 2231 |
|
|
|
| 2232 |
|
|
2005-11-18 12:50 gezelter |
| 2233 |
|
|
|
| 2234 |
|
|
* make/Makefile.in: Adding linking stuff |
| 2235 |
|
|
|
| 2236 |
|
|
2005-11-18 11:38 tim |
| 2237 |
|
|
|
| 2238 |
|
|
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
| 2239 |
|
|
src/applications/atom2mdin/atom2mdin.cpp, |
| 2240 |
chrisfen |
2762 |
src/applications/mdinConverter/Makefile, |
| 2241 |
|
|
src/applications/mdinConverter/mdinConverter.cpp, |
| 2242 |
gezelter |
2568 |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
| 2243 |
|
|
rename mdinConverter to atom2mdin |
| 2244 |
|
|
|
| 2245 |
|
|
2005-11-17 15:44 gezelter |
| 2246 |
|
|
|
| 2247 |
|
|
* src/openbabel/obconversion.cpp: fixed a bug |
| 2248 |
|
|
|
| 2249 |
|
|
2005-11-17 15:39 gezelter |
| 2250 |
|
|
|
| 2251 |
|
|
* configure: Adding some config checks for OpenBabel codes we are |
| 2252 |
|
|
using |
| 2253 |
|
|
|
| 2254 |
|
|
2005-11-17 15:39 gezelter |
| 2255 |
|
|
|
| 2256 |
|
|
* ac-tools/configure.in: Adding some checks for OpenBabel code |
| 2257 |
|
|
|
| 2258 |
|
|
2005-11-17 15:39 gezelter |
| 2259 |
|
|
|
| 2260 |
|
|
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
| 2261 |
|
|
|
| 2262 |
|
|
2005-11-17 15:38 gezelter |
| 2263 |
|
|
|
| 2264 |
|
|
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
| 2265 |
|
|
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
| 2266 |
|
|
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
| 2267 |
|
|
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
| 2268 |
|
|
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
| 2269 |
|
|
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
| 2270 |
|
|
Unifying config.h stuff and making sure the OpenBabel codes can |
| 2271 |
|
|
find our default (and environment variable) Force Field |
| 2272 |
|
|
directories. |
| 2273 |
|
|
|
| 2274 |
|
|
2005-11-17 13:35 tim |
| 2275 |
|
|
|
| 2276 |
|
|
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
| 2277 |
|
|
|
| 2278 |
|
|
2005-11-16 18:10 tim |
| 2279 |
|
|
|
| 2280 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 2281 |
|
|
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
| 2282 |
|
|
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
| 2283 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 2284 |
|
|
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
| 2285 |
|
|
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
| 2286 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 2287 |
|
|
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
| 2288 |
|
|
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
| 2289 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
| 2290 |
|
|
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
| 2291 |
|
|
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
| 2292 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
| 2293 |
|
|
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
| 2294 |
|
|
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
| 2295 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
| 2296 |
|
|
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
| 2297 |
|
|
get compiled |
| 2298 |
|
|
|
| 2299 |
|
|
2005-11-16 16:37 chuckv |
| 2300 |
|
|
|
| 2301 |
|
|
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
| 2302 |
|
|
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
| 2303 |
|
|
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
| 2304 |
|
|
optional parameters.... |
| 2305 |
|
|
|
| 2306 |
chrisfen |
2762 |
2005-11-16 16:24 tim |
| 2307 |
|
|
|
| 2308 |
|
|
* src/applications/mdinConverter/: Makefile, mdinConverter.cpp: |
| 2309 |
|
|
adding mdinConverter |
| 2310 |
|
|
|
| 2311 |
gezelter |
2568 |
2005-11-16 16:22 tim |
| 2312 |
|
|
|
| 2313 |
|
|
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
| 2314 |
|
|
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
| 2315 |
|
|
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
| 2316 |
|
|
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
| 2317 |
|
|
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
| 2318 |
|
|
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
| 2319 |
|
|
adding more readers/writers |
| 2320 |
|
|
|
| 2321 |
|
|
2005-11-16 16:20 tim |
| 2322 |
|
|
|
| 2323 |
|
|
* make/Makefile.in: adding openbabel |
| 2324 |
|
|
|
| 2325 |
|
|
2005-11-16 16:20 tim |
| 2326 |
|
|
|
| 2327 |
|
|
* src/brains/: Register.cpp, Register.hpp: register openbabel |
| 2328 |
|
|
readers/writers |
| 2329 |
|
|
|
| 2330 |
|
|
2005-11-16 14:57 chrisfen |
| 2331 |
|
|
|
| 2332 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
| 2333 |
|
|
potential self term |
| 2334 |
|
|
|
| 2335 |
|
|
2005-11-16 14:57 chrisfen |
| 2336 |
|
|
|
| 2337 |
|
|
* samples/water/spce/spce.md: just some parameters |
| 2338 |
|
|
|
| 2339 |
|
|
2005-11-16 14:42 tim |
| 2340 |
|
|
|
| 2341 |
|
|
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
| 2342 |
|
|
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
| 2343 |
|
|
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
| 2344 |
|
|
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
| 2345 |
|
|
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
| 2346 |
|
|
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
| 2347 |
|
|
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
| 2348 |
|
|
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
| 2349 |
|
|
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
| 2350 |
|
|
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
| 2351 |
|
|
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
| 2352 |
|
|
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
| 2353 |
|
|
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
| 2354 |
|
|
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
| 2355 |
|
|
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
| 2356 |
|
|
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
| 2357 |
|
|
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
| 2358 |
|
|
zipstreamimpl.hpp: adding openbabel |
| 2359 |
|
|
|
| 2360 |
|
|
2005-11-15 14:42 chrisfen |
| 2361 |
|
|
|
| 2362 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
| 2363 |
|
|
commented code |
| 2364 |
|
|
|
| 2365 |
|
|
2005-11-15 14:04 chrisfen |
| 2366 |
|
|
|
| 2367 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
| 2368 |
|
|
charge-charge interactions a bit... |
| 2369 |
|
|
|
| 2370 |
|
|
2005-11-15 14:03 chrisfen |
| 2371 |
|
|
|
| 2372 |
|
|
* samples/water/spce/: spce.md, water.md: just playing |
| 2373 |
|
|
|
| 2374 |
|
|
2005-11-15 11:38 chrisfen |
| 2375 |
|
|
|
| 2376 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
| 2377 |
|
|
shifted_potential case |
| 2378 |
|
|
|
| 2379 |
|
|
2005-11-15 11:37 chrisfen |
| 2380 |
|
|
|
| 2381 |
|
|
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
| 2382 |
|
|
just playing around - we need to refresh all the samples sometime |
| 2383 |
|
|
soon... |
| 2384 |
|
|
|
| 2385 |
|
|
2005-11-15 11:18 chuckv |
| 2386 |
|
|
|
| 2387 |
|
|
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
| 2388 |
|
|
preforce calc public in suttonchen. |
| 2389 |
|
|
|
| 2390 |
|
|
2005-11-15 11:05 chuckv |
| 2391 |
|
|
|
| 2392 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
| 2393 |
|
|
SimInfo |
| 2394 |
|
|
|
| 2395 |
|
|
2005-11-15 11:01 chuckv |
| 2396 |
|
|
|
| 2397 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
| 2398 |
|
|
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
| 2399 |
|
|
|
| 2400 |
|
|
2005-11-15 10:34 chuckv |
| 2401 |
|
|
|
| 2402 |
|
|
* forceFields/Makefile: Added sutton-chen to makefile. |
| 2403 |
|
|
|
| 2404 |
|
|
2005-11-14 17:20 chuckv |
| 2405 |
|
|
|
| 2406 |
|
|
* src/UseTheForce/DarkSide/: suttonchen.F90, |
| 2407 |
|
|
suttonchen_interface.h: Build Fixes for sutton-chen. |
| 2408 |
|
|
|
| 2409 |
|
|
2005-11-14 17:03 chuckv |
| 2410 |
|
|
|
| 2411 |
|
|
* src/io/Makefile: Missed makefile for sutton-chen. |
| 2412 |
|
|
|
| 2413 |
|
|
2005-11-14 17:03 chuckv |
| 2414 |
|
|
|
| 2415 |
|
|
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
| 2416 |
|
|
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
| 2417 |
|
|
|
| 2418 |
|
|
2005-11-14 16:29 chuckv |
| 2419 |
|
|
|
| 2420 |
|
|
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
| 2421 |
|
|
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
| 2422 |
|
|
UseTheForce/DarkSide/suttonchen.F90, |
| 2423 |
|
|
UseTheForce/DarkSide/suttonchen_interface.F90, |
| 2424 |
|
|
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
| 2425 |
|
|
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
| 2426 |
|
|
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
| 2427 |
|
|
fix do_forces to use Sutton-Chen. |
| 2428 |
|
|
|
| 2429 |
|
|
2005-11-11 12:21 chrisfen |
| 2430 |
|
|
|
| 2431 |
|
|
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
| 2432 |
|
|
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
| 2433 |
|
|
some files |
| 2434 |
|
|
|
| 2435 |
|
|
2005-11-11 10:22 chrisfen |
| 2436 |
|
|
|
| 2437 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
| 2438 |
|
|
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
| 2439 |
|
|
switching function option |
| 2440 |
|
|
|
| 2441 |
|
|
2005-11-11 10:21 chrisfen |
| 2442 |
|
|
|
| 2443 |
|
|
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
| 2444 |
|
|
5th order polynomial switching function |
| 2445 |
|
|
|
| 2446 |
|
|
2005-11-11 10:21 chrisfen |
| 2447 |
|
|
|
| 2448 |
|
|
* samples/water/ssd/ssd.md: playing with switching functions again |
| 2449 |
|
|
|
| 2450 |
|
|
2005-11-11 10:21 chrisfen |
| 2451 |
|
|
|
| 2452 |
|
|
* samples/argon/500.md: playing with switching functions |
| 2453 |
|
|
|
| 2454 |
|
|
2005-11-08 19:11 chuckv |
| 2455 |
|
|
|
| 2456 |
|
|
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
| 2457 |
|
|
files for Sutton-Chen and Quantum Sutton-Chen |
| 2458 |
|
|
|
| 2459 |
|
|
2005-11-08 08:32 chrisfen |
| 2460 |
|
|
|
| 2461 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
| 2462 |
|
|
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
| 2463 |
|
|
ability to output forces and torques |
| 2464 |
|
|
|
| 2465 |
|
|
2005-11-08 08:32 chrisfen |
| 2466 |
|
|
|
| 2467 |
|
|
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
| 2468 |
|
|
output of forces and torques |
| 2469 |
|
|
|
| 2470 |
|
|
2005-11-08 08:31 chrisfen |
| 2471 |
|
|
|
| 2472 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
| 2473 |
|
|
Working on shifted_force... |
| 2474 |
|
|
|
| 2475 |
|
|
2005-11-08 08:31 chrisfen |
| 2476 |
|
|
|
| 2477 |
|
|
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
| 2478 |
|
|
|
| 2479 |
|
|
2005-11-03 18:22 chrisfen |
| 2480 |
|
|
|
| 2481 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
| 2482 |
|
|
commented section |
| 2483 |
|
|
|
| 2484 |
|
|
2005-11-03 18:12 chrisfen |
| 2485 |
|
|
|
| 2486 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 2487 |
|
|
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
| 2488 |
|
|
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
| 2489 |
|
|
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
| 2490 |
|
|
|
| 2491 |
|
|
2005-11-03 18:11 chrisfen |
| 2492 |
|
|
|
| 2493 |
|
|
* samples/water/spce/spce.md: mmm... damped shifted force... |
| 2494 |
|
|
|
| 2495 |
|
|
2005-11-03 18:06 chuckv |
| 2496 |
|
|
|
| 2497 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
| 2498 |
|
|
|
| 2499 |
|
|
2005-11-02 18:50 chuckv |
| 2500 |
|
|
|
| 2501 |
|
|
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
| 2502 |
|
|
|
| 2503 |
|
|
2005-11-02 16:01 chrisfen |
| 2504 |
|
|
|
| 2505 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 2506 |
|
|
removed some test code |
| 2507 |
|
|
|
| 2508 |
|
|
2005-11-02 15:45 chrisfen |
| 2509 |
|
|
|
| 2510 |
|
|
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
| 2511 |
|
|
screening method header |
| 2512 |
|
|
|
| 2513 |
|
|
2005-11-02 15:36 chrisfen |
| 2514 |
|
|
|
| 2515 |
|
|
* src/brains/SimInfo.cpp: again, changing how we deal with |
| 2516 |
|
|
summation and screening methods |
| 2517 |
|
|
|
| 2518 |
|
|
2005-11-02 15:36 chrisfen |
| 2519 |
|
|
|
| 2520 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 2521 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 2522 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
| 2523 |
|
|
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
| 2524 |
|
|
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
| 2525 |
|
|
and screening methods |
| 2526 |
|
|
|
| 2527 |
|
|
2005-11-02 15:35 chrisfen |
| 2528 |
|
|
|
| 2529 |
|
|
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
| 2530 |
|
|
|
| 2531 |
|
|
2005-11-01 18:32 chuckv |
| 2532 |
|
|
|
| 2533 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
| 2534 |
|
|
UseTheForce/DarkSide/atype_interface.F90, |
| 2535 |
|
|
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
| 2536 |
|
|
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
| 2537 |
|
|
sutton-chen |
| 2538 |
|
|
|
| 2539 |
|
|
2005-11-01 14:24 chrisfen |
| 2540 |
|
|
|
| 2541 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 2542 |
|
|
removed some testing code... |
| 2543 |
|
|
|
| 2544 |
|
|
2005-11-01 14:14 chrisfen |
| 2545 |
|
|
|
| 2546 |
|
|
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
| 2547 |
|
|
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
| 2548 |
|
|
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
| 2549 |
|
|
initialization |
| 2550 |
|
|
|
| 2551 |
|
|
2005-11-01 14:13 chrisfen |
| 2552 |
|
|
|
| 2553 |
|
|
* src/applications/oopse/oopse.cpp: nothing |
| 2554 |
|
|
|
| 2555 |
|
|
2005-11-01 14:09 chrisfen |
| 2556 |
|
|
|
| 2557 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 2558 |
|
|
DarkSide/simulation.F90: still fixing up wolf... |
| 2559 |
|
|
|
| 2560 |
|
|
2005-11-01 13:29 chuckv |
| 2561 |
|
|
|
| 2562 |
|
|
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
| 2563 |
|
|
process of adding sutton-chen forcefield. |
| 2564 |
|
|
|
| 2565 |
chrisfen |
2762 |
2005-10-26 19:32 chrisfen |
| 2566 |
gezelter |
2568 |
|
| 2567 |
|
|
* src/brains/SimInfo.cpp: changed the default switching radius to |
| 2568 |
|
|
85% of rcut |
| 2569 |
|
|
|
| 2570 |
chrisfen |
2762 |
2005-10-26 19:31 chrisfen |
| 2571 |
gezelter |
2568 |
|
| 2572 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
| 2573 |
|
|
to be working now - for charges and dipoles alike |
| 2574 |
|
|
|
| 2575 |
chrisfen |
2762 |
2005-10-26 19:31 chrisfen |
| 2576 |
gezelter |
2568 |
|
| 2577 |
|
|
* src/UseTheForce/doForces.F90: reaction field looks to be working |
| 2578 |
|
|
now |
| 2579 |
|
|
|
| 2580 |
chrisfen |
2762 |
2005-10-26 19:30 chrisfen |
| 2581 |
gezelter |
2568 |
|
| 2582 |
|
|
* samples/water/ssdrf/water.md: added a test molecule |
| 2583 |
|
|
|
| 2584 |
chrisfen |
2762 |
2005-10-26 19:30 chrisfen |
| 2585 |
gezelter |
2568 |
|
| 2586 |
|
|
* forceFields/DUFF2.frc: added a test atom type |
| 2587 |
|
|
|
| 2588 |
chrisfen |
2762 |
2005-10-24 10:06 chrisfen |
| 2589 |
gezelter |
2568 |
|
| 2590 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
| 2591 |
|
|
reaction field - don't know if it works... |
| 2592 |
|
|
|
| 2593 |
chrisfen |
2762 |
2005-10-23 17:08 chrisfen |
| 2594 |
gezelter |
2568 |
|
| 2595 |
|
|
* src/: UseTheForce/doForces.F90, |
| 2596 |
|
|
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
| 2597 |
|
|
streamlined reaction field for dipoles (now a good bit faster) and |
| 2598 |
|
|
added reaction field for charges - still need to do charge-dipole |
| 2599 |
|
|
RF |
| 2600 |
|
|
|
| 2601 |
chrisfen |
2762 |
2005-10-23 17:07 chrisfen |
| 2602 |
gezelter |
2568 |
|
| 2603 |
|
|
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
| 2604 |
|
|
field |
| 2605 |
|
|
|
| 2606 |
chrisfen |
2762 |
2005-10-23 17:06 chrisfen |
| 2607 |
gezelter |
2568 |
|
| 2608 |
|
|
* samples/water/spce/spce.md: reaction field now works for charges |
| 2609 |
|
|
|
| 2610 |
chrisfen |
2762 |
2005-10-20 16:27 tim |
| 2611 |
gezelter |
2568 |
|
| 2612 |
|
|
* src/primitives/Torsion.cpp: Fix the other branch of force |
| 2613 |
|
|
calculation in Torision.cpp |
| 2614 |
|
|
|
| 2615 |
chrisfen |
2762 |
2005-10-19 15:24 chrisfen |
| 2616 |
gezelter |
2568 |
|
| 2617 |
|
|
* src/: UseTheForce/doForces.F90, |
| 2618 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 2619 |
|
|
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
| 2620 |
|
|
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
| 2621 |
|
|
toUpper problems - these changes should fix those... |
| 2622 |
|
|
|
| 2623 |
chrisfen |
2762 |
2005-10-19 15:23 chrisfen |
| 2624 |
gezelter |
2568 |
|
| 2625 |
|
|
* samples/water/ssdrf/ssdrf.md: nothing |
| 2626 |
|
|
|
| 2627 |
chrisfen |
2762 |
2005-10-19 13:03 gezelter |
| 2628 |
gezelter |
2568 |
|
| 2629 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
| 2630 |
|
|
GayBerne |
| 2631 |
|
|
|
| 2632 |
chrisfen |
2762 |
2005-10-19 12:49 tim |
| 2633 |
gezelter |
2568 |
|
| 2634 |
|
|
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
| 2635 |
|
|
brains/ForceManager.cpp: fix an index mismathcing between c and |
| 2636 |
|
|
fortran |
| 2637 |
|
|
|
| 2638 |
chrisfen |
2762 |
2005-10-18 19:03 gezelter |
| 2639 |
gezelter |
2568 |
|
| 2640 |
|
|
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
| 2641 |
|
|
samples for the cutoff methods that Yang Zheng has been working on |
| 2642 |
|
|
|
| 2643 |
chrisfen |
2762 |
2005-10-18 17:13 gezelter |
| 2644 |
gezelter |
2568 |
|
| 2645 |
|
|
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
| 2646 |
|
|
and a rotation matrix bug |
| 2647 |
|
|
|
| 2648 |
chrisfen |
2762 |
2005-10-18 17:13 gezelter |
| 2649 |
gezelter |
2568 |
|
| 2650 |
|
|
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
| 2651 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
| 2652 |
|
|
added a few GB test cases |
| 2653 |
|
|
|
| 2654 |
chrisfen |
2762 |
2005-10-18 17:13 gezelter |
| 2655 |
gezelter |
2568 |
|
| 2656 |
|
|
* forceFields/DUFF2.frc: Fixing GB parameters |
| 2657 |
|
|
|
| 2658 |
chrisfen |
2762 |
2005-10-18 14:36 kdaily |
| 2659 |
gezelter |
2568 |
|
| 2660 |
|
|
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
| 2661 |
|
|
type |
| 2662 |
|
|
|
| 2663 |
chrisfen |
2762 |
2005-10-18 11:01 chrisfen |
| 2664 |
gezelter |
2568 |
|
| 2665 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
| 2666 |
|
|
UseTheForce/DarkSide/Makefile, |
| 2667 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 2668 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 2669 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
| 2670 |
|
|
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
| 2671 |
|
|
reaction field with electrostatics.F90 |
| 2672 |
|
|
|
| 2673 |
chrisfen |
2762 |
2005-10-17 19:13 tim |
| 2674 |
gezelter |
2568 |
|
| 2675 |
|
|
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
| 2676 |
|
|
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
| 2677 |
|
|
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
| 2678 |
|
|
io/StatWriter.hpp: Customized StatWriter is working |
| 2679 |
|
|
|
| 2680 |
chrisfen |
2762 |
2005-10-17 18:42 kdaily |
| 2681 |
gezelter |
2568 |
|
| 2682 |
|
|
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
| 2683 |
|
|
paper |
| 2684 |
|
|
|
| 2685 |
chrisfen |
2762 |
2005-10-17 17:47 gezelter |
| 2686 |
gezelter |
2568 |
|
| 2687 |
|
|
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
| 2688 |
|
|
|
| 2689 |
chrisfen |
2762 |
2005-10-17 15:24 tim |
| 2690 |
gezelter |
2568 |
|
| 2691 |
|
|
* src/io/ParamConstraint.hpp: Another bug fix |
| 2692 |
|
|
|
| 2693 |
chrisfen |
2762 |
2005-10-17 15:22 tim |
| 2694 |
gezelter |
2568 |
|
| 2695 |
|
|
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
| 2696 |
|
|
issues in Globals |
| 2697 |
|
|
|
| 2698 |
chrisfen |
2762 |
2005-10-17 15:12 gezelter |
| 2699 |
gezelter |
2568 |
|
| 2700 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
| 2701 |
|
|
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
| 2702 |
|
|
UseTheForce/DarkSide/gb_interface.F90, |
| 2703 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
| 2704 |
|
|
io/GayBerneAtomTypesSectionParser.cpp, |
| 2705 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
| 2706 |
|
|
changing GB architecture |
| 2707 |
|
|
|
| 2708 |
chrisfen |
2762 |
2005-10-17 15:12 gezelter |
| 2709 |
gezelter |
2568 |
|
| 2710 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
| 2711 |
|
|
gbRotRoundZ.in: Adding samples for gb tests |
| 2712 |
|
|
|
| 2713 |
chrisfen |
2762 |
2005-10-16 23:06 tim |
| 2714 |
gezelter |
2568 |
|
| 2715 |
|
|
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
| 2716 |
|
|
a string to event's err_msg, there are still tons of memory |
| 2717 |
|
|
leaking problem in Globals |
| 2718 |
|
|
|
| 2719 |
chrisfen |
2762 |
2005-10-16 20:51 tim |
| 2720 |
gezelter |
2568 |
|
| 2721 |
|
|
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
| 2722 |
|
|
error message in Globals |
| 2723 |
|
|
|
| 2724 |
chrisfen |
2762 |
2005-10-14 17:43 tim |
| 2725 |
gezelter |
2568 |
|
| 2726 |
|
|
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
| 2727 |
|
|
parameters are working now |
| 2728 |
|
|
|
| 2729 |
chrisfen |
2762 |
2005-10-14 12:43 gezelter |
| 2730 |
gezelter |
2568 |
|
| 2731 |
|
|
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
| 2732 |
|
|
|
| 2733 |
chrisfen |
2762 |
2005-10-14 12:05 gezelter |
| 2734 |
gezelter |
2568 |
|
| 2735 |
|
|
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
| 2736 |
|
|
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
| 2737 |
|
|
Adding some Gay Berne tests |
| 2738 |
|
|
|
| 2739 |
chrisfen |
2762 |
2005-10-14 12:05 gezelter |
| 2740 |
gezelter |
2568 |
|
| 2741 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
| 2742 |
|
|
cutoff tests |
| 2743 |
|
|
|
| 2744 |
chrisfen |
2762 |
2005-10-14 11:44 kdaily |
| 2745 |
gezelter |
2568 |
|
| 2746 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
| 2747 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
| 2748 |
|
|
src/UseTheForce/DarkSide/gb_interface.F90, |
| 2749 |
|
|
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
| 2750 |
|
|
LJ |
| 2751 |
|
|
|
| 2752 |
chrisfen |
2762 |
2005-10-14 10:48 tim |
| 2753 |
gezelter |
2568 |
|
| 2754 |
|
|
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
| 2755 |
|
|
|
| 2756 |
chrisfen |
2762 |
2005-10-14 10:18 chrisfen |
| 2757 |
gezelter |
2568 |
|
| 2758 |
|
|
* samples/thermoIntegration/liquid/ssde.md, |
| 2759 |
|
|
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
| 2760 |
|
|
src/restraints/Restraints.cpp: added default restraint spring |
| 2761 |
|
|
constants into Globals |
| 2762 |
|
|
|
| 2763 |
chrisfen |
2762 |
2005-10-13 18:26 tim |
| 2764 |
gezelter |
2568 |
|
| 2765 |
|
|
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
| 2766 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
| 2767 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 2768 |
|
|
integrators/Integrator.cpp, integrators/NPT.cpp, |
| 2769 |
|
|
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
| 2770 |
|
|
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
| 2771 |
|
|
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
| 2772 |
|
|
restraints/ThermoIntegrationForceManager.cpp, |
| 2773 |
|
|
visitors/ZconsVisitor.cpp: rewrite Globals |
| 2774 |
|
|
|
| 2775 |
chrisfen |
2762 |
2005-10-12 17:57 chuckv |
| 2776 |
gezelter |
2568 |
|
| 2777 |
|
|
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
| 2778 |
|
|
potential array to fortran. |
| 2779 |
|
|
|
| 2780 |
chrisfen |
2762 |
2005-10-12 17:00 gezelter |
| 2781 |
gezelter |
2568 |
|
| 2782 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
| 2783 |
|
|
remember what we did |
| 2784 |
|
|
|
| 2785 |
chrisfen |
2762 |
2005-10-12 17:00 gezelter |
| 2786 |
gezelter |
2568 |
|
| 2787 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
| 2788 |
|
|
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
| 2789 |
|
|
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
| 2790 |
|
|
DarkSide/sticky.F90: simplifying long range potential array |
| 2791 |
|
|
|
| 2792 |
chrisfen |
2762 |
2005-10-12 17:00 gezelter |
| 2793 |
gezelter |
2568 |
|
| 2794 |
|
|
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
| 2795 |
|
|
cutoff methods |
| 2796 |
|
|
|
| 2797 |
chrisfen |
2762 |
2005-10-12 17:00 gezelter |
| 2798 |
gezelter |
2568 |
|
| 2799 |
|
|
* forceFields/DUFF2.frc: Messing with 2-point water models |
| 2800 |
|
|
|
| 2801 |
chrisfen |
2762 |
2005-10-12 16:22 chuckv |
| 2802 |
gezelter |
2568 |
|
| 2803 |
|
|
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
| 2804 |
|
|
interface now expects an array for pot. |
| 2805 |
|
|
|
| 2806 |
chrisfen |
2762 |
2005-10-12 16:18 chuckv |
| 2807 |
gezelter |
2568 |
|
| 2808 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
| 2809 |
|
|
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
| 2810 |
|
|
calculation of potential. |
| 2811 |
|
|
|
| 2812 |
chrisfen |
2762 |
2005-10-12 15:55 chuckv |
| 2813 |
gezelter |
2568 |
|
| 2814 |
|
|
* src/UseTheForce/doForces.F90: More changes to MPI potential |
| 2815 |
|
|
calculations. |
| 2816 |
|
|
|
| 2817 |
chrisfen |
2762 |
2005-10-12 14:59 chuckv |
| 2818 |
gezelter |
2568 |
|
| 2819 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
| 2820 |
|
|
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
| 2821 |
|
|
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
| 2822 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
| 2823 |
|
|
Breaky: Add Support for seperating potential contributions. |
| 2824 |
|
|
|
| 2825 |
chrisfen |
2762 |
2005-10-11 18:00 chuckv |
| 2826 |
gezelter |
2568 |
|
| 2827 |
|
|
* src/UseTheForce/doForces.F90: Free some variables that weren't |
| 2828 |
|
|
freed before. |
| 2829 |
|
|
|
| 2830 |
chrisfen |
2762 |
2005-10-11 17:59 chuckv |
| 2831 |
gezelter |
2568 |
|
| 2832 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 2833 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
| 2834 |
|
|
builder --twinned. |
| 2835 |
|
|
|
| 2836 |
chrisfen |
2762 |
2005-10-11 17:57 chuckv |
| 2837 |
gezelter |
2568 |
|
| 2838 |
|
|
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
| 2839 |
|
|
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
| 2840 |
|
|
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
| 2841 |
|
|
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
| 2842 |
|
|
cvs. |
| 2843 |
|
|
|
| 2844 |
chrisfen |
2762 |
2005-10-10 17:34 chuckv |
| 2845 |
gezelter |
2568 |
|
| 2846 |
|
|
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
| 2847 |
|
|
in MPI. |
| 2848 |
|
|
|
| 2849 |
chrisfen |
2762 |
2005-10-10 17:20 chuckv |
| 2850 |
gezelter |
2568 |
|
| 2851 |
|
|
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
| 2852 |
|
|
indexing of groupToGtype. We now have two seperate maps |
| 2853 |
|
|
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
| 2854 |
|
|
that is set to groupToGtypeRow in the single processor version. |
| 2855 |
|
|
|
| 2856 |
chrisfen |
2762 |
2005-10-06 14:44 chrisfen |
| 2857 |
gezelter |
2568 |
|
| 2858 |
|
|
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
| 2859 |
|
|
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
| 2860 |
|
|
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
| 2861 |
|
|
|
| 2862 |
chrisfen |
2762 |
2005-10-05 17:12 tim |
| 2863 |
gezelter |
2568 |
|
| 2864 |
|
|
* src/primitives/RigidBody.cpp: There is still something wrong with |
| 2865 |
|
|
inertia tensor projection |
| 2866 |
|
|
|
| 2867 |
chrisfen |
2762 |
2005-10-05 15:35 tim |
| 2868 |
gezelter |
2568 |
|
| 2869 |
|
|
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
| 2870 |
|
|
There is still something wrong with current implementation. |
| 2871 |
|
|
|
| 2872 |
chrisfen |
2762 |
2005-10-05 15:34 tim |
| 2873 |
gezelter |
2568 |
|
| 2874 |
|
|
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
| 2875 |
|
|
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
| 2876 |
|
|
between group and center of mass array |
| 2877 |
|
|
|
| 2878 |
chrisfen |
2762 |
2005-10-05 15:12 tim |
| 2879 |
gezelter |
2568 |
|
| 2880 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
| 2881 |
|
|
When cutoffGroup is turned off, there is a mismatch between group |
| 2882 |
|
|
and center of mass array |
| 2883 |
|
|
|
| 2884 |
chrisfen |
2762 |
2005-10-04 15:34 chrisfen |
| 2885 |
gezelter |
2568 |
|
| 2886 |
|
|
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
| 2887 |
|
|
mass ratio bug that results in simulation failure with massless |
| 2888 |
|
|
particles |
| 2889 |
|
|
|
| 2890 |
chrisfen |
2762 |
2005-10-04 15:33 chrisfen |
| 2891 |
gezelter |
2568 |
|
| 2892 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
| 2893 |
|
|
wolf |
| 2894 |
|
|
|
| 2895 |
chrisfen |
2762 |
2005-10-04 15:32 chrisfen |
| 2896 |
gezelter |
2568 |
|
| 2897 |
|
|
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
| 2898 |
|
|
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
| 2899 |
|
|
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
| 2900 |
|
|
random changes when testing |
| 2901 |
|
|
|
| 2902 |
chrisfen |
2762 |
2005-10-03 11:54 tim |
| 2903 |
gezelter |
2568 |
|
| 2904 |
|
|
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
| 2905 |
|
|
projecting the inertia tensor of directional atom in rigibody into |
| 2906 |
|
|
rigidbody's body frame (previous commit is wrong) |
| 2907 |
|
|
|
| 2908 |
chrisfen |
2762 |
2005-10-03 10:31 tim |
| 2909 |
gezelter |
2568 |
|
| 2910 |
|
|
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
| 2911 |
|
|
tensor of directional atom in rigibody into rigidbody's body frame |
| 2912 |
|
|
|
| 2913 |
chrisfen |
2762 |
2005-09-28 14:47 chrisfen |
| 2914 |
gezelter |
2568 |
|
| 2915 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
| 2916 |
|
|
|
| 2917 |
chrisfen |
2762 |
2005-09-28 14:46 chrisfen |
| 2918 |
gezelter |
2568 |
|
| 2919 |
|
|
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
| 2920 |
|
|
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
| 2921 |
|
|
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
| 2922 |
|
|
tip4p/tp4.md: fixed some samples |
| 2923 |
|
|
|
| 2924 |
chrisfen |
2762 |
2005-09-28 14:46 chrisfen |
| 2925 |
gezelter |
2568 |
|
| 2926 |
|
|
* ChangeLog: updated |
| 2927 |
|
|
|
| 2928 |
chrisfen |
2762 |
2005-09-28 12:55 tim |
| 2929 |
chrisfen |
2337 |
|
| 2930 |
|
|
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
| 2931 |
|
|
divergence in rotation matrix to quaternion transformation |
| 2932 |
|
|
|
| 2933 |
chrisfen |
2762 |
2005-09-28 12:32 gezelter |
| 2934 |
chrisfen |
2337 |
|
| 2935 |
|
|
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
| 2936 |
|
|
order error |
| 2937 |
|
|
|
| 2938 |
chrisfen |
2762 |
2005-09-28 12:32 gezelter |
| 2939 |
chrisfen |
2337 |
|
| 2940 |
|
|
* src/io/DumpReader.cpp: tracking down quaternion bug |
| 2941 |
|
|
|
| 2942 |
chrisfen |
2762 |
2005-09-28 12:32 gezelter |
| 2943 |
chrisfen |
2337 |
|
| 2944 |
|
|
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
| 2945 |
|
|
model |
| 2946 |
|
|
|
| 2947 |
chrisfen |
2762 |
2005-09-27 16:02 tim |
| 2948 |
chrisfen |
2337 |
|
| 2949 |
|
|
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
| 2950 |
|
|
to quaternion |
| 2951 |
|
|
|
| 2952 |
chrisfen |
2762 |
2005-09-26 14:38 chuckv |
| 2953 |
chrisfen |
2337 |
|
| 2954 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
| 2955 |
|
|
7 so derfc is external. Other compilers should treat erfc as |
| 2956 |
|
|
intrinsic. |
| 2957 |
|
|
|
| 2958 |
chrisfen |
2762 |
2005-09-26 13:07 chuckv |
| 2959 |
chrisfen |
2337 |
|
| 2960 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
| 2961 |
|
|
and declared it to be external to fix issure with ifc7. Hopefully |
| 2962 |
|
|
this will not cause a problem with other compilers where derfc is |
| 2963 |
|
|
an intrinsic function. |
| 2964 |
|
|
|
| 2965 |
chrisfen |
2762 |
2005-09-26 12:42 chuckv |
| 2966 |
chrisfen |
2337 |
|
| 2967 |
|
|
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
| 2968 |
|
|
in simulation module. We needed a seperate receive buffer. |
| 2969 |
|
|
|
| 2970 |
chrisfen |
2762 |
2005-09-26 11:58 chuckv |
| 2971 |
chrisfen |
2337 |
|
| 2972 |
|
|
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
| 2973 |
|
|
support for skinThickness keyword to Globals. |
| 2974 |
|
|
|
| 2975 |
chrisfen |
2762 |
2005-09-26 11:56 tim |
| 2976 |
chrisfen |
2337 |
|
| 2977 |
|
|
* src/io/DumpReader.cpp: fix a typo in DumpReader |
| 2978 |
|
|
|
| 2979 |
chrisfen |
2762 |
2005-09-26 10:27 chrisfen |
| 2980 |
chrisfen |
2337 |
|
| 2981 |
|
|
* samples/: minimizer/tip4p_two.md, |
| 2982 |
|
|
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
| 2983 |
|
|
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
| 2984 |
|
|
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
| 2985 |
|
|
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
| 2986 |
|
|
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
| 2987 |
|
|
water/tip4p/tp4.md: fixing up some samples |
| 2988 |
|
|
|
| 2989 |
chrisfen |
2762 |
2005-09-24 13:39 chrisfen |
| 2990 |
chrisfen |
2337 |
|
| 2991 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
| 2992 |
|
|
roughly the same speed as the old version when using dipoles |
| 2993 |
|
|
|
| 2994 |
|
|
energies are now exactly the same between the old version of OOPSE |
| 2995 |
|
|
and this version |
| 2996 |
|
|
|
| 2997 |
chrisfen |
2762 |
2005-09-24 13:38 chrisfen |
| 2998 |
chrisfen |
2337 |
|
| 2999 |
|
|
* samples/water/ssdrf/ssdrf.md: turned rf on |
| 3000 |
|
|
|
| 3001 |
chrisfen |
2762 |
2005-09-23 16:31 chuckv |
| 3002 |
chrisfen |
2337 |
|
| 3003 |
|
|
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
| 3004 |
|
|
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
| 3005 |
|
|
from skin. This will get fixed to where we can manually set skin |
| 3006 |
|
|
thickness. |
| 3007 |
|
|
|
| 3008 |
chrisfen |
2762 |
2005-09-22 14:50 gezelter |
| 3009 |
chrisfen |
2337 |
|
| 3010 |
|
|
* src/math/derfc.F90: added error function |
| 3011 |
|
|
|
| 3012 |
chrisfen |
2762 |
2005-09-21 20:08 chuckv |
| 3013 |
chrisfen |
2337 |
|
| 3014 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statement for |
| 3015 |
|
|
angular momentum and inertia tensor from velocitizer. |
| 3016 |
|
|
|
| 3017 |
chrisfen |
2762 |
2005-09-21 20:04 chuckv |
| 3018 |
chrisfen |
2337 |
|
| 3019 |
|
|
* src/integrators/Velocitizer.cpp: Removed print statements for |
| 3020 |
|
|
remove angular momentum. |
| 3021 |
|
|
|
| 3022 |
chrisfen |
2762 |
2005-09-21 19:45 chuckv |
| 3023 |
chrisfen |
2337 |
|
| 3024 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
| 3025 |
|
|
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
| 3026 |
|
|
map. |
| 3027 |
|
|
|
| 3028 |
chrisfen |
2762 |
2005-09-21 16:59 tim |
| 3029 |
chrisfen |
2337 |
|
| 3030 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
| 3031 |
|
|
DumpReader using pure c++ io |
| 3032 |
|
|
|
| 3033 |
chrisfen |
2762 |
2005-09-21 13:20 chrisfen |
| 3034 |
chrisfen |
2337 |
|
| 3035 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
| 3036 |
|
|
defaultCutoff bug (HEMES!) |
| 3037 |
|
|
|
| 3038 |
chrisfen |
2762 |
2005-09-20 18:13 gezelter |
| 3039 |
chrisfen |
2337 |
|
| 3040 |
|
|
* make/Makefile.in: libz additions |
| 3041 |
|
|
|
| 3042 |
chrisfen |
2762 |
2005-09-20 18:03 gezelter |
| 3043 |
chrisfen |
2337 |
|
| 3044 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 3045 |
|
|
src/config.h.in: added check for zlib in configure |
| 3046 |
|
|
|
| 3047 |
chrisfen |
2762 |
2005-09-20 17:22 tim |
| 3048 |
chrisfen |
2337 |
|
| 3049 |
|
|
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
| 3050 |
|
|
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
| 3051 |
|
|
|
| 3052 |
chrisfen |
2762 |
2005-09-20 12:22 tim |
| 3053 |
chrisfen |
2337 |
|
| 3054 |
|
|
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
| 3055 |
|
|
testcase for zipstream |
| 3056 |
|
|
|
| 3057 |
chrisfen |
2762 |
2005-09-20 11:41 tim |
| 3058 |
chrisfen |
2337 |
|
| 3059 |
|
|
* src/io/zipstream.hpp: adding zipstream.hpp |
| 3060 |
|
|
|
| 3061 |
chrisfen |
2762 |
2005-09-20 11:34 chrisfen |
| 3062 |
chrisfen |
2337 |
|
| 3063 |
|
|
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
| 3064 |
|
|
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
| 3065 |
|
|
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
| 3066 |
|
|
zcons/zconsMoving.md: fixed up some sample md files |
| 3067 |
|
|
|
| 3068 |
chrisfen |
2762 |
2005-09-19 19:21 chrisfen |
| 3069 |
chrisfen |
2337 |
|
| 3070 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
| 3071 |
|
|
src/UseTheForce/doForces.F90, |
| 3072 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 3073 |
|
|
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
| 3074 |
|
|
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
| 3075 |
|
|
appears as though it really is working... |
| 3076 |
|
|
|
| 3077 |
chrisfen |
2762 |
2005-09-18 16:45 chrisfen |
| 3078 |
chrisfen |
2310 |
|
| 3079 |
|
|
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
| 3080 |
|
|
src/UseTheForce/doForces.F90, |
| 3081 |
|
|
src/UseTheForce/doForces_interface.F90, |
| 3082 |
|
|
src/UseTheForce/doForces_interface.h, |
| 3083 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 3084 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 3085 |
|
|
src/brains/SimInfo.cpp: reaction field seems to work now, still |
| 3086 |
|
|
need to do some testing... |
| 3087 |
|
|
|
| 3088 |
chrisfen |
2762 |
2005-09-16 19:04 chuckv |
| 3089 |
chrisfen |
2309 |
|
| 3090 |
|
|
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
| 3091 |
|
|
dump files. |
| 3092 |
|
|
|
| 3093 |
chrisfen |
2762 |
2005-09-16 17:07 chrisfen |
| 3094 |
chrisfen |
2309 |
|
| 3095 |
|
|
* src/: UseTheForce/doForces_interface.F90, |
| 3096 |
|
|
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
| 3097 |
|
|
bug that ifc missed... |
| 3098 |
|
|
|
| 3099 |
chrisfen |
2762 |
2005-09-16 16:36 chrisfen |
| 3100 |
chrisfen |
2309 |
|
| 3101 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 3102 |
|
|
fixing some summation method issues |
| 3103 |
|
|
|
| 3104 |
chrisfen |
2762 |
2005-09-16 15:35 chrisfen |
| 3105 |
chrisfen |
2309 |
|
| 3106 |
|
|
* src/brains/SimInfo.cpp: fixed a capitalization error |
| 3107 |
|
|
|
| 3108 |
chrisfen |
2762 |
2005-09-16 15:34 chrisfen |
| 3109 |
chrisfen |
2309 |
|
| 3110 |
|
|
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
| 3111 |
|
|
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
| 3112 |
|
|
around |
| 3113 |
|
|
|
| 3114 |
chrisfen |
2762 |
2005-09-16 15:00 chrisfen |
| 3115 |
chrisfen |
2309 |
|
| 3116 |
|
|
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
| 3117 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
| 3118 |
|
|
are known issues - particularly with reaction field... |
| 3119 |
|
|
|
| 3120 |
chrisfen |
2762 |
2005-09-16 12:07 chrisfen |
| 3121 |
chrisfen |
2309 |
|
| 3122 |
|
|
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
| 3123 |
|
|
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
| 3124 |
|
|
(cutting out the old way to do reaction field) |
| 3125 |
|
|
|
| 3126 |
chrisfen |
2762 |
2005-09-15 18:05 gezelter |
| 3127 |
chrisfen |
2309 |
|
| 3128 |
|
|
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
| 3129 |
|
|
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
| 3130 |
|
|
DarkSide/electrostatic_interface.F90, |
| 3131 |
|
|
DarkSide/electrostatic_interface.h: Working on adding WOLF |
| 3132 |
|
|
|
| 3133 |
chrisfen |
2762 |
2005-09-15 15:17 tim |
| 3134 |
chrisfen |
2309 |
|
| 3135 |
|
|
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
| 3136 |
|
|
is called without calling getNFrames |
| 3137 |
|
|
|
| 3138 |
chrisfen |
2762 |
2005-09-15 09:47 chrisfen |
| 3139 |
chrisfen |
2309 |
|
| 3140 |
|
|
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
| 3141 |
|
|
|
| 3142 |
chrisfen |
2762 |
2005-09-14 22:48 chuckv |
| 3143 |
chrisfen |
2309 |
|
| 3144 |
|
|
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
| 3145 |
|
|
not initialized after creation. When maxval(gtypeMaxCutoff) was |
| 3146 |
|
|
called, the largest random garbage value was returned from the |
| 3147 |
|
|
array. |
| 3148 |
|
|
|
| 3149 |
chrisfen |
2762 |
2005-09-14 20:14 chrisfen |
| 3150 |
chrisfen |
2309 |
|
| 3151 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
| 3152 |
|
|
io/Globals.hpp: changes to include the coulombicCorrection selector |
| 3153 |
|
|
|
| 3154 |
chrisfen |
2762 |
2005-09-14 20:13 chrisfen |
| 3155 |
chrisfen |
2309 |
|
| 3156 |
|
|
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
| 3157 |
|
|
reactionField.F90: added in the undamped wolf, in the process of |
| 3158 |
|
|
doing the damped wolf |
| 3159 |
|
|
|
| 3160 |
chrisfen |
2762 |
2005-09-14 20:13 chrisfen |
| 3161 |
chrisfen |
2309 |
|
| 3162 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
| 3163 |
|
|
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
| 3164 |
|
|
the coulombicCorrection selector |
| 3165 |
|
|
|
| 3166 |
chrisfen |
2762 |
2005-09-14 20:11 chrisfen |
| 3167 |
chrisfen |
2309 |
|
| 3168 |
|
|
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
| 3169 |
|
|
|
| 3170 |
chrisfen |
2762 |
2005-09-14 20:11 chrisfen |
| 3171 |
chrisfen |
2309 |
|
| 3172 |
|
|
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
| 3173 |
|
|
|
| 3174 |
chrisfen |
2762 |
2005-09-14 20:10 chrisfen |
| 3175 |
chrisfen |
2309 |
|
| 3176 |
|
|
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
| 3177 |
|
|
|
| 3178 |
chrisfen |
2762 |
2005-09-14 16:31 chuckv |
| 3179 |
chrisfen |
2309 |
|
| 3180 |
|
|
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
| 3181 |
|
|
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
| 3182 |
|
|
|
| 3183 |
chrisfen |
2762 |
2005-09-14 16:28 gezelter |
| 3184 |
chrisfen |
2309 |
|
| 3185 |
|
|
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
| 3186 |
|
|
do_prepair |
| 3187 |
|
|
|
| 3188 |
chrisfen |
2762 |
2005-09-14 15:02 gezelter |
| 3189 |
chrisfen |
2309 |
|
| 3190 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
| 3191 |
|
|
createMixingMap routine. It should now set doShift correctly |
| 3192 |
|
|
|
| 3193 |
chrisfen |
2762 |
2005-09-07 18:44 chuckv |
| 3194 |
chrisfen |
2309 |
|
| 3195 |
|
|
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
| 3196 |
|
|
|
| 3197 |
chrisfen |
2762 |
2005-09-07 18:23 chuckv |
| 3198 |
chrisfen |
2309 |
|
| 3199 |
|
|
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
| 3200 |
|
|
logical variables |
| 3201 |
|
|
|
| 3202 |
chrisfen |
2762 |
2005-09-07 18:08 gezelter |
| 3203 |
chrisfen |
2309 |
|
| 3204 |
|
|
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
| 3205 |
|
|
algorithm |
| 3206 |
|
|
|
| 3207 |
chrisfen |
2762 |
2005-09-07 16:46 gezelter |
| 3208 |
chrisfen |
2309 |
|
| 3209 |
|
|
* src/: UseTheForce/doForces.F90, |
| 3210 |
|
|
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
| 3211 |
|
|
UseTheForce/notifyCutoffs_interface.F90, |
| 3212 |
|
|
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
| 3213 |
|
|
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
| 3214 |
|
|
cutoff Policy |
| 3215 |
|
|
|
| 3216 |
chrisfen |
2762 |
2005-09-07 15:18 gezelter |
| 3217 |
chrisfen |
2309 |
|
| 3218 |
|
|
* src/UseTheForce/doForces.F90: Some bug hunting |
| 3219 |
|
|
|
| 3220 |
chrisfen |
2762 |
2005-09-07 15:18 gezelter |
| 3221 |
chrisfen |
2309 |
|
| 3222 |
|
|
* samples/argon/argonNVT.md: Just a longer test |
| 3223 |
|
|
|
| 3224 |
chrisfen |
2762 |
2005-09-06 13:32 chuckv |
| 3225 |
chrisfen |
2309 |
|
| 3226 |
|
|
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
| 3227 |
|
|
etc.. |
| 3228 |
|
|
|
| 3229 |
chrisfen |
2762 |
2005-09-01 18:56 gezelter |
| 3230 |
chrisfen |
2309 |
|
| 3231 |
|
|
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
| 3232 |
|
|
zero |
| 3233 |
|
|
|
| 3234 |
chrisfen |
2762 |
2005-09-01 16:17 gezelter |
| 3235 |
chrisfen |
2309 |
|
| 3236 |
|
|
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
| 3237 |
|
|
createGtypeCutoffMap |
| 3238 |
|
|
|
| 3239 |
chrisfen |
2762 |
2005-08-30 14:23 chrisfen |
| 3240 |
chrisfen |
2309 |
|
| 3241 |
|
|
* src/: UseTheForce/doForces.F90, |
| 3242 |
|
|
UseTheForce/doForces_interface.F90, |
| 3243 |
|
|
UseTheForce/doForces_interface.h, |
| 3244 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 3245 |
|
|
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
| 3246 |
|
|
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
| 3247 |
|
|
changes for implementing the wolf potential |
| 3248 |
|
|
|
| 3249 |
chrisfen |
2762 |
2005-08-26 18:39 chrisfen |
| 3250 |
chrisfen |
2309 |
|
| 3251 |
|
|
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
| 3252 |
|
|
|
| 3253 |
chrisfen |
2762 |
2005-08-26 17:30 chrisfen |
| 3254 |
chrisfen |
2309 |
|
| 3255 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
| 3256 |
|
|
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
| 3257 |
|
|
some probably nonfunctional get*cut routines |
| 3258 |
|
|
|
| 3259 |
chrisfen |
2762 |
2005-08-26 16:34 chuckv |
| 3260 |
chrisfen |
2309 |
|
| 3261 |
|
|
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
| 3262 |
|
|
|
| 3263 |
chrisfen |
2762 |
2005-08-26 12:36 gezelter |
| 3264 |
chrisfen |
2309 |
|
| 3265 |
|
|
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
| 3266 |
|
|
interactionHash and gtypeCutoff routines |
| 3267 |
|
|
|
| 3268 |
chrisfen |
2762 |
2005-08-17 11:26 gezelter |
| 3269 |
chrisfen |
2309 |
|
| 3270 |
|
|
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
| 3271 |
|
|
DarkSide/simulation.F90: added fCutoffPolicy.h |
| 3272 |
|
|
|
| 3273 |
chrisfen |
2762 |
2005-08-11 17:04 gezelter |
| 3274 |
chrisfen |
2309 |
|
| 3275 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
| 3276 |
|
|
progress |
| 3277 |
|
|
|
| 3278 |
chrisfen |
2762 |
2005-08-10 15:17 gezelter |
| 3279 |
chrisfen |
2309 |
|
| 3280 |
|
|
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
| 3281 |
|
|
they belong |
| 3282 |
|
|
|
| 3283 |
chrisfen |
2762 |
2005-08-09 18:33 gezelter |
| 3284 |
chrisfen |
2309 |
|
| 3285 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
| 3286 |
|
|
Jones module |
| 3287 |
|
|
|
| 3288 |
chrisfen |
2762 |
2005-08-09 18:33 gezelter |
| 3289 |
chrisfen |
2309 |
|
| 3290 |
|
|
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
| 3291 |
|
|
|
| 3292 |
chrisfen |
2762 |
2005-08-09 15:40 chuckv |
| 3293 |
chrisfen |
2309 |
|
| 3294 |
|
|
* src/UseTheForce/doForces.F90: In process of re-write for group |
| 3295 |
|
|
based cutoff.... |
| 3296 |
|
|
|
| 3297 |
chrisfen |
2762 |
2005-07-29 15:38 gezelter |
| 3298 |
chrisfen |
2309 |
|
| 3299 |
|
|
* src/UseTheForce/doForces.F90: fixes in progress |
| 3300 |
|
|
|
| 3301 |
chrisfen |
2762 |
2005-07-29 13:34 tim |
| 3302 |
chrisfen |
2309 |
|
| 3303 |
|
|
* src/UseTheForce/doForces.F90: fix a bug which does not update |
| 3304 |
|
|
me_i and me_j correctly |
| 3305 |
|
|
|
| 3306 |
chrisfen |
2762 |
2005-07-28 18:12 chuckv |
| 3307 |
chrisfen |
2309 |
|
| 3308 |
|
|
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
| 3309 |
|
|
cutoffs... Segfaults nicely now... |
| 3310 |
|
|
|
| 3311 |
chrisfen |
2762 |
2005-07-20 13:04 gezelter |
| 3312 |
chrisfen |
2309 |
|
| 3313 |
|
|
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
| 3314 |
|
|
error messages from pathscale compiler |
| 3315 |
|
|
|
| 3316 |
chrisfen |
2762 |
2005-07-13 12:48 tim |
| 3317 |
chrisfen |
2309 |
|
| 3318 |
|
|
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
| 3319 |
|
|
<functional> |
| 3320 |
|
|
|
| 3321 |
chrisfen |
2762 |
2005-07-13 11:54 tim |
| 3322 |
chrisfen |
2309 |
|
| 3323 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
| 3324 |
|
|
UseTheForce/mpiComponentPlan.h, |
| 3325 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
| 3326 |
|
|
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
| 3327 |
|
|
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
| 3328 |
|
|
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
| 3329 |
|
|
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
| 3330 |
|
|
utils/simError.c, utils/simError.h: replace c++ style comment in c |
| 3331 |
|
|
files |
| 3332 |
|
|
|
| 3333 |
chrisfen |
2762 |
2005-07-03 16:53 chuckv |
| 3334 |
chrisfen |
2309 |
|
| 3335 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
| 3336 |
|
|
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
| 3337 |
|
|
subroutine to set cuttoff for Interaction map and function in |
| 3338 |
|
|
simulation.F90 to determine if a particular atype is present in a |
| 3339 |
|
|
simulation. |
| 3340 |
|
|
|
| 3341 |
chrisfen |
2762 |
2005-06-28 09:58 gezelter |
| 3342 |
chrisfen |
2309 |
|
| 3343 |
|
|
* src/UseTheForce/doForces.F90: [no log message] |
| 3344 |
|
|
|
| 3345 |
chrisfen |
2762 |
2005-06-27 18:21 chuckv |
| 3346 |
chrisfen |
2309 |
|
| 3347 |
|
|
* src/UseTheForce/doForces.F90: More breaking and destruction of |
| 3348 |
|
|
force code. Does not build at this point... |
| 3349 |
|
|
|
| 3350 |
chrisfen |
2762 |
2005-06-27 17:01 gezelter |
| 3351 |
chrisfen |
2309 |
|
| 3352 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
| 3353 |
|
|
UseTheForce/DarkSide/fInteractionMap.h, |
| 3354 |
|
|
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
| 3355 |
|
|
Breaky breaky! |
| 3356 |
|
|
|
| 3357 |
chrisfen |
2762 |
2005-06-20 12:03 gezelter |
| 3358 |
chrisfen |
2309 |
|
| 3359 |
|
|
* samples/water/ssd/ssd.md, |
| 3360 |
|
|
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
| 3361 |
|
|
simulation |
| 3362 |
|
|
|
| 3363 |
chrisfen |
2762 |
2005-06-13 14:25 tim |
| 3364 |
chrisfen |
2309 |
|
| 3365 |
|
|
* src/: applications/staticProps/DensityPlot.cpp, |
| 3366 |
|
|
applications/staticProps/DensityPlot.hpp, |
| 3367 |
|
|
applications/staticProps/SCDOrderParameter.cpp, |
| 3368 |
|
|
applications/staticProps/StaticProps.cpp, |
| 3369 |
|
|
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
| 3370 |
|
|
|
| 3371 |
chrisfen |
2762 |
2005-05-31 18:31 chuckv |
| 3372 |
chrisfen |
2309 |
|
| 3373 |
|
|
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
| 3374 |
|
|
remove angular momentum. |
| 3375 |
|
|
|
| 3376 |
chrisfen |
2762 |
2005-05-31 13:34 chuckv |
| 3377 |
chrisfen |
2309 |
|
| 3378 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
| 3379 |
|
|
typo in nanorodBuilder. |
| 3380 |
|
|
|
| 3381 |
chrisfen |
2762 |
2005-05-30 10:01 chuckv |
| 3382 |
chrisfen |
2309 |
|
| 3383 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3384 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
| 3385 |
|
|
brains/Stats.hpp, integrators/Velocitizer.cpp, |
| 3386 |
|
|
integrators/Velocitizer.hpp: Added method to remove system angular |
| 3387 |
|
|
momentum to velocitizer and added method to calculate system |
| 3388 |
|
|
angular momentum to siminfo. |
| 3389 |
|
|
|
| 3390 |
chrisfen |
2762 |
2005-05-29 17:16 chrisfen |
| 3391 |
chrisfen |
2309 |
|
| 3392 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
| 3393 |
|
|
balance from the Darkside (files) |
| 3394 |
|
|
|
| 3395 |
chrisfen |
2762 |
2005-05-29 17:15 chrisfen |
| 3396 |
chrisfen |
2309 |
|
| 3397 |
|
|
* src/UseTheForce/doForces.F90: Removed balance from doForces |
| 3398 |
|
|
|
| 3399 |
chrisfen |
2762 |
2005-05-29 17:15 chrisfen |
| 3400 |
chrisfen |
2309 |
|
| 3401 |
|
|
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
| 3402 |
|
|
|
| 3403 |
chrisfen |
2762 |
2005-05-29 17:15 chrisfen |
| 3404 |
chrisfen |
2309 |
|
| 3405 |
|
|
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
| 3406 |
|
|
dimer for testing purposes |
| 3407 |
|
|
|
| 3408 |
chrisfen |
2762 |
2005-05-29 17:14 chrisfen |
| 3409 |
chrisfen |
2309 |
|
| 3410 |
|
|
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
| 3411 |
|
|
was apparently wiped earlier this month... |
| 3412 |
|
|
|
| 3413 |
chrisfen |
2762 |
2005-05-29 17:13 chrisfen |
| 3414 |
chrisfen |
2309 |
|
| 3415 |
|
|
* ChangeLog: ran make cvslog |
| 3416 |
|
|
|
| 3417 |
chrisfen |
2762 |
2005-05-28 20:16 tim |
| 3418 |
chrisfen |
2246 |
|
| 3419 |
|
|
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
| 3420 |
|
|
AtomNameVisitor |
| 3421 |
|
|
|
| 3422 |
chrisfen |
2762 |
2005-05-28 20:09 tim |
| 3423 |
chrisfen |
2246 |
|
| 3424 |
|
|
* src/integrators/Integrator.cpp: dding resetIntegrator |
| 3425 |
|
|
|
| 3426 |
chrisfen |
2762 |
2005-05-28 20:06 tim |
| 3427 |
chrisfen |
2246 |
|
| 3428 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
| 3429 |
|
|
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
| 3430 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
| 3431 |
|
|
resetIntegrator |
| 3432 |
|
|
|
| 3433 |
chrisfen |
2762 |
2005-05-27 17:11 tim |
| 3434 |
chrisfen |
2246 |
|
| 3435 |
|
|
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
| 3436 |
|
|
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
| 3437 |
|
|
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
| 3438 |
|
|
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
| 3439 |
|
|
StaticProps |
| 3440 |
|
|
|
| 3441 |
chrisfen |
2762 |
2005-05-27 00:41 tim |
| 3442 |
chrisfen |
2246 |
|
| 3443 |
|
|
* src/: applications/staticProps/Makefile, |
| 3444 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
| 3445 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
| 3446 |
|
|
applications/staticProps/StaticProps.cpp, |
| 3447 |
|
|
applications/staticProps/StaticProps.ggo, |
| 3448 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 3449 |
|
|
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
| 3450 |
|
|
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
| 3451 |
|
|
|
| 3452 |
chrisfen |
2762 |
2005-05-26 18:45 tim |
| 3453 |
chrisfen |
2246 |
|
| 3454 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 3455 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 3456 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
| 3457 |
|
|
applications/staticProps/Makefile, |
| 3458 |
|
|
applications/staticProps/P2OrderParameter.cpp, |
| 3459 |
|
|
applications/staticProps/P2OrderParameter.hpp, |
| 3460 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 3461 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
| 3462 |
|
|
applications/staticProps/StaticAnalyser.hpp, |
| 3463 |
|
|
applications/staticProps/StaticProps.cpp, |
| 3464 |
|
|
applications/staticProps/StaticProps.ggo, |
| 3465 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 3466 |
|
|
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
| 3467 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
| 3468 |
|
|
AtomNameVisitor to convert atom name to its base name; |
| 3469 |
|
|
wrappingvisitor now wrap back to the center of the mass; adding |
| 3470 |
|
|
P2OrderParameter into StaticProps |
| 3471 |
|
|
|
| 3472 |
chrisfen |
2762 |
2005-05-22 17:36 chuckv |
| 3473 |
chrisfen |
2246 |
|
| 3474 |
gezelter |
2568 |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
| 3475 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 3476 |
|
|
applications/nanoRodBuilder/GeometryFactory.cpp, |
| 3477 |
|
|
applications/nanoRodBuilder/GeometryFactory.hpp, |
| 3478 |
|
|
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3479 |
|
|
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
| 3480 |
chrisfen |
2246 |
tensor. |
| 3481 |
|
|
|
| 3482 |
chrisfen |
2762 |
2005-05-22 17:05 tim |
| 3483 |
chrisfen |
2246 |
|
| 3484 |
|
|
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 3485 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 3486 |
|
|
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
| 3487 |
|
|
printPressureTensor |
| 3488 |
|
|
|
| 3489 |
chrisfen |
2762 |
2005-05-20 15:27 tim |
| 3490 |
chrisfen |
2246 |
|
| 3491 |
|
|
* src/integrators/NPrT.cpp: NPrT in progress |
| 3492 |
|
|
|
| 3493 |
chrisfen |
2762 |
2005-05-20 12:01 tim |
| 3494 |
chrisfen |
2246 |
|
| 3495 |
|
|
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
| 3496 |
|
|
utils/OOPSEConstant.hpp: NPrT in progress |
| 3497 |
|
|
|
| 3498 |
chrisfen |
2762 |
2005-05-19 17:31 tim |
| 3499 |
chrisfen |
2246 |
|
| 3500 |
|
|
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
| 3501 |
|
|
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
| 3502 |
|
|
io/Globals.hpp: NPAT is working |
| 3503 |
|
|
|
| 3504 |
chrisfen |
2762 |
2005-05-19 11:49 tim |
| 3505 |
chrisfen |
2246 |
|
| 3506 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
| 3507 |
|
|
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
| 3508 |
|
|
|
| 3509 |
chrisfen |
2762 |
2005-05-19 00:28 tim |
| 3510 |
chrisfen |
2246 |
|
| 3511 |
|
|
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
| 3512 |
|
|
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
| 3513 |
|
|
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
| 3514 |
|
|
|
| 3515 |
chrisfen |
2762 |
2005-05-18 15:06 chrisfen |
| 3516 |
chrisfen |
2246 |
|
| 3517 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
| 3518 |
|
|
some tap changes |
| 3519 |
|
|
|
| 3520 |
chrisfen |
2762 |
2005-05-18 14:31 chrisfen |
| 3521 |
chrisfen |
2246 |
|
| 3522 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 3523 |
|
|
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
| 3524 |
|
|
in the first solvation shell for tap |
| 3525 |
|
|
|
| 3526 |
chrisfen |
2762 |
2005-05-18 08:35 chrisfen |
| 3527 |
chrisfen |
2246 |
|
| 3528 |
|
|
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
| 3529 |
|
|
for testing purposes |
| 3530 |
|
|
|
| 3531 |
chrisfen |
2762 |
2005-05-17 18:35 chrisfen |
| 3532 |
chrisfen |
2246 |
|
| 3533 |
|
|
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
| 3534 |
|
|
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
| 3535 |
|
|
src/UseTheForce/doForces.F90, |
| 3536 |
|
|
src/UseTheForce/DarkSide/electrostatic.F90, |
| 3537 |
|
|
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 3538 |
|
|
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
| 3539 |
|
|
correcting changes to the previous merge that were not caught |
| 3540 |
|
|
|
| 3541 |
chrisfen |
2762 |
2005-05-17 00:20 chuckv |
| 3542 |
chrisfen |
2229 |
|
| 3543 |
|
|
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
| 3544 |
|
|
Fixed merge issues between Kyle and Chris so OOPSE will actually |
| 3545 |
|
|
build. |
| 3546 |
|
|
|
| 3547 |
chrisfen |
2762 |
2005-05-16 23:46 kdaily |
| 3548 |
chrisfen |
2229 |
|
| 3549 |
|
|
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
| 3550 |
|
|
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
| 3551 |
|
|
|
| 3552 |
chrisfen |
2762 |
2005-05-16 22:08 kdaily |
| 3553 |
chrisfen |
2229 |
|
| 3554 |
|
|
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
| 3555 |
|
|
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
| 3556 |
|
|
src/types/DirectionalAtomType.cpp, |
| 3557 |
|
|
src/types/DirectionalAtomType.hpp: added gb |
| 3558 |
|
|
|
| 3559 |
chrisfen |
2762 |
2005-05-13 16:36 chrisfen |
| 3560 |
chrisfen |
2229 |
|
| 3561 |
|
|
* forceFields/DUFF2.frc: Better tap |
| 3562 |
|
|
|
| 3563 |
chrisfen |
2762 |
2005-05-12 15:43 chrisfen |
| 3564 |
chrisfen |
2229 |
|
| 3565 |
|
|
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
| 3566 |
|
|
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
| 3567 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 3568 |
|
|
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
| 3569 |
|
|
Need to parametrize. |
| 3570 |
|
|
|
| 3571 |
chrisfen |
2762 |
2005-05-11 19:15 chuckv |
| 3572 |
chrisfen |
2229 |
|
| 3573 |
|
|
* src/: io/ShapeAtomTypesSectionParser.cpp, |
| 3574 |
|
|
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
| 3575 |
|
|
build issues under ifc7. |
| 3576 |
|
|
|
| 3577 |
chrisfen |
2762 |
2005-05-09 18:07 chuckv |
| 3578 |
chrisfen |
2229 |
|
| 3579 |
|
|
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
| 3580 |
|
|
builder changes. |
| 3581 |
|
|
|
| 3582 |
chrisfen |
2762 |
2005-05-05 11:06 chrisfen |
| 3583 |
chrisfen |
2229 |
|
| 3584 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
| 3585 |
|
|
to TAP |
| 3586 |
|
|
|
| 3587 |
chrisfen |
2762 |
2005-05-05 10:47 chrisfen |
| 3588 |
chrisfen |
2229 |
|
| 3589 |
|
|
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
| 3590 |
|
|
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
| 3591 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
| 3592 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
| 3593 |
|
|
src/UseTheForce/DarkSide/atype_interface.F90, |
| 3594 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
| 3595 |
|
|
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
| 3596 |
|
|
src/brains/fSimulation.h, src/io/Makefile, |
| 3597 |
|
|
src/io/StickyAtomTypesSectionParser.cpp, |
| 3598 |
|
|
src/io/StickyPowerAtomTypesSectionParser.cpp, |
| 3599 |
|
|
src/io/StickyPowerAtomTypesSectionParser.hpp, |
| 3600 |
|
|
src/types/AtomType.cpp, src/types/AtomType.hpp, |
| 3601 |
|
|
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
| 3602 |
|
|
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
| 3603 |
|
|
not parametrized, but OOPSE will now let me run it... |
| 3604 |
|
|
|
| 3605 |
chrisfen |
2762 |
2005-05-03 18:55 chuckv |
| 3606 |
chrisfen |
2229 |
|
| 3607 |
|
|
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 3608 |
|
|
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
| 3609 |
|
|
Adding support for generic geometry to nanorodbuilder. |
| 3610 |
|
|
|
| 3611 |
chrisfen |
2762 |
2005-05-03 13:55 chuckv |
| 3612 |
chrisfen |
2229 |
|
| 3613 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 3614 |
|
|
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
| 3615 |
|
|
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
| 3616 |
|
|
|
| 3617 |
chrisfen |
2762 |
2005-04-29 15:16 gezelter |
| 3618 |
chrisfen |
2229 |
|
| 3619 |
|
|
* make/Makefile.in: [no log message] |
| 3620 |
|
|
|
| 3621 |
chrisfen |
2762 |
2005-04-29 12:26 chrisfen |
| 3622 |
chrisfen |
2229 |
|
| 3623 |
|
|
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
| 3624 |
|
|
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
| 3625 |
|
|
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
| 3626 |
|
|
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
| 3627 |
|
|
samples/water/tip4p/water.md: Added TIP4P-Ew |
| 3628 |
|
|
|
| 3629 |
chrisfen |
2762 |
2005-04-27 20:24 chuckv |
| 3630 |
chrisfen |
2229 |
|
| 3631 |
|
|
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 3632 |
|
|
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
| 3633 |
|
|
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
| 3634 |
|
|
nanoRodBuilder.... |
| 3635 |
|
|
|
| 3636 |
chrisfen |
2762 |
2005-04-27 16:13 chrisfen |
| 3637 |
chrisfen |
2229 |
|
| 3638 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
| 3639 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
| 3640 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
| 3641 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 3642 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
| 3643 |
|
|
write statements and am closer to a working shapes |
| 3644 |
|
|
|
| 3645 |
chrisfen |
2762 |
2005-04-22 17:57 chuckv |
| 3646 |
chrisfen |
2229 |
|
| 3647 |
|
|
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
| 3648 |
|
|
|
| 3649 |
chrisfen |
2762 |
2005-04-22 17:52 tim |
| 3650 |
chrisfen |
2229 |
|
| 3651 |
|
|
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
| 3652 |
|
|
Trim.hpp: adding CharClassificationFunctor to fix the locale |
| 3653 |
|
|
problem of c++ |
| 3654 |
|
|
|
| 3655 |
chrisfen |
2762 |
2005-04-21 10:12 chrisfen |
| 3656 |
chrisfen |
2229 |
|
| 3657 |
|
|
* samples/shape/Shapes.frc, samples/shape/linear.in, |
| 3658 |
|
|
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
| 3659 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
| 3660 |
|
|
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
| 3661 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
| 3662 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
| 3663 |
|
|
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 3664 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
| 3665 |
|
|
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
| 3666 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
| 3667 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 3668 |
|
|
src/io/ShapeAtomTypesSectionParser.cpp, |
| 3669 |
|
|
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
| 3670 |
|
|
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
| 3671 |
|
|
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
| 3672 |
|
|
bounds overwrite (I think...). At least the parser loads the |
| 3673 |
|
|
forcefield fine... |
| 3674 |
|
|
|
| 3675 |
chrisfen |
2762 |
2005-04-18 11:44 chrisfen |
| 3676 |
chrisfen |
2229 |
|
| 3677 |
|
|
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
| 3678 |
|
|
Mac (capitalization confusion of filenames) |
| 3679 |
|
|
|
| 3680 |
chrisfen |
2762 |
2005-04-17 23:50 chrisfen |
| 3681 |
chrisfen |
2229 |
|
| 3682 |
|
|
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
| 3683 |
|
|
UseTheForce/Shapes_FF.cpp, |
| 3684 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 3685 |
|
|
io/ShapeAtomTypesSectionParser.cpp, |
| 3686 |
|
|
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
| 3687 |
|
|
|
| 3688 |
chrisfen |
2762 |
2005-04-15 18:43 gezelter |
| 3689 |
chrisfen |
2229 |
|
| 3690 |
|
|
* README: gmake in case people forget |
| 3691 |
|
|
|
| 3692 |
chrisfen |
2762 |
2005-04-15 18:40 gezelter |
| 3693 |
chrisfen |
2229 |
|
| 3694 |
|
|
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
| 3695 |
|
|
banner. Vanity. |
| 3696 |
|
|
|
| 3697 |
chrisfen |
2762 |
2005-04-15 18:22 gezelter |
| 3698 |
chrisfen |
2229 |
|
| 3699 |
|
|
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
| 3700 |
|
|
in banner (and version numbers in config.h) |
| 3701 |
|
|
|
| 3702 |
chrisfen |
2762 |
2005-04-15 18:22 gezelter |
| 3703 |
chrisfen |
2229 |
|
| 3704 |
|
|
* ChangeLog, LICENSE, README: Documentation changes |
| 3705 |
|
|
|
| 3706 |
chrisfen |
2762 |
2005-04-15 18:03 gezelter |
| 3707 |
gezelter |
2205 |
|
| 3708 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3709 |
|
|
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
| 3710 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 3711 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
| 3712 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
| 3713 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 3714 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
| 3715 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
| 3716 |
|
|
UseTheForce/notifyCutoffs.F90, |
| 3717 |
|
|
UseTheForce/notifyCutoffs_interface.F90, |
| 3718 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 3719 |
|
|
UseTheForce/DarkSide/atype.F90, |
| 3720 |
|
|
UseTheForce/DarkSide/atype_interface.F90, |
| 3721 |
|
|
UseTheForce/DarkSide/eam.F90, |
| 3722 |
|
|
UseTheForce/DarkSide/eam_interface.F90, |
| 3723 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
| 3724 |
|
|
UseTheForce/DarkSide/electrostatic.F90, |
| 3725 |
|
|
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 3726 |
|
|
UseTheForce/DarkSide/electrostatic_interface.h, |
| 3727 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
| 3728 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 3729 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
| 3730 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
| 3731 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
| 3732 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
| 3733 |
|
|
UseTheForce/DarkSide/shapes.F90, |
| 3734 |
|
|
UseTheForce/DarkSide/shapes_interface.F90, |
| 3735 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
| 3736 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
| 3737 |
|
|
UseTheForce/DarkSide/simParallel_interface.F90, |
| 3738 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
| 3739 |
|
|
UseTheForce/DarkSide/simulation.F90, |
| 3740 |
|
|
UseTheForce/DarkSide/simulation_interface.F90, |
| 3741 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
| 3742 |
|
|
UseTheForce/DarkSide/sticky.F90, |
| 3743 |
|
|
UseTheForce/DarkSide/sticky_interface.F90, |
| 3744 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
| 3745 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
| 3746 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
| 3747 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 3748 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
| 3749 |
|
|
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
| 3750 |
|
|
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
| 3751 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 3752 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 3753 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
| 3754 |
|
|
applications/dynamicProps/DynamicPropsCmd.c, |
| 3755 |
|
|
applications/dynamicProps/DynamicPropsCmd.h, |
| 3756 |
|
|
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
| 3757 |
|
|
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
| 3758 |
|
|
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
| 3759 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
| 3760 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
| 3761 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
| 3762 |
|
|
applications/dynamicProps/TimeCorrFunc.hpp, |
| 3763 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
| 3764 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
| 3765 |
|
|
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 3766 |
|
|
applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 3767 |
|
|
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3768 |
|
|
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 3769 |
|
|
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
| 3770 |
|
|
applications/oopse/oopse.cpp, |
| 3771 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 3772 |
|
|
applications/simpleBuilder/simpleBuilderCmd.c, |
| 3773 |
|
|
applications/simpleBuilder/simpleBuilderCmd.h, |
| 3774 |
|
|
applications/staticProps/GofAngle2.cpp, |
| 3775 |
|
|
applications/staticProps/GofAngle2.hpp, |
| 3776 |
|
|
applications/staticProps/GofR.cpp, |
| 3777 |
|
|
applications/staticProps/GofR.hpp, |
| 3778 |
|
|
applications/staticProps/GofRAngle.cpp, |
| 3779 |
|
|
applications/staticProps/GofRAngle.hpp, |
| 3780 |
|
|
applications/staticProps/GofXyz.cpp, |
| 3781 |
|
|
applications/staticProps/GofXyz.hpp, |
| 3782 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 3783 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
| 3784 |
|
|
applications/staticProps/StaticProps.cpp, |
| 3785 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 3786 |
|
|
applications/staticProps/StaticPropsCmd.h, |
| 3787 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 3788 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 3789 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 3790 |
|
|
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
| 3791 |
|
|
brains/MoleculeCreator.hpp, brains/Register.cpp, |
| 3792 |
|
|
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 3793 |
|
|
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 3794 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
| 3795 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 3796 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 3797 |
|
|
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
| 3798 |
|
|
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
| 3799 |
|
|
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
| 3800 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 3801 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 3802 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 3803 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 3804 |
|
|
integrators/IntegratorFactory.cpp, |
| 3805 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 3806 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 3807 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 3808 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 3809 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
| 3810 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 3811 |
|
|
integrators/Velocitizer.hpp, |
| 3812 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 3813 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
| 3814 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 3815 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 3816 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 3817 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 3818 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 3819 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
| 3820 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 3821 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 3822 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 3823 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 3824 |
|
|
io/Globals.cpp, io/Globals.hpp, |
| 3825 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
| 3826 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 3827 |
|
|
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
| 3828 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
| 3829 |
|
|
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
| 3830 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
| 3831 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 3832 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
| 3833 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
| 3834 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
| 3835 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 3836 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 3837 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
| 3838 |
|
|
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
| 3839 |
|
|
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 3840 |
|
|
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
| 3841 |
|
|
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
| 3842 |
|
|
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 3843 |
|
|
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
| 3844 |
|
|
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
| 3845 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 3846 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 3847 |
|
|
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
| 3848 |
|
|
math/Quaternion.hpp, math/RandNumGen.hpp, |
| 3849 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 3850 |
|
|
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
| 3851 |
|
|
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
| 3852 |
|
|
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
| 3853 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
| 3854 |
|
|
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
| 3855 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 3856 |
|
|
minimizers/MinimizerFactory.hpp, |
| 3857 |
|
|
minimizers/MinimizerParameterSet.cpp, |
| 3858 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 3859 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 3860 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 3861 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 3862 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 3863 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 3864 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 3865 |
|
|
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
| 3866 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 3867 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 3868 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 3869 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 3870 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 3871 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 3872 |
|
|
profiling/timing.F90, restraints/Restraints.cpp, |
| 3873 |
|
|
restraints/Restraints.hpp, |
| 3874 |
|
|
restraints/ThermoIntegrationForceManager.cpp, |
| 3875 |
|
|
restraints/ThermoIntegrationForceManager.hpp, |
| 3876 |
|
|
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 3877 |
|
|
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 3878 |
|
|
selection/NameFinder.cpp, selection/NameFinder.hpp, |
| 3879 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
| 3880 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 3881 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 3882 |
|
|
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
| 3883 |
|
|
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 3884 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 3885 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 3886 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 3887 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 3888 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 3889 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 3890 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 3891 |
|
|
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
| 3892 |
|
|
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
| 3893 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 3894 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 3895 |
|
|
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
| 3896 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 3897 |
|
|
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
| 3898 |
|
|
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
| 3899 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 3900 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 3901 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 3902 |
|
|
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
| 3903 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
| 3904 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 3905 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 3906 |
|
|
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 3907 |
|
|
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
| 3908 |
|
|
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
| 3909 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 3910 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 3911 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 3912 |
|
|
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
| 3913 |
|
|
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
| 3914 |
|
|
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
| 3915 |
|
|
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
| 3916 |
|
|
utils/residentMem.h, utils/simError.c, utils/simError.h, |
| 3917 |
|
|
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
| 3918 |
|
|
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
| 3919 |
|
|
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
| 3920 |
|
|
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
| 3921 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 3922 |
|
|
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
| 3923 |
|
|
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
| 3924 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
| 3925 |
|
|
been drafted to perform our indentation services |
| 3926 |
|
|
|
| 3927 |
chrisfen |
2762 |
2005-04-15 18:03 gezelter |
| 3928 |
gezelter |
2205 |
|
| 3929 |
|
|
* configure, ac-tools/configure.in: Jedi mind-trick warning |
| 3930 |
|
|
messages have been added to make users ignore CGAL. |
| 3931 |
|
|
|
| 3932 |
chrisfen |
2762 |
2005-04-15 14:41 tim |
| 3933 |
gezelter |
2205 |
|
| 3934 |
|
|
* make/Makefile.in: fix make install |
| 3935 |
|
|
|
| 3936 |
chrisfen |
2762 |
2005-04-15 14:41 tim |
| 3937 |
gezelter |
2205 |
|
| 3938 |
|
|
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
| 3939 |
|
|
add Makefile of samples |
| 3940 |
|
|
|
| 3941 |
chrisfen |
2762 |
2005-04-15 14:33 tim |
| 3942 |
gezelter |
2205 |
|
| 3943 |
|
|
* samples/: lipid/Makefile, water/dimer/Makefile, |
| 3944 |
|
|
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
| 3945 |
|
|
installed correctly |
| 3946 |
|
|
|
| 3947 |
chrisfen |
2762 |
2005-04-14 17:41 gezelter |
| 3948 |
gezelter |
2205 |
|
| 3949 |
|
|
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 3950 |
|
|
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
| 3951 |
|
|
scripts/filepp, scripts/filepp.in: configure now searches for perl |
| 3952 |
|
|
to use with filepp |
| 3953 |
|
|
|
| 3954 |
chrisfen |
2762 |
2005-04-14 17:20 gezelter |
| 3955 |
tim |
2102 |
|
| 3956 |
gezelter |
2199 |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
| 3957 |
|
|
MoLocator |
| 3958 |
|
|
|
| 3959 |
chrisfen |
2762 |
2005-04-14 15:12 gezelter |
| 3960 |
gezelter |
2199 |
|
| 3961 |
|
|
* LICENSE: [no log message] |
| 3962 |
|
|
|
| 3963 |
chrisfen |
2762 |
2005-04-14 12:10 chuckv |
| 3964 |
gezelter |
2199 |
|
| 3965 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
| 3966 |
|
|
nanorodbuilder now exit's when libCGAL is not present. |
| 3967 |
|
|
|
| 3968 |
chrisfen |
2762 |
2005-04-14 11:20 tim |
| 3969 |
gezelter |
2199 |
|
| 3970 |
|
|
* src/io/make_nodes.h: fix one more warning message in make_nodes |
| 3971 |
|
|
|
| 3972 |
chrisfen |
2762 |
2005-04-13 19:36 chuckv |
| 3973 |
gezelter |
2199 |
|
| 3974 |
|
|
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
| 3975 |
|
|
interface name for SGI Compiler |
| 3976 |
|
|
|
| 3977 |
chrisfen |
2762 |
2005-04-13 19:29 chrisfen |
| 3978 |
gezelter |
2199 |
|
| 3979 |
|
|
* samples/water/ssde/ssde.md: oops... bad sample |
| 3980 |
|
|
|
| 3981 |
chrisfen |
2762 |
2005-04-13 19:00 chuckv |
| 3982 |
gezelter |
2199 |
|
| 3983 |
|
|
* src/config.h.in: Change typo in CGAL. |
| 3984 |
|
|
|
| 3985 |
chrisfen |
2762 |
2005-04-13 18:43 tim |
| 3986 |
gezelter |
2199 |
|
| 3987 |
|
|
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
| 3988 |
|
|
selection/SelectionCompiler.hpp: fix some warning messages |
| 3989 |
|
|
|
| 3990 |
chrisfen |
2762 |
2005-04-13 18:30 gezelter |
| 3991 |
gezelter |
2199 |
|
| 3992 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 3993 |
|
|
make/Makefile.in, src/config.h.in, |
| 3994 |
|
|
src/applications/nanoRodBuilder/Makefile, |
| 3995 |
|
|
src/applications/nanoRodBuilder/Makefile.in, |
| 3996 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
| 3997 |
|
|
checks |
| 3998 |
|
|
|
| 3999 |
chrisfen |
2762 |
2005-04-13 16:36 chuckv |
| 4000 |
gezelter |
2199 |
|
| 4001 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
| 4002 |
|
|
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
| 4003 |
|
|
DarkSide/electrostatic_interface.F90, |
| 4004 |
|
|
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
| 4005 |
|
|
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
| 4006 |
|
|
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
| 4007 |
|
|
destroy methods for Fortran modules. |
| 4008 |
|
|
|
| 4009 |
chrisfen |
2762 |
2005-04-13 16:17 chuckv |
| 4010 |
gezelter |
2199 |
|
| 4011 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
| 4012 |
|
|
shapes_interface.h: Added destroy method to clean up memory |
| 4013 |
|
|
|
| 4014 |
chrisfen |
2762 |
2005-04-13 14:41 tim |
| 4015 |
gezelter |
2199 |
|
| 4016 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 4017 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 4018 |
|
|
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
| 4019 |
|
|
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
| 4020 |
|
|
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
| 4021 |
|
|
fixed |
| 4022 |
|
|
|
| 4023 |
chrisfen |
2762 |
2005-04-12 18:44 chuckv |
| 4024 |
gezelter |
2199 |
|
| 4025 |
|
|
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
| 4026 |
|
|
for nanoRodBuilder. |
| 4027 |
|
|
|
| 4028 |
chrisfen |
2762 |
2005-04-12 18:42 tim |
| 4029 |
gezelter |
2199 |
|
| 4030 |
|
|
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
| 4031 |
|
|
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
| 4032 |
|
|
and simpleBuilder(forget to delete lattice) |
| 4033 |
|
|
|
| 4034 |
chrisfen |
2762 |
2005-04-12 18:33 tim |
| 4035 |
gezelter |
2199 |
|
| 4036 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 4037 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
| 4038 |
|
|
refactory lattice |
| 4039 |
|
|
|
| 4040 |
chrisfen |
2762 |
2005-04-12 18:07 tim |
| 4041 |
gezelter |
2199 |
|
| 4042 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
| 4043 |
|
|
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
| 4044 |
|
|
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
| 4045 |
|
|
LatticeFactory and LatticeCreator |
| 4046 |
|
|
|
| 4047 |
chrisfen |
2762 |
2005-04-12 17:58 tim |
| 4048 |
gezelter |
2199 |
|
| 4049 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 4050 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
| 4051 |
|
|
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 4052 |
|
|
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
| 4053 |
|
|
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
| 4054 |
|
|
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
| 4055 |
|
|
|
| 4056 |
chrisfen |
2762 |
2005-04-12 17:28 gezelter |
| 4057 |
gezelter |
2199 |
|
| 4058 |
|
|
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
| 4059 |
|
|
vector_class.F90: cleaned up vector_class memory leak fix by |
| 4060 |
|
|
deallocating in reverse order of how we allocated. Also migrated |
| 4061 |
|
|
MoLocator into utils directory |
| 4062 |
|
|
|
| 4063 |
chrisfen |
2762 |
2005-04-12 17:27 gezelter |
| 4064 |
gezelter |
2199 |
|
| 4065 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
| 4066 |
|
|
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 4067 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
| 4068 |
|
|
directory |
| 4069 |
|
|
|
| 4070 |
chrisfen |
2762 |
2005-04-12 17:27 gezelter |
| 4071 |
gezelter |
2199 |
|
| 4072 |
|
|
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
| 4073 |
|
|
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
| 4074 |
|
|
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
| 4075 |
|
|
nanoRodBuilder/LatticeCreator.hpp, |
| 4076 |
|
|
nanoRodBuilder/LatticeFactory.cpp, |
| 4077 |
|
|
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
| 4078 |
|
|
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
| 4079 |
|
|
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
| 4080 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 4081 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 4082 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 4083 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
| 4084 |
|
|
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
| 4085 |
|
|
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
| 4086 |
|
|
these files are now redundant |
| 4087 |
|
|
|
| 4088 |
chrisfen |
2762 |
2005-04-12 17:27 gezelter |
| 4089 |
gezelter |
2199 |
|
| 4090 |
|
|
* src/UseTheForce/DarkSide/: atype_interface.F90, |
| 4091 |
|
|
atype_interface.h: cleaned up memory leak fix |
| 4092 |
|
|
|
| 4093 |
chrisfen |
2762 |
2005-04-12 17:26 gezelter |
| 4094 |
gezelter |
2199 |
|
| 4095 |
|
|
* make/Makefile.in: added lattice subdirectory |
| 4096 |
|
|
|
| 4097 |
chrisfen |
2762 |
2005-04-12 16:57 chrisfen |
| 4098 |
gezelter |
2199 |
|
| 4099 |
|
|
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
| 4100 |
|
|
a space by accident |
| 4101 |
|
|
|
| 4102 |
chrisfen |
2762 |
2005-04-12 16:56 chrisfen |
| 4103 |
gezelter |
2199 |
|
| 4104 |
|
|
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
| 4105 |
|
|
quadrupole sample |
| 4106 |
|
|
|
| 4107 |
chrisfen |
2762 |
2005-04-12 16:56 chrisfen |
| 4108 |
gezelter |
2199 |
|
| 4109 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
| 4110 |
|
|
samples |
| 4111 |
|
|
|
| 4112 |
chrisfen |
2762 |
2005-04-12 14:30 tim |
| 4113 |
gezelter |
2199 |
|
| 4114 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
| 4115 |
|
|
type in fortran side |
| 4116 |
|
|
|
| 4117 |
chrisfen |
2762 |
2005-04-12 13:45 chuckv |
| 4118 |
gezelter |
2199 |
|
| 4119 |
|
|
* src/utils/vector_class.F90: Further changes to vector_class |
| 4120 |
|
|
destroy function. |
| 4121 |
|
|
|
| 4122 |
chrisfen |
2762 |
2005-04-12 13:39 chuckv |
| 4123 |
gezelter |
2199 |
|
| 4124 |
|
|
* src/utils/vector_class.F90: Fixed pointer memory leak in |
| 4125 |
|
|
vector_class. |
| 4126 |
|
|
|
| 4127 |
chrisfen |
2762 |
2005-04-12 13:12 chuckv |
| 4128 |
gezelter |
2199 |
|
| 4129 |
|
|
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
| 4130 |
|
|
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
| 4131 |
|
|
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
| 4132 |
|
|
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
| 4133 |
|
|
|
| 4134 |
chrisfen |
2762 |
2005-04-12 10:24 chrisfen |
| 4135 |
gezelter |
2199 |
|
| 4136 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
| 4137 |
|
|
output |
| 4138 |
|
|
|
| 4139 |
chrisfen |
2762 |
2005-04-11 20:29 chuckv |
| 4140 |
gezelter |
2199 |
|
| 4141 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
| 4142 |
|
|
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
| 4143 |
|
|
|
| 4144 |
chrisfen |
2762 |
2005-04-11 20:28 chuckv |
| 4145 |
gezelter |
2199 |
|
| 4146 |
|
|
* src/utils/vector_class.F90: Added code to delete vector. |
| 4147 |
|
|
|
| 4148 |
chrisfen |
2762 |
2005-04-11 17:58 tim |
| 4149 |
gezelter |
2199 |
|
| 4150 |
|
|
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
| 4151 |
|
|
basic_ifstrstream |
| 4152 |
|
|
|
| 4153 |
chrisfen |
2762 |
2005-04-11 17:37 chuckv |
| 4154 |
gezelter |
2199 |
|
| 4155 |
|
|
* make/Makefile.in, |
| 4156 |
|
|
src/applications/nanoRodBuilder/BaseLattice.cpp, |
| 4157 |
|
|
src/applications/nanoRodBuilder/BaseLattice.hpp, |
| 4158 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 4159 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 4160 |
|
|
src/applications/nanoRodBuilder/Lattice.cpp, |
| 4161 |
|
|
src/applications/nanoRodBuilder/Lattice.hpp, |
| 4162 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
| 4163 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
| 4164 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
| 4165 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
| 4166 |
|
|
src/applications/nanoRodBuilder/Makefile, |
| 4167 |
|
|
src/applications/nanoRodBuilder/MoLocator.cpp, |
| 4168 |
|
|
src/applications/nanoRodBuilder/MoLocator.hpp, |
| 4169 |
|
|
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
| 4170 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 4171 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
| 4172 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 4173 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
| 4174 |
|
|
nanoRodBuilder application (may not work yet). ((Doesn't work |
| 4175 |
|
|
yet.)) (((May never work....))) |
| 4176 |
|
|
|
| 4177 |
chrisfen |
2762 |
2005-04-11 16:54 tim |
| 4178 |
gezelter |
2199 |
|
| 4179 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
| 4180 |
|
|
prepareVisitor in Dump2XYZ |
| 4181 |
|
|
|
| 4182 |
chrisfen |
2762 |
2005-04-11 16:19 chrisfen |
| 4183 |
gezelter |
2199 |
|
| 4184 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
| 4185 |
|
|
quadrupoles. look! it's divide by 3 like stone says! |
| 4186 |
|
|
|
| 4187 |
chrisfen |
2762 |
2005-04-11 16:18 chrisfen |
| 4188 |
gezelter |
2199 |
|
| 4189 |
|
|
* forceFields/DUFF2.frc: fixing of the quadrupoles |
| 4190 |
|
|
|
| 4191 |
chrisfen |
2762 |
2005-04-11 16:16 tim |
| 4192 |
gezelter |
2199 |
|
| 4193 |
|
|
* src/selection/Token.hpp: change the parameter name in |
| 4194 |
|
|
constructors |
| 4195 |
|
|
|
| 4196 |
chrisfen |
2762 |
2005-04-11 15:49 gezelter |
| 4197 |
gezelter |
2199 |
|
| 4198 |
|
|
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
| 4199 |
|
|
|
| 4200 |
chrisfen |
2762 |
2005-04-11 15:06 gezelter |
| 4201 |
gezelter |
2199 |
|
| 4202 |
|
|
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
| 4203 |
|
|
versions < 3.80 |
| 4204 |
|
|
|
| 4205 |
chrisfen |
2762 |
2005-04-11 12:13 gezelter |
| 4206 |
gezelter |
2199 |
|
| 4207 |
|
|
* make/Makefile.in, src/UseTheForce/Makefile, |
| 4208 |
|
|
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
| 4209 |
|
|
some stuff to clean out module files during "make clean" |
| 4210 |
|
|
|
| 4211 |
chrisfen |
2762 |
2005-04-08 18:13 chrisfen |
| 4212 |
gezelter |
2199 |
|
| 4213 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
| 4214 |
|
|
interactions should be working with a remaining question of |
| 4215 |
|
|
interaction magnitude |
| 4216 |
|
|
|
| 4217 |
chrisfen |
2762 |
2005-04-08 18:12 chrisfen |
| 4218 |
gezelter |
2199 |
|
| 4219 |
|
|
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
| 4220 |
|
|
samples |
| 4221 |
|
|
|
| 4222 |
chrisfen |
2762 |
2005-04-08 14:48 chrisfen |
| 4223 |
gezelter |
2199 |
|
| 4224 |
|
|
* samples/water/ssd/ssd.md: oops... messed up a sample |
| 4225 |
|
|
|
| 4226 |
chrisfen |
2762 |
2005-04-08 10:43 chrisfen |
| 4227 |
gezelter |
2199 |
|
| 4228 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
| 4229 |
|
|
charge-dipole interactions |
| 4230 |
|
|
|
| 4231 |
chrisfen |
2762 |
2005-04-08 10:42 chrisfen |
| 4232 |
gezelter |
2199 |
|
| 4233 |
|
|
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
| 4234 |
|
|
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
| 4235 |
|
|
|
| 4236 |
chrisfen |
2762 |
2005-04-08 10:41 chrisfen |
| 4237 |
gezelter |
2199 |
|
| 4238 |
|
|
* forceFields/DUFF2.frc: added Cl- and Na+ |
| 4239 |
|
|
|
| 4240 |
chrisfen |
2762 |
2005-04-06 19:59 tim |
| 4241 |
gezelter |
2199 |
|
| 4242 |
|
|
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
| 4243 |
|
|
|
| 4244 |
chrisfen |
2762 |
2005-04-05 19:09 tim |
| 4245 |
gezelter |
2199 |
|
| 4246 |
|
|
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
| 4247 |
|
|
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
| 4248 |
|
|
in atom type name;clean the code a little bit |
| 4249 |
|
|
|
| 4250 |
|
|
2005-03-29 16:00 tim |
| 4251 |
|
|
|
| 4252 |
|
|
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
| 4253 |
|
|
in converting rotation matrix to quaternion |
| 4254 |
|
|
|
| 4255 |
|
|
2005-03-28 17:41 tim |
| 4256 |
|
|
|
| 4257 |
|
|
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
| 4258 |
|
|
|
| 4259 |
|
|
2005-03-28 17:30 tim |
| 4260 |
|
|
|
| 4261 |
|
|
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
| 4262 |
|
|
the wrapping |
| 4263 |
|
|
|
| 4264 |
|
|
2005-03-28 10:54 tim |
| 4265 |
|
|
|
| 4266 |
|
|
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
| 4267 |
|
|
dimension of histogram |
| 4268 |
|
|
|
| 4269 |
|
|
2005-03-22 11:38 tim |
| 4270 |
|
|
|
| 4271 |
|
|
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
| 4272 |
|
|
src/applications/dynamicProps/Makefile, |
| 4273 |
|
|
src/applications/oopse/Makefile, |
| 4274 |
|
|
src/applications/simpleBuilder/Makefile, |
| 4275 |
|
|
src/applications/staticProps/Makefile: avoid building parallel |
| 4276 |
|
|
executable for dump2XYZ, simpleBuilder, staticProps and |
| 4277 |
|
|
dynamicProps |
| 4278 |
|
|
|
| 4279 |
|
|
2005-03-21 17:34 chrisfen |
| 4280 |
|
|
|
| 4281 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
| 4282 |
|
|
forcefield files |
| 4283 |
|
|
|
| 4284 |
|
|
2005-03-21 15:51 chrisfen |
| 4285 |
|
|
|
| 4286 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 4287 |
|
|
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
| 4288 |
|
|
data for reaction_field |
| 4289 |
|
|
|
| 4290 |
|
|
2005-03-21 15:50 chrisfen |
| 4291 |
|
|
|
| 4292 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
| 4293 |
|
|
WILL CHANGE THIS BACK, RIGHT? |
| 4294 |
|
|
|
| 4295 |
|
|
2005-03-21 14:23 gezelter |
| 4296 |
|
|
|
| 4297 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
| 4298 |
|
|
correct value |
| 4299 |
|
|
|
| 4300 |
|
|
2005-03-21 14:22 gezelter |
| 4301 |
|
|
|
| 4302 |
|
|
* make/Makefile.in: fixed an install-related bug. |
| 4303 |
|
|
$(InstallCommand) had been set to $(InstallData) |
| 4304 |
|
|
|
| 4305 |
|
|
2005-03-15 09:21 gezelter |
| 4306 |
|
|
|
| 4307 |
|
|
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
| 4308 |
|
|
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
| 4309 |
|
|
|
| 4310 |
|
|
2005-03-15 09:20 gezelter |
| 4311 |
|
|
|
| 4312 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
| 4313 |
|
|
|
| 4314 |
|
|
2005-03-13 02:39 gezelter |
| 4315 |
|
|
|
| 4316 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
| 4317 |
|
|
charge-quadrupole interactions |
| 4318 |
|
|
|
| 4319 |
|
|
2005-03-12 14:12 chrisfen |
| 4320 |
|
|
|
| 4321 |
|
|
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
| 4322 |
|
|
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
| 4323 |
|
|
|
| 4324 |
|
|
2005-03-12 14:05 chrisfen |
| 4325 |
|
|
|
| 4326 |
|
|
* samples/thermoIntegration/liquid/ssde.in, |
| 4327 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
| 4328 |
|
|
samples/thermoIntegration/liquid/water.md, |
| 4329 |
|
|
samples/thermoIntegration/solid/idealCrystal.in, |
| 4330 |
|
|
samples/thermoIntegration/solid/ssde.in, |
| 4331 |
|
|
samples/thermoIntegration/solid/ssde.md, |
| 4332 |
|
|
samples/thermoIntegration/solid/ssde.zang0, |
| 4333 |
|
|
samples/thermoIntegration/solid/water.md, |
| 4334 |
|
|
samples/water/tip3p_ice/tp3.md, |
| 4335 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
| 4336 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: added some |
| 4337 |
|
|
samples |
| 4338 |
|
|
|
| 4339 |
|
|
2005-03-11 12:50 tim |
| 4340 |
|
|
|
| 4341 |
|
|
* src/: brains/SimCreator.cpp, |
| 4342 |
|
|
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
| 4343 |
|
|
MultipoleAtomTypesSectionParser |
| 4344 |
|
|
|
| 4345 |
|
|
2005-03-11 10:55 tim |
| 4346 |
|
|
|
| 4347 |
|
|
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
| 4348 |
|
|
excluded |
| 4349 |
|
|
|
| 4350 |
|
|
2005-03-11 10:53 gezelter |
| 4351 |
|
|
|
| 4352 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
| 4353 |
|
|
quadrupoles |
| 4354 |
|
|
|
| 4355 |
|
|
2005-03-11 10:52 gezelter |
| 4356 |
|
|
|
| 4357 |
|
|
* forceFields/DUFF2.frc: quadrupoles for SSD models |
| 4358 |
|
|
|
| 4359 |
|
|
2005-03-11 10:00 tim |
| 4360 |
|
|
|
| 4361 |
|
|
* ChangeLog, doc/SelectionExpression.html, |
| 4362 |
|
|
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
| 4363 |
|
|
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
| 4364 |
|
|
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
| 4365 |
|
|
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
| 4366 |
|
|
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
| 4367 |
|
|
SelectionExpression.html |
| 4368 |
|
|
|
| 4369 |
|
|
2005-03-10 19:43 chrisfen |
| 4370 |
|
|
|
| 4371 |
tim |
2116 |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
| 4372 |
|
|
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
| 4373 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
| 4374 |
|
|
MPI restraints |
| 4375 |
|
|
|
| 4376 |
gezelter |
2199 |
2005-03-10 18:56 tim |
| 4377 |
tim |
2116 |
|
| 4378 |
|
|
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
| 4379 |
|
|
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
| 4380 |
|
|
and cutoff group |
| 4381 |
|
|
|
| 4382 |
gezelter |
2199 |
2005-03-10 17:06 gezelter |
| 4383 |
tim |
2116 |
|
| 4384 |
|
|
* src/types/MorseBondType.hpp: fixed a doxygen problem |
| 4385 |
|
|
|
| 4386 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
| 4387 |
tim |
2116 |
|
| 4388 |
|
|
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
| 4389 |
|
|
the split dipole test cases |
| 4390 |
|
|
|
| 4391 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
| 4392 |
tim |
2116 |
|
| 4393 |
|
|
* doc/SelectionExpression.html: updated some documentation |
| 4394 |
|
|
|
| 4395 |
gezelter |
2199 |
2005-03-10 15:40 gezelter |
| 4396 |
tim |
2116 |
|
| 4397 |
|
|
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
| 4398 |
|
|
Makefile: LinkedList removal project starts now |
| 4399 |
|
|
|
| 4400 |
gezelter |
2199 |
2005-03-10 15:28 tim |
| 4401 |
tim |
2116 |
|
| 4402 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 4403 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
| 4404 |
|
|
using map to replace link list |
| 4405 |
|
|
|
| 4406 |
gezelter |
2199 |
2005-03-10 14:11 tim |
| 4407 |
tim |
2116 |
|
| 4408 |
|
|
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
| 4409 |
|
|
case of split dipole |
| 4410 |
|
|
|
| 4411 |
gezelter |
2199 |
2005-03-10 14:10 chrisfen |
| 4412 |
tim |
2116 |
|
| 4413 |
|
|
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
| 4414 |
|
|
src/io/RestWriter.cpp, |
| 4415 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
| 4416 |
|
|
builds... |
| 4417 |
|
|
|
| 4418 |
gezelter |
2199 |
2005-03-10 13:44 tim |
| 4419 |
tim |
2116 |
|
| 4420 |
|
|
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
| 4421 |
|
|
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
| 4422 |
|
|
adding test case for split dipole |
| 4423 |
|
|
|
| 4424 |
gezelter |
2199 |
2005-03-10 12:54 gezelter |
| 4425 |
tim |
2116 |
|
| 4426 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
| 4427 |
|
|
support for split dipoles |
| 4428 |
|
|
|
| 4429 |
gezelter |
2199 |
2005-03-10 11:27 chrisfen |
| 4430 |
tim |
2116 |
|
| 4431 |
|
|
* samples/water/tip3p_ice/tp3.md, |
| 4432 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
| 4433 |
|
|
restraints |
| 4434 |
|
|
|
| 4435 |
gezelter |
2199 |
2005-03-10 11:15 chrisfen |
| 4436 |
tim |
2116 |
|
| 4437 |
|
|
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
| 4438 |
|
|
src/UseTheForce/ForceFields.hpp, |
| 4439 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
| 4440 |
|
|
|
| 4441 |
gezelter |
2199 |
2005-03-10 11:14 tim |
| 4442 |
tim |
2116 |
|
| 4443 |
|
|
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
| 4444 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
| 4445 |
|
|
src/selection/SelectionEvaluator.cpp: minor change |
| 4446 |
|
|
|
| 4447 |
gezelter |
2199 |
2005-03-10 10:10 chrisfen |
| 4448 |
tim |
2116 |
|
| 4449 |
tim |
2102 |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
| 4450 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
| 4451 |
|
|
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
| 4452 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
| 4453 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
| 4454 |
|
|
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
| 4455 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
| 4456 |
|
|
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
| 4457 |
|
|
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
| 4458 |
|
|
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
| 4459 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
| 4460 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp, |
| 4461 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
| 4462 |
|
|
the new restraints code |
| 4463 |
|
|
|
| 4464 |
gezelter |
2199 |
2005-03-09 13:48 tim |
| 4465 |
tim |
2102 |
|
| 4466 |
|
|
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
| 4467 |
|
|
IndexFinder |
| 4468 |
|
|
|
| 4469 |
gezelter |
2199 |
2005-03-09 13:46 tim |
| 4470 |
tim |
2102 |
|
| 4471 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
| 4472 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 4473 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
| 4474 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
| 4475 |
|
|
fix compilation issue |
| 4476 |
|
|
|
| 4477 |
gezelter |
2199 |
2005-03-09 12:58 tim |
| 4478 |
tim |
2102 |
|
| 4479 |
|
|
* forceFields/DUFF2.frc, scripts/filepp, |
| 4480 |
|
|
src/UseTheForce/EAM_FF.cpp, |
| 4481 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
| 4482 |
|
|
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
| 4483 |
|
|
in SectionParser (lineNo is not updated) |
| 4484 |
|
|
|
| 4485 |
gezelter |
2199 |
2005-03-09 12:30 tim |
| 4486 |
tim |
2102 |
|
| 4487 |
|
|
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
| 4488 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
| 4489 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 4490 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
| 4491 |
|
|
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 4492 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
| 4493 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 4494 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
| 4495 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
| 4496 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
| 4497 |
|
|
io/SectionParserManager.cpp, selection/Makefile, |
| 4498 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 4499 |
|
|
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
| 4500 |
|
|
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
| 4501 |
|
|
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
| 4502 |
|
|
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
| 4503 |
|
|
into ChargeAtomTypesSectionParser and |
| 4504 |
|
|
MultipoleAtomTypesSectionParser;remove print dipole option from |
| 4505 |
|
|
Dump2XYZ; |
| 4506 |
|
|
|
| 4507 |
gezelter |
2199 |
2005-03-09 12:28 tim |
| 4508 |
tim |
2102 |
|
| 4509 |
|
|
* forceFields/DUFF2.frc: change the format of DUFF2 |
| 4510 |
|
|
|
| 4511 |
gezelter |
2199 |
2005-03-09 10:44 gezelter |
| 4512 |
tim |
2102 |
|
| 4513 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, |
| 4514 |
|
|
electrostatic_interface.F90, electrostatic_interface.h: new |
| 4515 |
|
|
electrostatic module |
| 4516 |
|
|
|
| 4517 |
gezelter |
2199 |
2005-03-09 09:26 gezelter |
| 4518 |
tim |
2102 |
|
| 4519 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 4520 |
|
|
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
| 4521 |
|
|
and fixed quadrupole stuff |
| 4522 |
|
|
|
| 4523 |
gezelter |
2199 |
2005-03-09 09:25 gezelter |
| 4524 |
tim |
2102 |
|
| 4525 |
|
|
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
| 4526 |
|
|
for outdated charge and dipole interfaces |
| 4527 |
|
|
|
| 4528 |
gezelter |
2199 |
2005-03-08 16:08 gezelter |
| 4529 |
tim |
2102 |
|
| 4530 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
| 4531 |
|
|
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
| 4532 |
|
|
charge-dipole test cases |
| 4533 |
|
|
|
| 4534 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
| 4535 |
tim |
2102 |
|
| 4536 |
|
|
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
| 4537 |
|
|
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
| 4538 |
|
|
strange icc8 bug (we think). |
| 4539 |
|
|
|
| 4540 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
| 4541 |
tim |
2102 |
|
| 4542 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
| 4543 |
|
|
|
| 4544 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
| 4545 |
tim |
2102 |
|
| 4546 |
|
|
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
| 4547 |
|
|
Unification Project |
| 4548 |
|
|
|
| 4549 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
| 4550 |
tim |
2102 |
|
| 4551 |
|
|
* src/io/Globals.cpp: Dunno |
| 4552 |
|
|
|
| 4553 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
| 4554 |
tim |
2102 |
|
| 4555 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
| 4556 |
|
|
OOPSE_itoa and checking a NULL left over from the LinkedList days |
| 4557 |
|
|
|
| 4558 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
| 4559 |
tim |
2102 |
|
| 4560 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 4561 |
|
|
atype_interface.F90, atype_interface.h, charge.F90, |
| 4562 |
|
|
charge_interface.F90, charge_interface.h, dipole.F90, |
| 4563 |
|
|
dipole_interface.F90, dipole_interface.h: electrostatic unification |
| 4564 |
|
|
project fixed an uninitialized variable in Lennard Jones mixing map |
| 4565 |
|
|
|
| 4566 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
| 4567 |
tim |
2102 |
|
| 4568 |
|
|
* src/UseTheForce/doForces.F90: electrostatic unification project |
| 4569 |
|
|
|
| 4570 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
| 4571 |
tim |
2102 |
|
| 4572 |
|
|
* samples/water/dimer/: two.md, water.md: making some cool test |
| 4573 |
|
|
cases |
| 4574 |
|
|
|
| 4575 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
| 4576 |
tim |
2102 |
|
| 4577 |
|
|
* forceFields/DUFF2.frc: Added a charge for Chlorine |
| 4578 |
|
|
|
| 4579 |
gezelter |
2199 |
2005-03-07 17:39 tim |
| 4580 |
tim |
2102 |
|
| 4581 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
| 4582 |
|
|
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
| 4583 |
|
|
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
| 4584 |
|
|
Fixing a bug in BitSet.cpp |
| 4585 |
|
|
|
| 4586 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
| 4587 |
tim |
2102 |
|
| 4588 |
|
|
* src/config.h.in: Cleaning up config.h.in by adding comments |
| 4589 |
|
|
|
| 4590 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
| 4591 |
tim |
2102 |
|
| 4592 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
| 4593 |
|
|
src/brains/SimCreator.cpp: SPRNG eradication project |
| 4594 |
|
|
|
| 4595 |
gezelter |
2199 |
2005-03-03 09:40 tim |
| 4596 |
tim |
2102 |
|
| 4597 |
|
|
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
| 4598 |
|
|
missing atom type problem) |
| 4599 |
|
|
|
| 4600 |
gezelter |
2199 |
2005-03-02 11:29 tim |
| 4601 |
tim |
2102 |
|
| 4602 |
|
|
* src/math/RandNumGen.hpp: adding base class of Random Number |
| 4603 |
|
|
generator |
| 4604 |
|
|
|
| 4605 |
gezelter |
2199 |
2005-03-02 11:28 tim |
| 4606 |
tim |
2102 |
|
| 4607 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 4608 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
| 4609 |
|
|
Velocitizer is not initialized which causes a seg fault |
| 4610 |
|
|
|
| 4611 |
gezelter |
2199 |
2005-03-02 10:36 tim |
| 4612 |
tim |
2102 |
|
| 4613 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 4614 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
| 4615 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 4616 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
| 4617 |
|
|
math/SeqRandNumGen.hpp: remove default parameter from |
| 4618 |
|
|
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
| 4619 |
|
|
random number generator |
| 4620 |
|
|
|
| 4621 |
gezelter |
2199 |
2005-03-02 02:32 tim |
| 4622 |
tim |
2102 |
|
| 4623 |
|
|
* test/math/testRandNumGen.cpp: Adding unit test for random number |
| 4624 |
|
|
generator |
| 4625 |
|
|
|
| 4626 |
gezelter |
2199 |
2005-03-01 18:17 tim |
| 4627 |
tim |
2102 |
|
| 4628 |
|
|
* src/brains/Thermo.hpp: fixed a file inclusion problem |
| 4629 |
|
|
|
| 4630 |
gezelter |
2199 |
2005-03-01 18:17 tim |
| 4631 |
tim |
2102 |
|
| 4632 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
| 4633 |
|
|
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
| 4634 |
|
|
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
| 4635 |
|
|
RandNumGenTestCase.hpp: fixed compilation problem |
| 4636 |
|
|
|
| 4637 |
gezelter |
2199 |
2005-03-01 18:02 tim |
| 4638 |
tim |
2102 |
|
| 4639 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
| 4640 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
| 4641 |
|
|
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
| 4642 |
|
|
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
| 4643 |
|
|
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
| 4644 |
|
|
|
| 4645 |
gezelter |
2199 |
2005-03-01 18:00 tim |
| 4646 |
tim |
2102 |
|
| 4647 |
|
|
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
| 4648 |
|
|
ParallelandNumGenTestCase.hpp: Change the name of test case |
| 4649 |
|
|
|
| 4650 |
gezelter |
2199 |
2005-03-01 16:00 tim |
| 4651 |
tim |
2102 |
|
| 4652 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
| 4653 |
|
|
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
| 4654 |
|
|
generator |
| 4655 |
|
|
|
| 4656 |
gezelter |
2199 |
2005-03-01 15:10 tim |
| 4657 |
tim |
2102 |
|
| 4658 |
|
|
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
| 4659 |
|
|
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
| 4660 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
| 4661 |
|
|
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
| 4662 |
|
|
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
| 4663 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 4664 |
|
|
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
| 4665 |
|
|
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
| 4666 |
|
|
|
| 4667 |
gezelter |
2199 |
2005-03-01 14:11 tim |
| 4668 |
tim |
2102 |
|
| 4669 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
| 4670 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 4671 |
|
|
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
| 4672 |
|
|
OOPSERandNumGen |
| 4673 |
|
|
|
| 4674 |
gezelter |
2199 |
2005-03-01 10:44 gezelter |
| 4675 |
tim |
2102 |
|
| 4676 |
|
|
* make/Makefile.in: Fixed the damned build problem with the |
| 4677 |
|
|
libraries not being removed in make clean and make distclean (at |
| 4678 |
|
|
least we think it is fixed). |
| 4679 |
|
|
|
| 4680 |
gezelter |
2199 |
2005-03-01 10:26 gezelter |
| 4681 |
tim |
2102 |
|
| 4682 |
|
|
* src/math/MersenneTwister.hpp: Making small modifications to allow |
| 4683 |
|
|
for use on MPI machines |
| 4684 |
|
|
|
| 4685 |
gezelter |
2199 |
2005-03-01 09:45 tim |
| 4686 |
tim |
2102 |
|
| 4687 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
| 4688 |
|
|
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
| 4689 |
|
|
math/MersenneTwister.hpp: adding MersenneTwister random number |
| 4690 |
|
|
generator |
| 4691 |
|
|
|
| 4692 |
gezelter |
2199 |
2005-02-28 22:55 tim |
| 4693 |
tim |
2102 |
|
| 4694 |
|
|
* src/math/MersenneTwister.hpp: Adding a modified version of |
| 4695 |
|
|
MersenneTwister.hpp |
| 4696 |
|
|
|
| 4697 |
gezelter |
2199 |
2005-02-28 12:24 tim |
| 4698 |
tim |
2102 |
|
| 4699 |
|
|
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
| 4700 |
|
|
definition.jpg: selection expression |
| 4701 |
|
|
|
| 4702 |
gezelter |
2199 |
2005-02-25 16:22 tim |
| 4703 |
tim |
2102 |
|
| 4704 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
| 4705 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
| 4706 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
| 4707 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
| 4708 |
|
|
types/AtomType.hpp: adding soft potential to LJ Module |
| 4709 |
|
|
|
| 4710 |
gezelter |
2199 |
2005-02-25 11:38 tim |
| 4711 |
tim |
2102 |
|
| 4712 |
|
|
* doc/SelectionExpression.html: adding documentation for selection |
| 4713 |
|
|
expression |
| 4714 |
|
|
|
| 4715 |
gezelter |
2199 |
2005-02-24 15:55 tim |
| 4716 |
tim |
2102 |
|
| 4717 |
|
|
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
| 4718 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
| 4719 |
|
|
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
| 4720 |
|
|
adding basic_teebuf which can operate on multiple stream |
| 4721 |
|
|
simutaneously. |
| 4722 |
|
|
|
| 4723 |
gezelter |
2199 |
2005-02-22 14:26 chrisfen |
| 4724 |
tim |
2102 |
|
| 4725 |
gezelter |
2199 |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
| 4726 |
|
|
sample |
| 4727 |
|
|
|
| 4728 |
|
|
2005-02-22 13:56 tim |
| 4729 |
|
|
|
| 4730 |
tim |
2102 |
* src/: UseTheForce/DarkSide/reactionField.F90, |
| 4731 |
|
|
primitives/RigidBody.cpp: reactionfield get fixed |
| 4732 |
|
|
|
| 4733 |
gezelter |
2199 |
2005-02-21 11:57 tim |
| 4734 |
tim |
2102 |
|
| 4735 |
|
|
* src/: applications/staticProps/GofRAngle.cpp, |
| 4736 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
| 4737 |
|
|
a bug in GofRAngle |
| 4738 |
|
|
|
| 4739 |
gezelter |
2199 |
2005-02-21 10:28 tim |
| 4740 |
tim |
2102 |
|
| 4741 |
|
|
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
| 4742 |
|
|
|
| 4743 |
gezelter |
2199 |
2005-02-21 10:22 tim |
| 4744 |
tim |
2102 |
|
| 4745 |
|
|
* src/utils/next_combination.hpp: fix for compilation on the Sun |
| 4746 |
|
|
|
| 4747 |
gezelter |
2199 |
2005-02-21 10:21 tim |
| 4748 |
tim |
2102 |
|
| 4749 |
|
|
* src/utils/GenericData.hpp: fix problem in sun |
| 4750 |
|
|
|
| 4751 |
gezelter |
2199 |
2005-02-18 18:07 tim |
| 4752 |
tim |
2102 |
|
| 4753 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 4754 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
| 4755 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
| 4756 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
| 4757 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
| 4758 |
|
|
applications/staticProps/GofXyz.cpp, |
| 4759 |
|
|
applications/staticProps/GofXyz.hpp, |
| 4760 |
|
|
applications/staticProps/StaticProps.cpp, |
| 4761 |
|
|
applications/staticProps/StaticProps.ggo, |
| 4762 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 4763 |
|
|
applications/staticProps/StaticPropsCmd.h, |
| 4764 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 4765 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 4766 |
|
|
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
| 4767 |
|
|
|
| 4768 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
| 4769 |
tim |
2102 |
|
| 4770 |
|
|
* src/brains/Register.cpp: Corrected filename collision for EAM on |
| 4771 |
|
|
Mac OS X |
| 4772 |
|
|
|
| 4773 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
| 4774 |
tim |
2102 |
|
| 4775 |
|
|
* src/applications/oopse/oopse.cpp: Updated copyright information |
| 4776 |
|
|
|
| 4777 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
| 4778 |
tim |
2102 |
|
| 4779 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
| 4780 |
|
|
Makefile: corrected filename collision for EAM on operating systems |
| 4781 |
|
|
which are not case sensitive (aka Mac OS X) |
| 4782 |
|
|
|
| 4783 |
gezelter |
2199 |
2005-02-17 15:15 tim |
| 4784 |
tim |
2102 |
|
| 4785 |
|
|
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
| 4786 |
|
|
|
| 4787 |
gezelter |
2199 |
2005-02-17 14:50 tim |
| 4788 |
tim |
2102 |
|
| 4789 |
|
|
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
| 4790 |
|
|
in GofXyz |
| 4791 |
|
|
|
| 4792 |
gezelter |
2199 |
2005-02-17 14:09 tim |
| 4793 |
tim |
2102 |
|
| 4794 |
|
|
* src/applications/staticProps/RadialDistrFunc.hpp: make |
| 4795 |
|
|
processHistogram non-abstrct function |
| 4796 |
|
|
|
| 4797 |
gezelter |
2199 |
2005-02-17 13:41 tim |
| 4798 |
tim |
2102 |
|
| 4799 |
|
|
* src/applications/staticProps/GofXyz.cpp: [no log message] |
| 4800 |
|
|
|
| 4801 |
gezelter |
2199 |
2005-02-17 13:30 tim |
| 4802 |
tim |
2102 |
|
| 4803 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
| 4804 |
|
|
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
| 4805 |
|
|
finish GofXyz |
| 4806 |
|
|
|
| 4807 |
gezelter |
2199 |
2005-02-17 11:21 tim |
| 4808 |
tim |
2102 |
|
| 4809 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
| 4810 |
|
|
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
| 4811 |
|
|
distribution function |
| 4812 |
|
|
|
| 4813 |
gezelter |
2199 |
2005-02-17 10:23 tim |
| 4814 |
tim |
2102 |
|
| 4815 |
|
|
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
| 4816 |
|
|
|
| 4817 |
gezelter |
2199 |
2005-02-17 10:18 tim |
| 4818 |
tim |
2102 |
|
| 4819 |
|
|
* src/: brains/BlockSnapshotManager.cpp, |
| 4820 |
|
|
selection/DistanceFinder.cpp: The change of interface of BitSet |
| 4821 |
|
|
cause a bug in SelectionEvaluation |
| 4822 |
|
|
|
| 4823 |
gezelter |
2199 |
2005-02-16 16:13 tim |
| 4824 |
tim |
2102 |
|
| 4825 |
|
|
* src/utils/residentMem.c: return residentMem in byte |
| 4826 |
|
|
|
| 4827 |
gezelter |
2199 |
2005-02-16 16:00 tim |
| 4828 |
tim |
2102 |
|
| 4829 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
| 4830 |
|
|
a bug in writing out the value of cosang |
| 4831 |
|
|
|
| 4832 |
gezelter |
2199 |
2005-02-16 15:43 tim |
| 4833 |
tim |
2102 |
|
| 4834 |
|
|
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
| 4835 |
|
|
estimate avaliable memory |
| 4836 |
|
|
|
| 4837 |
gezelter |
2199 |
2005-02-16 15:30 tim |
| 4838 |
tim |
2102 |
|
| 4839 |
|
|
* src/: applications/staticProps/GofAngle2.cpp, |
| 4840 |
|
|
applications/staticProps/GofAngle2.hpp, |
| 4841 |
|
|
applications/staticProps/GofR.cpp, |
| 4842 |
|
|
applications/staticProps/GofR.hpp, |
| 4843 |
|
|
applications/staticProps/GofRAngle.cpp, |
| 4844 |
|
|
applications/staticProps/GofRAngle.hpp, |
| 4845 |
|
|
applications/staticProps/GofXyz.cpp, |
| 4846 |
|
|
applications/staticProps/GofXyz.hpp, |
| 4847 |
|
|
applications/staticProps/StaticProps.cpp, |
| 4848 |
|
|
applications/staticProps/StaticProps.ggo, |
| 4849 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 4850 |
|
|
applications/staticProps/StaticPropsCmd.h, |
| 4851 |
|
|
brains/BlockSnapshotManager.cpp: change the default bin number |
| 4852 |
|
|
|
| 4853 |
gezelter |
2199 |
2005-02-16 14:36 tim |
| 4854 |
tim |
2102 |
|
| 4855 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
| 4856 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
| 4857 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
| 4858 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
| 4859 |
|
|
applications/staticProps/GofAngle2.cpp, |
| 4860 |
|
|
applications/staticProps/GofR.cpp, |
| 4861 |
|
|
applications/staticProps/GofR.hpp, |
| 4862 |
|
|
applications/staticProps/GofRAngle.cpp, |
| 4863 |
|
|
applications/staticProps/GofRAngle.hpp, |
| 4864 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 4865 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
| 4866 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 4867 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
| 4868 |
|
|
files;fix the problem of counting in staticProps |
| 4869 |
|
|
|
| 4870 |
gezelter |
2199 |
2005-02-15 14:39 tim |
| 4871 |
tim |
2102 |
|
| 4872 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
| 4873 |
|
|
BlockSnapshotManager |
| 4874 |
|
|
|
| 4875 |
gezelter |
2199 |
2005-02-15 14:36 tim |
| 4876 |
tim |
2102 |
|
| 4877 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
| 4878 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 4879 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 4880 |
|
|
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
| 4881 |
|
|
reference counting now |
| 4882 |
|
|
|
| 4883 |
gezelter |
2199 |
2005-02-15 12:49 tim |
| 4884 |
tim |
2102 |
|
| 4885 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 4886 |
|
|
replace std::make_pair by VariablesType::value_type to make Sun |
| 4887 |
|
|
Compiler happy |
| 4888 |
|
|
|
| 4889 |
gezelter |
2199 |
2005-02-15 12:35 tim |
| 4890 |
tim |
2102 |
|
| 4891 |
|
|
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
| 4892 |
|
|
TokenMap, using TokenMapType::value_type instead of std::make_pair |
| 4893 |
|
|
to make Sun compiler happy |
| 4894 |
|
|
|
| 4895 |
gezelter |
2199 |
2005-02-15 12:24 tim |
| 4896 |
tim |
2102 |
|
| 4897 |
|
|
* src/applications/staticProps/: GofRAngle.cpp, |
| 4898 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
| 4899 |
|
|
|
| 4900 |
gezelter |
2199 |
2005-02-15 12:11 tim |
| 4901 |
tim |
2102 |
|
| 4902 |
|
|
* src/: applications/staticProps/GofR.cpp, |
| 4903 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 4904 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
| 4905 |
|
|
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
| 4906 |
|
|
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
| 4907 |
|
|
calculation problem when two selections intersect with each other |
| 4908 |
|
|
|
| 4909 |
gezelter |
2199 |
2005-02-15 10:24 gezelter |
| 4910 |
tim |
2102 |
|
| 4911 |
|
|
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
| 4912 |
|
|
xlc++ |
| 4913 |
|
|
|
| 4914 |
gezelter |
2199 |
2005-02-15 10:17 gezelter |
| 4915 |
tim |
2102 |
|
| 4916 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
| 4917 |
|
|
src/utils/residentMem.c: [no log message] |
| 4918 |
|
|
|
| 4919 |
gezelter |
2199 |
2005-02-15 01:17 gezelter |
| 4920 |
tim |
2102 |
|
| 4921 |
|
|
* src/utils/residentMem.c: bug fix for null termination |
| 4922 |
|
|
|
| 4923 |
gezelter |
2199 |
2005-02-15 01:11 gezelter |
| 4924 |
tim |
2102 |
|
| 4925 |
|
|
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
| 4926 |
|
|
bugfixing residentMem |
| 4927 |
|
|
|
| 4928 |
gezelter |
2199 |
2005-02-15 00:59 gezelter |
| 4929 |
tim |
2102 |
|
| 4930 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
| 4931 |
|
|
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
| 4932 |
|
|
|
| 4933 |
gezelter |
2199 |
2005-02-15 00:08 gezelter |
| 4934 |
tim |
2102 |
|
| 4935 |
|
|
* src/utils/Makefile.in: added residentMem |
| 4936 |
|
|
|
| 4937 |
gezelter |
2199 |
2005-02-15 00:05 gezelter |
| 4938 |
tim |
2102 |
|
| 4939 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
| 4940 |
|
|
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
| 4941 |
|
|
src/utils/residentMem.h: modifications to estimate memory in use by |
| 4942 |
|
|
other processes autoconf fixes ps syntax checking config.h file |
| 4943 |
|
|
cleaning |
| 4944 |
|
|
|
| 4945 |
gezelter |
2199 |
2005-02-14 18:26 gezelter |
| 4946 |
tim |
2102 |
|
| 4947 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
| 4948 |
|
|
|
| 4949 |
gezelter |
2199 |
2005-02-14 18:16 gezelter |
| 4950 |
tim |
2102 |
|
| 4951 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
| 4952 |
|
|
strangeness |
| 4953 |
|
|
|
| 4954 |
gezelter |
2199 |
2005-02-14 14:42 tim |
| 4955 |
tim |
2102 |
|
| 4956 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
| 4957 |
|
|
BlockSnapshotManager.hpp |
| 4958 |
|
|
|
| 4959 |
gezelter |
2199 |
2005-02-14 13:51 tim |
| 4960 |
tim |
2102 |
|
| 4961 |
|
|
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
| 4962 |
|
|
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
| 4963 |
|
|
length of first frame |
| 4964 |
|
|
|
| 4965 |
gezelter |
2199 |
2005-02-14 13:12 tim |
| 4966 |
tim |
2102 |
|
| 4967 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
| 4968 |
|
|
VelocityVerletIntegrator : last frame is written twice |
| 4969 |
|
|
|
| 4970 |
gezelter |
2199 |
2005-02-14 12:57 tim |
| 4971 |
tim |
2102 |
|
| 4972 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
| 4973 |
|
|
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
| 4974 |
|
|
primitives/StuntDouble.hpp: begin bug fix |
| 4975 |
|
|
|
| 4976 |
gezelter |
2199 |
2005-02-14 12:35 tim |
| 4977 |
tim |
2102 |
|
| 4978 |
|
|
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
| 4979 |
|
|
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
| 4980 |
|
|
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
| 4981 |
|
|
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
| 4982 |
|
|
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
| 4983 |
|
|
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
| 4984 |
|
|
VCorrFunc.hpp: refactory CorrelationFunction |
| 4985 |
|
|
|
| 4986 |
gezelter |
2199 |
2005-02-14 10:18 gezelter |
| 4987 |
tim |
2102 |
|
| 4988 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
| 4989 |
|
|
and start of switch for type of correlation function |
| 4990 |
|
|
|
| 4991 |
gezelter |
2199 |
2005-02-13 16:18 tim |
| 4992 |
tim |
2102 |
|
| 4993 |
|
|
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
| 4994 |
|
|
calculating bytes per stuntdouble |
| 4995 |
|
|
|
| 4996 |
gezelter |
2199 |
2005-02-13 16:03 tim |
| 4997 |
tim |
2102 |
|
| 4998 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
| 4999 |
|
|
|
| 5000 |
gezelter |
2199 |
2005-02-13 15:57 tim |
| 5001 |
tim |
2102 |
|
| 5002 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
| 5003 |
|
|
bug in CorrelationFunction |
| 5004 |
|
|
|
| 5005 |
gezelter |
2199 |
2005-02-13 15:36 tim |
| 5006 |
tim |
2102 |
|
| 5007 |
|
|
* src/: applications/staticProps/GofR.cpp, |
| 5008 |
|
|
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
| 5009 |
|
|
bug in SimInfo::getCutoff() |
| 5010 |
|
|
|
| 5011 |
gezelter |
2199 |
2005-02-13 15:08 tim |
| 5012 |
tim |
2102 |
|
| 5013 |
|
|
* make/Makefile.in: adding staticProps and dynamicProps into |
| 5014 |
|
|
Makefile.in |
| 5015 |
|
|
|
| 5016 |
gezelter |
2199 |
2005-02-13 15:05 tim |
| 5017 |
tim |
2102 |
|
| 5018 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 5019 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
| 5020 |
|
|
applications/staticProps/StaticProps.cpp, |
| 5021 |
|
|
applications/staticProps/StaticProps.ggo, |
| 5022 |
|
|
applications/staticProps/StaticPropsCmd.c, |
| 5023 |
|
|
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
| 5024 |
|
|
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
| 5025 |
|
|
defaults to the cutoff radius |
| 5026 |
|
|
|
| 5027 |
gezelter |
2199 |
2005-02-13 14:14 tim |
| 5028 |
tim |
2102 |
|
| 5029 |
|
|
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
| 5030 |
|
|
|
| 5031 |
gezelter |
2199 |
2005-02-13 14:10 tim |
| 5032 |
tim |
2102 |
|
| 5033 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 5034 |
|
|
applications/dynamicProps/CorrelationFunction.cpp, |
| 5035 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
| 5036 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
| 5037 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 5038 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
| 5039 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 5040 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
| 5041 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
| 5042 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
| 5043 |
|
|
visitors/OtherVisitor.cpp: dynamicProps get built |
| 5044 |
|
|
|
| 5045 |
gezelter |
2199 |
2005-02-13 10:56 tim |
| 5046 |
tim |
2102 |
|
| 5047 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 5048 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 5049 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
| 5050 |
|
|
progress |
| 5051 |
|
|
|
| 5052 |
gezelter |
2199 |
2005-02-13 03:04 tim |
| 5053 |
tim |
2102 |
|
| 5054 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
| 5055 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 5056 |
|
|
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 5057 |
|
|
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
| 5058 |
|
|
work in dynamicProps |
| 5059 |
|
|
|
| 5060 |
gezelter |
2199 |
2005-02-13 02:25 tim |
| 5061 |
tim |
2102 |
|
| 5062 |
|
|
* src/applications/dynamicProps/DynamicProps.cpp: adding |
| 5063 |
|
|
dynamicProps |
| 5064 |
|
|
|
| 5065 |
gezelter |
2199 |
2005-02-13 02:14 tim |
| 5066 |
tim |
2102 |
|
| 5067 |
|
|
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
| 5068 |
|
|
DynamicPropsCmd.h: adding command line option to DynamicProps |
| 5069 |
|
|
|
| 5070 |
gezelter |
2199 |
2005-02-13 02:13 tim |
| 5071 |
tim |
2102 |
|
| 5072 |
|
|
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
| 5073 |
|
|
adding command line option for DynamicProps |
| 5074 |
|
|
|
| 5075 |
gezelter |
2199 |
2005-02-13 01:57 tim |
| 5076 |
tim |
2102 |
|
| 5077 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
| 5078 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
| 5079 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 5080 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 5081 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
| 5082 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
| 5083 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
| 5084 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
| 5085 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
| 5086 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 5087 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 5088 |
|
|
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
| 5089 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
| 5090 |
|
|
dynamicProps |
| 5091 |
|
|
|
| 5092 |
gezelter |
2199 |
2005-02-12 15:09 tim |
| 5093 |
tim |
2102 |
|
| 5094 |
|
|
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
| 5095 |
|
|
|
| 5096 |
gezelter |
2199 |
2005-02-11 17:41 tim |
| 5097 |
tim |
2102 |
|
| 5098 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
| 5099 |
|
|
more constructor to Snapshot to create customized DataStorage |
| 5100 |
|
|
|
| 5101 |
gezelter |
2199 |
2005-02-11 17:39 tim |
| 5102 |
tim |
2102 |
|
| 5103 |
|
|
* src/selection/: DistanceFinder.hpp, Makefile, |
| 5104 |
|
|
SelectionManager.hpp: adding beginSelected, nextSelected method to |
| 5105 |
|
|
SelectionManager |
| 5106 |
|
|
|
| 5107 |
gezelter |
2199 |
2005-02-11 17:36 tim |
| 5108 |
tim |
2102 |
|
| 5109 |
|
|
* src/config.h.in, configure: adding support for physmem |
| 5110 |
|
|
|
| 5111 |
gezelter |
2199 |
2005-02-11 17:35 tim |
| 5112 |
tim |
2102 |
|
| 5113 |
|
|
* ac-tools/configure.in: adding supprot for physmem |
| 5114 |
|
|
|
| 5115 |
gezelter |
2199 |
2005-02-11 17:35 tim |
| 5116 |
tim |
2102 |
|
| 5117 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
| 5118 |
|
|
physmem |
| 5119 |
|
|
|
| 5120 |
gezelter |
2199 |
2005-02-10 17:37 tim |
| 5121 |
tim |
2102 |
|
| 5122 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
| 5123 |
|
|
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
| 5124 |
|
|
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
| 5125 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 5126 |
|
|
StaticPropsCmd.h: more work in StaticProps |
| 5127 |
|
|
|
| 5128 |
gezelter |
2199 |
2005-02-10 13:14 tim |
| 5129 |
tim |
2102 |
|
| 5130 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
| 5131 |
|
|
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
| 5132 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
| 5133 |
|
|
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
| 5134 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 5135 |
|
|
StaticPropsCmd.h: change the filenames |
| 5136 |
|
|
|
| 5137 |
gezelter |
2199 |
2005-02-10 09:15 tim |
| 5138 |
tim |
2102 |
|
| 5139 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
| 5140 |
|
|
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
| 5141 |
|
|
RadialDistrFunc.hpp: adding GofRAngle |
| 5142 |
|
|
|
| 5143 |
gezelter |
2199 |
2005-02-09 13:21 tim |
| 5144 |
tim |
2102 |
|
| 5145 |
|
|
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
| 5146 |
|
|
useless files |
| 5147 |
|
|
|
| 5148 |
gezelter |
2199 |
2005-02-09 13:12 tim |
| 5149 |
tim |
2102 |
|
| 5150 |
|
|
* src/applications/staticProps/: GofR.cpp, Makefile, |
| 5151 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
| 5152 |
|
|
|
| 5153 |
gezelter |
2199 |
2005-02-09 12:08 tim |
| 5154 |
tim |
2102 |
|
| 5155 |
|
|
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
| 5156 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
| 5157 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
| 5158 |
|
|
|
| 5159 |
gezelter |
2199 |
2005-02-07 17:39 tim |
| 5160 |
tim |
2102 |
|
| 5161 |
|
|
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
| 5162 |
|
|
Molecule class |
| 5163 |
|
|
|
| 5164 |
gezelter |
2199 |
2005-02-07 17:38 tim |
| 5165 |
tim |
2102 |
|
| 5166 |
|
|
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
| 5167 |
|
|
|
| 5168 |
gezelter |
2199 |
2005-02-07 17:36 tim |
| 5169 |
tim |
2102 |
|
| 5170 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 5171 |
|
|
SelectionCompiler.cpp: support select internal index selection, for |
| 5172 |
|
|
example, select DMPC.3 |
| 5173 |
|
|
|
| 5174 |
gezelter |
2199 |
2005-02-07 16:11 tim |
| 5175 |
tim |
2102 |
|
| 5176 |
|
|
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
| 5177 |
|
|
help info for Dump2XYZ |
| 5178 |
|
|
|
| 5179 |
gezelter |
2199 |
2005-02-07 15:39 chrisfen |
| 5180 |
tim |
2102 |
|
| 5181 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 5182 |
|
|
selection librarys added |
| 5183 |
|
|
|
| 5184 |
gezelter |
2199 |
2005-02-07 15:31 tim |
| 5185 |
tim |
2102 |
|
| 5186 |
|
|
* src/selection/Makefile, make/Makefile.in: adding Makefile |
| 5187 |
|
|
|
| 5188 |
gezelter |
2199 |
2005-02-07 15:20 chrisfen |
| 5189 |
tim |
2102 |
|
| 5190 |
|
|
* src/utils/wildcards.hpp: issue commented out in wildcards |
| 5191 |
|
|
|
| 5192 |
gezelter |
2199 |
2005-02-07 15:06 tim |
| 5193 |
tim |
2102 |
|
| 5194 |
|
|
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
| 5195 |
|
|
which cause reevaluate return NULL |
| 5196 |
|
|
|
| 5197 |
gezelter |
2199 |
2005-02-07 14:14 tim |
| 5198 |
tim |
2102 |
|
| 5199 |
|
|
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
| 5200 |
|
|
SimSnapshotManager.hpp: fix a bug in determing the global index for |
| 5201 |
|
|
rigidbodies |
| 5202 |
|
|
|
| 5203 |
gezelter |
2199 |
2005-02-07 14:13 tim |
| 5204 |
tim |
2102 |
|
| 5205 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
| 5206 |
|
|
in Bitset |
| 5207 |
|
|
|
| 5208 |
gezelter |
2199 |
2005-02-07 14:13 tim |
| 5209 |
tim |
2102 |
|
| 5210 |
|
|
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
| 5211 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 5212 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
| 5213 |
|
|
TokenMap.cpp: selection library is working |
| 5214 |
|
|
|
| 5215 |
gezelter |
2199 |
2005-02-04 17:46 tim |
| 5216 |
tim |
2102 |
|
| 5217 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
| 5218 |
|
|
|
| 5219 |
gezelter |
2199 |
2005-02-04 17:45 tim |
| 5220 |
tim |
2102 |
|
| 5221 |
|
|
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
| 5222 |
|
|
and XYZVisitor now use selection library |
| 5223 |
|
|
|
| 5224 |
gezelter |
2199 |
2005-02-04 17:44 tim |
| 5225 |
tim |
2102 |
|
| 5226 |
|
|
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
| 5227 |
|
|
adding SelectionManager into SimInfo |
| 5228 |
|
|
|
| 5229 |
gezelter |
2199 |
2005-02-04 17:43 tim |
| 5230 |
tim |
2102 |
|
| 5231 |
|
|
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
| 5232 |
|
|
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
| 5233 |
|
|
selection library |
| 5234 |
|
|
|
| 5235 |
gezelter |
2199 |
2005-02-04 17:42 tim |
| 5236 |
tim |
2102 |
|
| 5237 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
| 5238 |
|
|
in BitSet |
| 5239 |
|
|
|
| 5240 |
gezelter |
2199 |
2005-02-04 17:41 tim |
| 5241 |
tim |
2102 |
|
| 5242 |
|
|
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
| 5243 |
|
|
implementation |
| 5244 |
|
|
|
| 5245 |
gezelter |
2199 |
2005-02-04 17:39 tim |
| 5246 |
tim |
2102 |
|
| 5247 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 5248 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 5249 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
| 5250 |
|
|
SelectionManager.hpp, Token.hpp: half of the selection utility is |
| 5251 |
|
|
working need to debug within keyword and atomproperty keyword |
| 5252 |
|
|
|
| 5253 |
gezelter |
2199 |
2005-02-04 00:42 tim |
| 5254 |
tim |
2102 |
|
| 5255 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
| 5256 |
|
|
get built |
| 5257 |
|
|
|
| 5258 |
gezelter |
2199 |
2005-02-04 00:42 tim |
| 5259 |
tim |
2102 |
|
| 5260 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
| 5261 |
|
|
|
| 5262 |
gezelter |
2199 |
2005-02-04 00:26 tim |
| 5263 |
tim |
2102 |
|
| 5264 |
|
|
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
| 5265 |
|
|
remove some useless files |
| 5266 |
|
|
|
| 5267 |
gezelter |
2199 |
2005-02-03 23:57 tim |
| 5268 |
tim |
2102 |
|
| 5269 |
|
|
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
| 5270 |
|
|
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
| 5271 |
|
|
adding wildcard class; NameFinder is finished |
| 5272 |
|
|
|
| 5273 |
gezelter |
2199 |
2005-02-03 18:14 tim |
| 5274 |
tim |
2102 |
|
| 5275 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
| 5276 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 5277 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
| 5278 |
|
|
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
| 5279 |
|
|
selection library |
| 5280 |
|
|
|
| 5281 |
gezelter |
2199 |
2005-02-03 09:04 tim |
| 5282 |
tim |
2102 |
|
| 5283 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
| 5284 |
|
|
selection in progress |
| 5285 |
|
|
|
| 5286 |
gezelter |
2199 |
2005-02-02 18:13 tim |
| 5287 |
tim |
2102 |
|
| 5288 |
|
|
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
| 5289 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
| 5290 |
|
|
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
| 5291 |
|
|
progress, except SelectionEvaluator, other files are compiled |
| 5292 |
|
|
|
| 5293 |
gezelter |
2199 |
2005-02-02 18:12 tim |
| 5294 |
tim |
2102 |
|
| 5295 |
|
|
* src/utils/: Makefile.in, any.hpp: adding boost::any |
| 5296 |
|
|
|
| 5297 |
gezelter |
2199 |
2005-02-02 07:51 tim |
| 5298 |
tim |
2102 |
|
| 5299 |
|
|
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
| 5300 |
|
|
|
| 5301 |
gezelter |
2199 |
2005-02-01 17:49 tim |
| 5302 |
tim |
2102 |
|
| 5303 |
|
|
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
| 5304 |
|
|
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
| 5305 |
|
|
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
| 5306 |
|
|
selection/Token.hpp: Selection in progress |
| 5307 |
|
|
|
| 5308 |
gezelter |
2199 |
2005-02-01 01:55 tim |
| 5309 |
tim |
2102 |
|
| 5310 |
|
|
* src/: selection/SelectionCompiler.hpp, |
| 5311 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 5312 |
|
|
selection/SelectionManager.hpp, selection/Token.hpp, |
| 5313 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
| 5314 |
|
|
|
| 5315 |
gezelter |
2199 |
2005-01-26 10:26 tim |
| 5316 |
tim |
2102 |
|
| 5317 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, |
| 5318 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
| 5319 |
|
|
to add eorWriter |
| 5320 |
|
|
|
| 5321 |
gezelter |
2199 |
2005-01-26 10:15 tim |
| 5322 |
tim |
2102 |
|
| 5323 |
|
|
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
| 5324 |
|
|
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
| 5325 |
|
|
wrong column of electroframe |
| 5326 |
|
|
|
| 5327 |
gezelter |
2199 |
2005-01-25 16:59 tim |
| 5328 |
tim |
2102 |
|
| 5329 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
| 5330 |
|
|
SimInfo, use number of cutoff stamp as counter to loop over |
| 5331 |
|
|
rigidbody stamp |
| 5332 |
|
|
|
| 5333 |
gezelter |
2199 |
2005-01-25 12:45 tim |
| 5334 |
tim |
2102 |
|
| 5335 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 5336 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 5337 |
|
|
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
| 5338 |
|
|
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
| 5339 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
| 5340 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
| 5341 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
| 5342 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
| 5343 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
| 5344 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 5345 |
|
|
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
| 5346 |
|
|
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
| 5347 |
|
|
primitives/GhostTorsion.hpp, primitives/Makefile, |
| 5348 |
|
|
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
| 5349 |
|
|
section parser's error message (2) add GhostTorsion (3) accumulate |
| 5350 |
|
|
inertial tensor from the directional atoms before calculate |
| 5351 |
|
|
rigidbody's inertial tensor |
| 5352 |
|
|
|
| 5353 |
gezelter |
2199 |
2005-01-17 17:17 tim |
| 5354 |
tim |
2102 |
|
| 5355 |
|
|
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
| 5356 |
|
|
|
| 5357 |
gezelter |
2199 |
2005-01-17 11:58 tim |
| 5358 |
tim |
2102 |
|
| 5359 |
|
|
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
| 5360 |
|
|
system parameters |
| 5361 |
|
|
|
| 5362 |
gezelter |
2199 |
2005-01-17 11:05 tim |
| 5363 |
tim |
2102 |
|
| 5364 |
|
|
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
| 5365 |
|
|
|
| 5366 |
gezelter |
2199 |
2005-01-14 17:02 tim |
| 5367 |
tim |
2102 |
|
| 5368 |
|
|
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
| 5369 |
|
|
|
| 5370 |
gezelter |
2199 |
2005-01-14 16:37 tim |
| 5371 |
tim |
2102 |
|
| 5372 |
|
|
* forceFields/Makefile: sync Makefile |
| 5373 |
|
|
|
| 5374 |
gezelter |
2199 |
2005-01-14 16:13 gezelter |
| 5375 |
tim |
2102 |
|
| 5376 |
|
|
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
| 5377 |
|
|
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
| 5378 |
|
|
src/applications/dump2Xyz/Makefile, |
| 5379 |
|
|
src/applications/oopse/Makefile, |
| 5380 |
|
|
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
| 5381 |
|
|
src/constraints/Makefile, src/integrators/Makefile, |
| 5382 |
|
|
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
| 5383 |
|
|
src/primitives/Makefile, src/profiling/Makefile, |
| 5384 |
|
|
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
| 5385 |
|
|
src/visitors/Makefile: moved Package variable into subdirectory |
| 5386 |
|
|
makefiles to speed up the building process |
| 5387 |
|
|
|
| 5388 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
| 5389 |
tim |
2102 |
|
| 5390 |
|
|
* src/applications/oopse/oopse.cpp: Fixed publication details in |
| 5391 |
|
|
banner |
| 5392 |
|
|
|
| 5393 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
| 5394 |
tim |
2102 |
|
| 5395 |
|
|
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
| 5396 |
|
|
simParallel_interface.h: added dummy subroutine to avoid empty |
| 5397 |
|
|
unit, synchronized this dummy routine between C and fortran |
| 5398 |
|
|
|
| 5399 |
gezelter |
2199 |
2005-01-14 15:31 gezelter |
| 5400 |
tim |
2102 |
|
| 5401 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
| 5402 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
| 5403 |
|
|
DarkSide/Makefile, DarkSide/atype.F90, |
| 5404 |
|
|
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
| 5405 |
|
|
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
| 5406 |
|
|
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
| 5407 |
|
|
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
| 5408 |
|
|
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
| 5409 |
|
|
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
| 5410 |
|
|
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
| 5411 |
|
|
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
| 5412 |
|
|
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
| 5413 |
|
|
modules and C/Fortran interface subroutines |
| 5414 |
|
|
|
| 5415 |
gezelter |
2199 |
2005-01-14 15:15 gezelter |
| 5416 |
tim |
2102 |
|
| 5417 |
|
|
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
| 5418 |
|
|
|
| 5419 |
gezelter |
2199 |
2005-01-14 15:09 gezelter |
| 5420 |
tim |
2102 |
|
| 5421 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
| 5422 |
|
|
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
| 5423 |
|
|
|
| 5424 |
gezelter |
2199 |
2005-01-14 11:49 tim |
| 5425 |
tim |
2102 |
|
| 5426 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
| 5427 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 5428 |
|
|
utils/StringUtils.hpp: using c library to do conversion instead of |
| 5429 |
|
|
using iostream due to a bug in libstdc++(GCC 3.2) |
| 5430 |
|
|
|
| 5431 |
gezelter |
2199 |
2005-01-13 21:40 tim |
| 5432 |
tim |
2102 |
|
| 5433 |
|
|
* src/brains/SimSetup.cpp: no message |
| 5434 |
|
|
|
| 5435 |
gezelter |
2199 |
2005-01-13 20:56 tim |
| 5436 |
tim |
2102 |
|
| 5437 |
|
|
* src/primitives/Molecule.hpp: fix a bug in global index |
| 5438 |
|
|
|
| 5439 |
gezelter |
2199 |
2005-01-13 20:04 tim |
| 5440 |
tim |
2102 |
|
| 5441 |
|
|
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
| 5442 |
|
|
Integrator.hpp in Minimizer |
| 5443 |
|
|
|
| 5444 |
gezelter |
2199 |
2005-01-13 17:14 gezelter |
| 5445 |
tim |
2102 |
|
| 5446 |
|
|
* src/utils/Makefile: compile getopt and getopt1 if we need to |
| 5447 |
|
|
|
| 5448 |
gezelter |
2199 |
2005-01-13 16:56 gezelter |
| 5449 |
tim |
2102 |
|
| 5450 |
|
|
* make/Makefile.in: template flags |
| 5451 |
|
|
|
| 5452 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
| 5453 |
tim |
2102 |
|
| 5454 |
|
|
* src/applications/oopse/Makefile: formatting |
| 5455 |
|
|
|
| 5456 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
| 5457 |
tim |
2102 |
|
| 5458 |
|
|
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
| 5459 |
|
|
target |
| 5460 |
|
|
|
| 5461 |
gezelter |
2199 |
2005-01-13 14:40 tim |
| 5462 |
tim |
2102 |
|
| 5463 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
| 5464 |
|
|
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
| 5465 |
|
|
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
| 5466 |
|
|
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
| 5467 |
|
|
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
| 5468 |
|
|
|
| 5469 |
gezelter |
2199 |
2005-01-13 13:26 tim |
| 5470 |
tim |
2102 |
|
| 5471 |
|
|
* make/Makefile.in: change the order of linking (object file comes |
| 5472 |
|
|
first and then follow by user built library) |
| 5473 |
|
|
|
| 5474 |
gezelter |
2199 |
2005-01-12 18:24 tim |
| 5475 |
tim |
2102 |
|
| 5476 |
|
|
* src/io/DumpWriter.cpp: remove useless debug info |
| 5477 |
|
|
|
| 5478 |
gezelter |
2199 |
2005-01-12 18:21 tim |
| 5479 |
tim |
2102 |
|
| 5480 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
| 5481 |
|
|
|
| 5482 |
gezelter |
2199 |
2005-01-12 18:17 tim |
| 5483 |
tim |
2102 |
|
| 5484 |
|
|
* make/: Makefile.in, Makefile.in: missing tab |
| 5485 |
|
|
|
| 5486 |
gezelter |
2199 |
2005-01-12 18:15 tim |
| 5487 |
tim |
2102 |
|
| 5488 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
| 5489 |
|
|
get fixed |
| 5490 |
|
|
|
| 5491 |
gezelter |
2199 |
2005-01-12 17:40 gezelter |
| 5492 |
tim |
2102 |
|
| 5493 |
|
|
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
| 5494 |
|
|
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
| 5495 |
|
|
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
| 5496 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
| 5497 |
|
|
src/UseTheForce/ForceFieldCreator.hpp, |
| 5498 |
|
|
src/UseTheForce/ForceFieldFactory.cpp, |
| 5499 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
| 5500 |
|
|
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
| 5501 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
| 5502 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 5503 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
| 5504 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 5505 |
|
|
src/UseTheForce/notifyCutoffs.F90, |
| 5506 |
|
|
src/UseTheForce/notifyCutoffs_interface.h, |
| 5507 |
|
|
src/UseTheForce/DarkSide/LJ.F90, |
| 5508 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
| 5509 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
| 5510 |
|
|
src/UseTheForce/DarkSide/charge.F90, |
| 5511 |
|
|
src/UseTheForce/DarkSide/charge_interface.h, |
| 5512 |
|
|
src/UseTheForce/DarkSide/dipole.F90, |
| 5513 |
|
|
src/UseTheForce/DarkSide/dipole_interface.h, |
| 5514 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
| 5515 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
| 5516 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
| 5517 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
| 5518 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
| 5519 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
| 5520 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 5521 |
|
|
src/UseTheForce/DarkSide/reactionField.F90, |
| 5522 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
| 5523 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
| 5524 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
| 5525 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 5526 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
| 5527 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
| 5528 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
| 5529 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
| 5530 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
| 5531 |
|
|
src/applications/Makedepend, src/applications/quickLate.c, |
| 5532 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 5533 |
|
|
src/applications/oopse/oopse.cpp, |
| 5534 |
|
|
src/applications/simpleBuilder/BaseLattice.cpp, |
| 5535 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
| 5536 |
|
|
src/applications/simpleBuilder/Lattice.cpp, |
| 5537 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
| 5538 |
|
|
src/applications/simpleBuilder/LatticeCreator.cpp, |
| 5539 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
| 5540 |
|
|
src/applications/simpleBuilder/LatticeFactory.cpp, |
| 5541 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
| 5542 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
| 5543 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
| 5544 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 5545 |
|
|
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
| 5546 |
|
|
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
| 5547 |
|
|
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
| 5548 |
|
|
src/brains/Makefile, src/brains/Migrator.hpp, |
| 5549 |
|
|
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
| 5550 |
|
|
src/brains/Register.cpp, src/brains/Register.hpp, |
| 5551 |
|
|
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
| 5552 |
|
|
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
| 5553 |
|
|
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
| 5554 |
|
|
src/brains/SimSnapshotManager.cpp, |
| 5555 |
|
|
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
| 5556 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 5557 |
|
|
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
| 5558 |
|
|
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
| 5559 |
|
|
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
| 5560 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 5561 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 5562 |
|
|
src/constraints/AbstractClasses.hpp, |
| 5563 |
|
|
src/constraints/ConstraintElem.hpp, |
| 5564 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
| 5565 |
|
|
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
| 5566 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 5567 |
|
|
src/constraints/ZconsStruct.hpp, |
| 5568 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
| 5569 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
| 5570 |
|
|
src/integrators/AbstractClasses.hpp, |
| 5571 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
| 5572 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
| 5573 |
|
|
src/integrators/Integrator.hpp, |
| 5574 |
|
|
src/integrators/IntegratorCreator.hpp, |
| 5575 |
|
|
src/integrators/IntegratorFactory.cpp, |
| 5576 |
|
|
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
| 5577 |
|
|
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
| 5578 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
| 5579 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
| 5580 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
| 5581 |
|
|
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
| 5582 |
|
|
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
| 5583 |
|
|
src/integrators/RotationAlgorithm.hpp, |
| 5584 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
| 5585 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
| 5586 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
| 5587 |
|
|
src/io/AtomTypesSectionParser.cpp, |
| 5588 |
|
|
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
| 5589 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 5590 |
|
|
src/io/BendTypesSectionParser.cpp, |
| 5591 |
|
|
src/io/BendTypesSectionParser.hpp, |
| 5592 |
|
|
src/io/BondTypesSectionParser.cpp, |
| 5593 |
|
|
src/io/BondTypesSectionParser.hpp, |
| 5594 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
| 5595 |
|
|
src/io/DirectionalAtomTypesSectionParser.hpp, |
| 5596 |
|
|
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
| 5597 |
|
|
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
| 5598 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
| 5599 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, |
| 5600 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
| 5601 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
| 5602 |
|
|
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
| 5603 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
| 5604 |
|
|
src/io/LennardJonesAtomTypesSectionParser.hpp, |
| 5605 |
|
|
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
| 5606 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 5607 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
| 5608 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 5609 |
|
|
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
| 5610 |
|
|
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
| 5611 |
|
|
src/io/StickyAtomTypesSectionParser.hpp, |
| 5612 |
|
|
src/io/TorsionTypesSectionParser.cpp, |
| 5613 |
|
|
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
| 5614 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 5615 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
| 5616 |
|
|
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
| 5617 |
|
|
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
| 5618 |
|
|
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
| 5619 |
|
|
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
| 5620 |
|
|
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
| 5621 |
|
|
src/math/MatVec3.h, src/math/Polynomial.hpp, |
| 5622 |
|
|
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
| 5623 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
| 5624 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 5625 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 5626 |
|
|
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
| 5627 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
| 5628 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
| 5629 |
|
|
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
| 5630 |
|
|
src/minimizers/MinimizerCreator.hpp, |
| 5631 |
|
|
src/minimizers/MinimizerFactory.cpp, |
| 5632 |
|
|
src/minimizers/MinimizerFactory.hpp, |
| 5633 |
|
|
src/minimizers/MinimizerParameterSet.cpp, |
| 5634 |
|
|
src/minimizers/MinimizerParameterSet.hpp, |
| 5635 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
| 5636 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 5637 |
|
|
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
| 5638 |
|
|
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
| 5639 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 5640 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
| 5641 |
|
|
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
| 5642 |
|
|
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
| 5643 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 5644 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 5645 |
|
|
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
| 5646 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
| 5647 |
|
|
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
| 5648 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
| 5649 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
| 5650 |
|
|
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
| 5651 |
|
|
src/primitives/UreyBradleyBend.cpp, |
| 5652 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
| 5653 |
|
|
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
| 5654 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
| 5655 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
| 5656 |
|
|
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
| 5657 |
|
|
src/types/BendType.hpp, src/types/BondStamp.cpp, |
| 5658 |
|
|
src/types/BondStamp.hpp, src/types/BondType.hpp, |
| 5659 |
|
|
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
| 5660 |
|
|
src/types/Component.cpp, src/types/Component.hpp, |
| 5661 |
|
|
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
| 5662 |
|
|
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
| 5663 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
| 5664 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
| 5665 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
| 5666 |
|
|
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
| 5667 |
|
|
src/types/Makefile, src/types/MoleculeStamp.cpp, |
| 5668 |
|
|
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
| 5669 |
|
|
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
| 5670 |
|
|
src/types/PolynomialBondType.hpp, |
| 5671 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
| 5672 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
| 5673 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 5674 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
| 5675 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 5676 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
| 5677 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 5678 |
|
|
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
| 5679 |
|
|
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
| 5680 |
|
|
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
| 5681 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
| 5682 |
|
|
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
| 5683 |
|
|
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
| 5684 |
|
|
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
| 5685 |
|
|
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
| 5686 |
|
|
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
| 5687 |
|
|
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
| 5688 |
|
|
src/utils/Utility.cpp, src/utils/Utility.hpp, |
| 5689 |
|
|
src/utils/definitions.F90, src/utils/fError.c, |
| 5690 |
|
|
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
| 5691 |
|
|
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
| 5692 |
|
|
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
| 5693 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 5694 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 5695 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 5696 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 5697 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 5698 |
|
|
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
| 5699 |
|
|
OOPSE-2.0 |
| 5700 |
|
|
|
| 5701 |
gezelter |
2199 |
2005-01-12 13:13 tim |
| 5702 |
tim |
2102 |
|
| 5703 |
|
|
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
| 5704 |
|
|
utils/TypeContainer.hpp: forget to include <algorithm> |
| 5705 |
|
|
|
| 5706 |
gezelter |
2199 |
2005-01-12 12:25 tim |
| 5707 |
tim |
2102 |
|
| 5708 |
|
|
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
| 5709 |
|
|
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
| 5710 |
|
|
fields |
| 5711 |
|
|
|
| 5712 |
gezelter |
2199 |
2005-01-12 12:14 tim |
| 5713 |
tim |
2102 |
|
| 5714 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 5715 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
| 5716 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 5717 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
| 5718 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
| 5719 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 5720 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
| 5721 |
|
|
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
| 5722 |
|
|
UseTheForce/notifyCutoffs.F90, |
| 5723 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 5724 |
|
|
UseTheForce/DarkSide/atype.F90, |
| 5725 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
| 5726 |
|
|
UseTheForce/DarkSide/charge.F90, |
| 5727 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
| 5728 |
|
|
UseTheForce/DarkSide/dipole.F90, |
| 5729 |
|
|
UseTheForce/DarkSide/dipole_interface.h, |
| 5730 |
|
|
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
| 5731 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
| 5732 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 5733 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
| 5734 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
| 5735 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
| 5736 |
|
|
UseTheForce/DarkSide/shapes.F90, |
| 5737 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
| 5738 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
| 5739 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
| 5740 |
|
|
UseTheForce/DarkSide/simulation.F90, |
| 5741 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
| 5742 |
|
|
UseTheForce/DarkSide/sticky.F90, |
| 5743 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
| 5744 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
| 5745 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 5746 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
| 5747 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
| 5748 |
|
|
applications/simpleBuilder/Lattice.cpp, |
| 5749 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 5750 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
| 5751 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 5752 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 5753 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 5754 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
| 5755 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
| 5756 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 5757 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 5758 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 5759 |
|
|
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
| 5760 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 5761 |
|
|
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
| 5762 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 5763 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 5764 |
|
|
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
| 5765 |
|
|
brains/Snapshot.cpp, brains/Snapshot.hpp, |
| 5766 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
| 5767 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
| 5768 |
|
|
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
| 5769 |
|
|
constraints/Rattle.cpp, constraints/Rattle.hpp, |
| 5770 |
|
|
constraints/ZconsStruct.hpp, |
| 5771 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 5772 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 5773 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 5774 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 5775 |
|
|
integrators/IntegratorFactory.cpp, |
| 5776 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 5777 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 5778 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 5779 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 5780 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
| 5781 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 5782 |
|
|
integrators/Velocitizer.hpp, |
| 5783 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 5784 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
| 5785 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 5786 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 5787 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 5788 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 5789 |
|
|
io/BondTypesSectionParser.hpp, |
| 5790 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 5791 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 5792 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 5793 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 5794 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 5795 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
| 5796 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
| 5797 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 5798 |
|
|
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
| 5799 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
| 5800 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 5801 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
| 5802 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
| 5803 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
| 5804 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 5805 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 5806 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
| 5807 |
|
|
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
| 5808 |
|
|
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 5809 |
|
|
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
| 5810 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 5811 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, |
| 5812 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 5813 |
|
|
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
| 5814 |
|
|
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
| 5815 |
|
|
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
| 5816 |
|
|
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
| 5817 |
|
|
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
| 5818 |
|
|
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
| 5819 |
|
|
minimizers/MinimizerParameterSet.cpp, |
| 5820 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 5821 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 5822 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 5823 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 5824 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 5825 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 5826 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 5827 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 5828 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 5829 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 5830 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 5831 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 5832 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 5833 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
| 5834 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
| 5835 |
|
|
types/AtomType.hpp, types/AtomTypeProperties.h, |
| 5836 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 5837 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 5838 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 5839 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 5840 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 5841 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 5842 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
| 5843 |
|
|
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
| 5844 |
|
|
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
| 5845 |
|
|
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
| 5846 |
|
|
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
| 5847 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
| 5848 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
| 5849 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
| 5850 |
|
|
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
| 5851 |
|
|
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
| 5852 |
|
|
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
| 5853 |
|
|
types/TorsionStamp.hpp, types/TorsionType.hpp, |
| 5854 |
|
|
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
| 5855 |
|
|
types/ZconStamp.hpp, utils/GenericData.hpp, |
| 5856 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 5857 |
|
|
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
| 5858 |
|
|
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
| 5859 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
| 5860 |
|
|
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
| 5861 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 5862 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 5863 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
| 5864 |
|
|
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
| 5865 |
|
|
utils/simError.c, utils/simError.h, utils/status.F90, |
| 5866 |
|
|
utils/vector_class.F90, visitors/AtomData.hpp, |
| 5867 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
| 5868 |
|
|
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 5869 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 5870 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 5871 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 5872 |
|
|
visitors/ZconsVisitor.hpp: change license |
| 5873 |
|
|
|
| 5874 |
gezelter |
2199 |
2005-01-12 12:14 tim |
| 5875 |
tim |
2102 |
|
| 5876 |
|
|
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
| 5877 |
|
|
branch new_design. |
| 5878 |
|
|
|
| 5879 |
gezelter |
2199 |
2005-01-11 16:03 tim |
| 5880 |
tim |
2102 |
|
| 5881 |
|
|
* src/: constraints/ZconstraintForceManager.cpp, |
| 5882 |
|
|
constraints/ZconstraintForceManager.hpp, |
| 5883 |
|
|
minimizers/MinimizerParameterSet.cpp, |
| 5884 |
|
|
minimizers/MinimizerParameterSet.hpp: change const static double |
| 5885 |
|
|
data member to const double |
| 5886 |
|
|
|
| 5887 |
gezelter |
2199 |
2005-01-11 15:50 tim |
| 5888 |
tim |
2102 |
|
| 5889 |
|
|
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
| 5890 |
|
|
|
| 5891 |
gezelter |
2199 |
2005-01-11 15:39 tim |
| 5892 |
tim |
2102 |
|
| 5893 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
| 5894 |
|
|
change data type from logical to integer in AtomTypeProperties.h |
| 5895 |
|
|
|
| 5896 |
gezelter |
2199 |
2005-01-11 11:36 tim |
| 5897 |
tim |
2102 |
|
| 5898 |
|
|
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
| 5899 |
|
|
new format of EAM force field |
| 5900 |
|
|
|
| 5901 |
gezelter |
2199 |
2005-01-11 11:24 tim |
| 5902 |
tim |
2102 |
|
| 5903 |
|
|
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
| 5904 |
|
|
to DUFF2.frc |
| 5905 |
|
|
|
| 5906 |
gezelter |
2199 |
2005-01-11 11:23 tim |
| 5907 |
tim |
2102 |
|
| 5908 |
|
|
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
| 5909 |
|
|
DUFF2.frc |
| 5910 |
|
|
|
| 5911 |
gezelter |
2199 |
2005-01-11 11:09 tim |
| 5912 |
tim |
2102 |
|
| 5913 |
|
|
* make/Makefile.in: adding constraints and minimizers into |
| 5914 |
|
|
Makefile.in |
| 5915 |
|
|
|
| 5916 |
gezelter |
2199 |
2005-01-11 11:03 tim |
| 5917 |
tim |
2102 |
|
| 5918 |
|
|
* src/io/: ChargeAtomTypesSectionParser.cpp, |
| 5919 |
|
|
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
| 5920 |
|
|
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
| 5921 |
|
|
files |
| 5922 |
|
|
|
| 5923 |
gezelter |
2199 |
2005-01-11 10:59 tim |
| 5924 |
tim |
2102 |
|
| 5925 |
|
|
* src/io/ZConsWriter.cpp: [no log message] |
| 5926 |
|
|
|
| 5927 |
gezelter |
2199 |
2005-01-11 10:53 tim |
| 5928 |
tim |
2102 |
|
| 5929 |
|
|
* src/UseTheForce/EAM.cpp: minor fix |
| 5930 |
|
|
|
| 5931 |
gezelter |
2199 |
2005-01-11 10:52 tim |
| 5932 |
tim |
2102 |
|
| 5933 |
tim |
2116 |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
| 5934 |
|
|
on branch new_design. |
| 5935 |
|
|
|
| 5936 |
gezelter |
2199 |
2005-01-11 10:52 tim |
| 5937 |
tim |
2116 |
|
| 5938 |
tim |
2102 |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
| 5939 |
|
|
on branch new_design. |
| 5940 |
|
|
|
| 5941 |
gezelter |
2199 |
2005-01-11 10:52 tim |
| 5942 |
tim |
2102 |
|
| 5943 |
|
|
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
| 5944 |
|
|
|
| 5945 |
gezelter |
2199 |
2005-01-11 10:47 tim |
| 5946 |
tim |
2102 |
|
| 5947 |
|
|
* make/Makefile.in: forget a '$' sign |
| 5948 |
|
|
|
| 5949 |
gezelter |
2199 |
2005-01-11 10:46 tim |
| 5950 |
tim |
2102 |
|
| 5951 |
|
|
* make/Makefile.in: missing tab in rules |
| 5952 |
|
|
|
| 5953 |
gezelter |
2199 |
2005-01-10 17:04 tim |
| 5954 |
tim |
2102 |
|
| 5955 |
|
|
* src/: UseTheForce/ForceFieldCreator.cpp, |
| 5956 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
| 5957 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
| 5958 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
| 5959 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 5960 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
| 5961 |
|
|
brains/Register.cpp, brains/Register.hpp, |
| 5962 |
|
|
integrators/IntegratorCreator.cpp, |
| 5963 |
|
|
integrators/IntegratorCreator.hpp, |
| 5964 |
|
|
integrators/IntegratorFactory.cpp, |
| 5965 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 5966 |
|
|
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 5967 |
|
|
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
| 5968 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 5969 |
|
|
minimizers/MinimizerFactory.hpp: create a register module to |
| 5970 |
|
|
register force fields, integrators and minimizers |
| 5971 |
|
|
|
| 5972 |
gezelter |
2199 |
2005-01-10 17:04 tim |
| 5973 |
tim |
2102 |
|
| 5974 |
|
|
* src/brains/Register.cpp: file Register.cpp was initially added on |
| 5975 |
|
|
branch new_design. |
| 5976 |
|
|
|
| 5977 |
gezelter |
2199 |
2005-01-10 17:04 tim |
| 5978 |
tim |
2102 |
|
| 5979 |
|
|
* src/brains/Register.hpp: file Register.hpp was initially added on |
| 5980 |
|
|
branch new_design. |
| 5981 |
|
|
|
| 5982 |
gezelter |
2199 |
2005-01-10 15:52 tim |
| 5983 |
tim |
2102 |
|
| 5984 |
|
|
* src/: UseTheForce/ForceFieldFactory.cpp, |
| 5985 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
| 5986 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 5987 |
|
|
constraints/ZconstraintForceManager.hpp, |
| 5988 |
|
|
integrators/IntegratorFactory.cpp, |
| 5989 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
| 5990 |
|
|
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
| 5991 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
| 5992 |
|
|
method is working now |
| 5993 |
|
|
|
| 5994 |
gezelter |
2199 |
2005-01-10 13:05 tim |
| 5995 |
tim |
2102 |
|
| 5996 |
|
|
* src/: constraints/ConstraintElem.hpp, |
| 5997 |
|
|
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
| 5998 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 5999 |
|
|
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
| 6000 |
|
|
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
| 6001 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
| 6002 |
|
|
zconstraint |
| 6003 |
|
|
|
| 6004 |
gezelter |
2199 |
2005-01-10 13:05 tim |
| 6005 |
tim |
2102 |
|
| 6006 |
|
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
| 6007 |
|
|
initially added on branch new_design. |
| 6008 |
|
|
|
| 6009 |
gezelter |
2199 |
2005-01-07 16:50 tim |
| 6010 |
tim |
2102 |
|
| 6011 |
tim |
2116 |
* src/constraints/ZconstraintForceManager.cpp: file |
| 6012 |
|
|
ZconstraintForceManager.cpp was initially added on branch |
| 6013 |
|
|
new_design. |
| 6014 |
|
|
|
| 6015 |
gezelter |
2199 |
2005-01-07 16:50 tim |
| 6016 |
tim |
2116 |
|
| 6017 |
|
|
* src/constraints/ZconstraintForceManager.hpp: file |
| 6018 |
|
|
ZconstraintForceManager.hpp was initially added on branch |
| 6019 |
|
|
new_design. |
| 6020 |
|
|
|
| 6021 |
gezelter |
2199 |
2005-01-07 16:50 tim |
| 6022 |
tim |
2116 |
|
| 6023 |
tim |
2102 |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
| 6024 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 6025 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 6026 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6027 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
| 6028 |
|
|
constraints/ConstraintElem.hpp, constraints/Makefile, |
| 6029 |
|
|
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
| 6030 |
|
|
constraints/ZconstraintForceManager.cpp, |
| 6031 |
|
|
constraints/ZconstraintForceManager.hpp, |
| 6032 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
| 6033 |
|
|
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
| 6034 |
|
|
|
| 6035 |
gezelter |
2199 |
2005-01-07 16:50 tim |
| 6036 |
tim |
2102 |
|
| 6037 |
|
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
| 6038 |
|
|
initially added on branch new_design. |
| 6039 |
|
|
|
| 6040 |
gezelter |
2199 |
2005-01-06 17:31 tim |
| 6041 |
tim |
2102 |
|
| 6042 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 6043 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6044 |
|
|
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
| 6045 |
|
|
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 6046 |
|
|
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
| 6047 |
|
|
constraint is almost working |
| 6048 |
|
|
|
| 6049 |
gezelter |
2199 |
2005-01-05 19:36 tim |
| 6050 |
tim |
2102 |
|
| 6051 |
|
|
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
| 6052 |
|
|
working |
| 6053 |
|
|
|
| 6054 |
gezelter |
2199 |
2005-01-05 19:16 tim |
| 6055 |
tim |
2102 |
|
| 6056 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 6057 |
|
|
applications/oopse/oopse.cpp, |
| 6058 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
| 6059 |
|
|
applications/simpleBuilder/Lattice.cpp, |
| 6060 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6061 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6062 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
| 6063 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
| 6064 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 6065 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
| 6066 |
|
|
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
| 6067 |
|
|
in progress |
| 6068 |
|
|
|
| 6069 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6070 |
tim |
2102 |
|
| 6071 |
|
|
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
| 6072 |
|
|
was initially added on branch new_design. |
| 6073 |
|
|
|
| 6074 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6075 |
tim |
2102 |
|
| 6076 |
tim |
2116 |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
| 6077 |
|
|
added on branch new_design. |
| 6078 |
|
|
|
| 6079 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6080 |
tim |
2116 |
|
| 6081 |
tim |
2102 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 6082 |
|
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
| 6083 |
|
|
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
| 6084 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
| 6085 |
|
|
SDMinimizer.hpp: minimizer in progress |
| 6086 |
|
|
|
| 6087 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6088 |
tim |
2102 |
|
| 6089 |
tim |
2116 |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
| 6090 |
|
|
was initially added on branch new_design. |
| 6091 |
tim |
2102 |
|
| 6092 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6093 |
tim |
2102 |
|
| 6094 |
tim |
2116 |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
| 6095 |
tim |
2102 |
was initially added on branch new_design. |
| 6096 |
|
|
|
| 6097 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6098 |
tim |
2102 |
|
| 6099 |
tim |
2116 |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
| 6100 |
tim |
2102 |
was initially added on branch new_design. |
| 6101 |
|
|
|
| 6102 |
gezelter |
2199 |
2005-01-05 12:35 tim |
| 6103 |
tim |
2102 |
|
| 6104 |
|
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
| 6105 |
|
|
added on branch new_design. |
| 6106 |
|
|
|
| 6107 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6108 |
tim |
2102 |
|
| 6109 |
|
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
| 6110 |
|
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
| 6111 |
|
|
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
| 6112 |
|
|
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
| 6113 |
|
|
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 6114 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
| 6115 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
| 6116 |
|
|
progress |
| 6117 |
|
|
|
| 6118 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6119 |
tim |
2102 |
|
| 6120 |
tim |
2116 |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
| 6121 |
|
|
initially added on branch new_design. |
| 6122 |
tim |
2102 |
|
| 6123 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6124 |
tim |
2102 |
|
| 6125 |
|
|
* src/minimizers/MinimizerParameterSet.cpp: file |
| 6126 |
|
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
| 6127 |
|
|
|
| 6128 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6129 |
tim |
2102 |
|
| 6130 |
|
|
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
| 6131 |
|
|
initially added on branch new_design. |
| 6132 |
|
|
|
| 6133 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6134 |
tim |
2102 |
|
| 6135 |
tim |
2116 |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
| 6136 |
|
|
was initially added on branch new_design. |
| 6137 |
|
|
|
| 6138 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6139 |
tim |
2116 |
|
| 6140 |
|
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 6141 |
|
|
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
| 6142 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
| 6143 |
|
|
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
| 6144 |
|
|
|
| 6145 |
gezelter |
2199 |
2005-01-04 17:18 tim |
| 6146 |
tim |
2116 |
|
| 6147 |
tim |
2102 |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
| 6148 |
|
|
branch new_design. |
| 6149 |
|
|
|
| 6150 |
gezelter |
2199 |
2004-12-20 15:50 chuckv |
| 6151 |
tim |
2102 |
|
| 6152 |
|
|
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
| 6153 |
|
|
other BSD's, replaced test -f *.mod with ls function since BSD test |
| 6154 |
|
|
apparently doesn't support wildcards. |
| 6155 |
|
|
|
| 6156 |
gezelter |
2199 |
2004-12-20 15:36 tim |
| 6157 |
tim |
2102 |
|
| 6158 |
|
|
* make/Makefile.in: fix a test command incompatiable problem |
| 6159 |
|
|
|
| 6160 |
gezelter |
2199 |
2004-12-20 14:49 tim |
| 6161 |
tim |
2102 |
|
| 6162 |
|
|
* src/integrators/NPTi.cpp: NPT is working now |
| 6163 |
|
|
|
| 6164 |
gezelter |
2199 |
2004-12-16 14:20 tim |
| 6165 |
tim |
2102 |
|
| 6166 |
|
|
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
| 6167 |
|
|
invalid stamp id |
| 6168 |
|
|
|
| 6169 |
gezelter |
2199 |
2004-12-16 14:00 tim |
| 6170 |
tim |
2102 |
|
| 6171 |
|
|
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
| 6172 |
|
|
newEAM.u6.frc: adding new EAM force field files |
| 6173 |
|
|
|
| 6174 |
gezelter |
2199 |
2004-12-16 13:55 tim |
| 6175 |
tim |
2102 |
|
| 6176 |
|
|
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
| 6177 |
|
|
in EAM parameter file is incorrect |
| 6178 |
|
|
|
| 6179 |
gezelter |
2199 |
2004-12-16 12:27 tim |
| 6180 |
tim |
2102 |
|
| 6181 |
|
|
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
| 6182 |
|
|
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
| 6183 |
|
|
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
| 6184 |
|
|
|
| 6185 |
gezelter |
2199 |
2004-12-15 17:34 tim |
| 6186 |
tim |
2102 |
|
| 6187 |
|
|
* src/: applications/simpleBuilder/BaseLattice.cpp, |
| 6188 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
| 6189 |
|
|
applications/simpleBuilder/Lattice.cpp, |
| 6190 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 6191 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
| 6192 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 6193 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6194 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6195 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 6196 |
|
|
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
| 6197 |
|
|
|
| 6198 |
gezelter |
2199 |
2004-12-15 16:07 tim |
| 6199 |
tim |
2102 |
|
| 6200 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 6201 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
| 6202 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
| 6203 |
|
|
add EAM Force Field |
| 6204 |
|
|
|
| 6205 |
gezelter |
2199 |
2004-12-15 14:40 tim |
| 6206 |
tim |
2102 |
|
| 6207 |
|
|
* src/applications/oopse/oopse.cpp: add more force fields |
| 6208 |
|
|
|
| 6209 |
gezelter |
2199 |
2004-12-15 11:44 tim |
| 6210 |
tim |
2102 |
|
| 6211 |
|
|
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
| 6212 |
|
|
to call All_reduce in MPI version) |
| 6213 |
|
|
|
| 6214 |
gezelter |
2199 |
2004-12-15 11:13 tim |
| 6215 |
tim |
2102 |
|
| 6216 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
| 6217 |
|
|
io/DumpReader.cpp: MPI in NVE is working |
| 6218 |
|
|
|
| 6219 |
gezelter |
2199 |
2004-12-14 16:57 tim |
| 6220 |
tim |
2102 |
|
| 6221 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
| 6222 |
|
|
Master nodes does not brocast the total number of frames |
| 6223 |
|
|
|
| 6224 |
gezelter |
2199 |
2004-12-14 14:08 tim |
| 6225 |
tim |
2102 |
|
| 6226 |
|
|
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
| 6227 |
|
|
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 6228 |
|
|
minimizers/CGFamilyMinimizer.cpp, |
| 6229 |
|
|
minimizers/MinimizerParameterSet.hpp, |
| 6230 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
| 6231 |
|
|
minimizers/SDMinimizer.cpp: more fix in MPI version |
| 6232 |
|
|
|
| 6233 |
gezelter |
2199 |
2004-12-13 17:30 tim |
| 6234 |
tim |
2102 |
|
| 6235 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, |
| 6236 |
|
|
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
| 6237 |
|
|
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
| 6238 |
|
|
integrators/DLM.cpp, integrators/Integrator.cpp, |
| 6239 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
| 6240 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
| 6241 |
|
|
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
| 6242 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
| 6243 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
| 6244 |
|
|
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
| 6245 |
|
|
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
| 6246 |
|
|
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
| 6247 |
|
|
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
| 6248 |
|
|
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
| 6249 |
|
|
is built |
| 6250 |
|
|
|
| 6251 |
gezelter |
2199 |
2004-12-10 13:41 tim |
| 6252 |
tim |
2102 |
|
| 6253 |
|
|
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
| 6254 |
|
|
|
| 6255 |
gezelter |
2199 |
2004-12-10 11:14 tim |
| 6256 |
tim |
2102 |
|
| 6257 |
|
|
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
| 6258 |
|
|
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
| 6259 |
|
|
and Dipole is working now |
| 6260 |
|
|
|
| 6261 |
gezelter |
2199 |
2004-12-09 18:15 tim |
| 6262 |
tim |
2102 |
|
| 6263 |
|
|
* src/: UseTheForce/DarkSide/dipole.F90, |
| 6264 |
|
|
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
| 6265 |
|
|
fix an index problem in eFrame matrix |
| 6266 |
|
|
|
| 6267 |
gezelter |
2199 |
2004-12-09 18:09 tim |
| 6268 |
tim |
2102 |
|
| 6269 |
|
|
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
| 6270 |
|
|
initializing the new Charge AtomType |
| 6271 |
|
|
|
| 6272 |
gezelter |
2199 |
2004-12-09 16:15 tim |
| 6273 |
tim |
2102 |
|
| 6274 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
| 6275 |
|
|
types/DirectionalAtomType.cpp: sticky module get compiled |
| 6276 |
|
|
|
| 6277 |
gezelter |
2199 |
2004-12-09 15:43 gezelter |
| 6278 |
tim |
2102 |
|
| 6279 |
|
|
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
| 6280 |
|
|
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
| 6281 |
|
|
GB |
| 6282 |
|
|
|
| 6283 |
gezelter |
2199 |
2004-12-09 15:42 gezelter |
| 6284 |
tim |
2102 |
|
| 6285 |
|
|
* src/UseTheForce/doForces.F90: u_l -> eFrame |
| 6286 |
|
|
|
| 6287 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
| 6288 |
tim |
2102 |
|
| 6289 |
|
|
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
| 6290 |
|
|
module now has the option for multiple sticky types |
| 6291 |
|
|
|
| 6292 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
| 6293 |
tim |
2102 |
|
| 6294 |
|
|
* src/UseTheForce/doForces.F90: sticky |
| 6295 |
|
|
|
| 6296 |
gezelter |
2199 |
2004-12-09 11:22 tim |
| 6297 |
tim |
2102 |
|
| 6298 |
|
|
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
| 6299 |
|
|
inconsistency in lab2Bidy |
| 6300 |
|
|
|
| 6301 |
gezelter |
2199 |
2004-12-09 10:45 tim |
| 6302 |
tim |
2102 |
|
| 6303 |
|
|
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
| 6304 |
|
|
in calculating torque in rigid body |
| 6305 |
|
|
|
| 6306 |
gezelter |
2199 |
2004-12-08 15:37 tim |
| 6307 |
tim |
2102 |
|
| 6308 |
|
|
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
| 6309 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, |
| 6310 |
|
|
integrators/Integrator.cpp, |
| 6311 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
| 6312 |
|
|
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
| 6313 |
|
|
|
| 6314 |
gezelter |
2199 |
2004-12-08 12:03 tim |
| 6315 |
tim |
2102 |
|
| 6316 |
|
|
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
| 6317 |
|
|
in NVT is working |
| 6318 |
|
|
|
| 6319 |
gezelter |
2199 |
2004-12-07 18:08 tim |
| 6320 |
tim |
2102 |
|
| 6321 |
|
|
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
| 6322 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
| 6323 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
| 6324 |
|
|
io/DumpWriter.cpp: NPT in progress |
| 6325 |
|
|
|
| 6326 |
gezelter |
2199 |
2004-12-07 09:43 tim |
| 6327 |
tim |
2102 |
|
| 6328 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
| 6329 |
|
|
message] |
| 6330 |
|
|
|
| 6331 |
gezelter |
2199 |
2004-12-07 00:12 tim |
| 6332 |
tim |
2102 |
|
| 6333 |
|
|
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
| 6334 |
|
|
UseInitXSstate |
| 6335 |
|
|
|
| 6336 |
gezelter |
2199 |
2004-12-07 00:00 tim |
| 6337 |
tim |
2102 |
|
| 6338 |
|
|
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
| 6339 |
|
|
|
| 6340 |
gezelter |
2199 |
2004-12-06 23:47 tim |
| 6341 |
tim |
2102 |
|
| 6342 |
|
|
* src/types/DirectionalAtomType.cpp: [no log message] |
| 6343 |
|
|
|
| 6344 |
gezelter |
2199 |
2004-12-06 21:18 tim |
| 6345 |
tim |
2102 |
|
| 6346 |
|
|
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
| 6347 |
|
|
|
| 6348 |
gezelter |
2199 |
2004-12-06 20:33 tim |
| 6349 |
tim |
2102 |
|
| 6350 |
|
|
* forceFields/newDUFF.frc: change the force constant of bonds |
| 6351 |
|
|
|
| 6352 |
gezelter |
2199 |
2004-12-06 18:29 tim |
| 6353 |
tim |
2102 |
|
| 6354 |
|
|
* src/: UseTheForce/DarkSide/charge.F90, |
| 6355 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
| 6356 |
|
|
UseTheForce/DarkSide/dipole.F90, |
| 6357 |
|
|
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
| 6358 |
|
|
fix atom type ident in Charge and Dipole Module |
| 6359 |
|
|
|
| 6360 |
gezelter |
2199 |
2004-12-06 17:56 tim |
| 6361 |
tim |
2102 |
|
| 6362 |
|
|
* src/primitives/Torsion.cpp: butane is working now |
| 6363 |
|
|
|
| 6364 |
gezelter |
2199 |
2004-12-06 15:15 tim |
| 6365 |
tim |
2102 |
|
| 6366 |
|
|
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
| 6367 |
|
|
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
| 6368 |
|
|
interaction for butane is correct.Still something wrong with long |
| 6369 |
|
|
range one |
| 6370 |
|
|
|
| 6371 |
gezelter |
2199 |
2004-12-05 23:49 tim |
| 6372 |
tim |
2102 |
|
| 6373 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 6374 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6375 |
|
|
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
| 6376 |
|
|
primitives/Atom.hpp, utils/NumericConstant.hpp, |
| 6377 |
|
|
utils/TypeContainer.hpp: fix a bug in Exclude List |
| 6378 |
|
|
|
| 6379 |
gezelter |
2199 |
2004-12-05 17:21 tim |
| 6380 |
tim |
2102 |
|
| 6381 |
|
|
* forceFields/newDUFF.frc: minor fix in DUFF |
| 6382 |
|
|
|
| 6383 |
gezelter |
2199 |
2004-12-05 17:02 tim |
| 6384 |
tim |
2102 |
|
| 6385 |
|
|
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
| 6386 |
|
|
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
| 6387 |
|
|
fix a bug in filling MolMembership |
| 6388 |
|
|
|
| 6389 |
gezelter |
2199 |
2004-12-05 12:12 tim |
| 6390 |
tim |
2102 |
|
| 6391 |
|
|
* forceFields/newDUFF.frc: minor fix in force field file |
| 6392 |
|
|
|
| 6393 |
gezelter |
2199 |
2004-12-05 12:09 tim |
| 6394 |
tim |
2102 |
|
| 6395 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
| 6396 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
| 6397 |
|
|
|
| 6398 |
gezelter |
2199 |
2004-12-04 15:09 tim |
| 6399 |
tim |
2102 |
|
| 6400 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
| 6401 |
|
|
math/Vector3.hpp: NVE is working now, get the same result as |
| 6402 |
|
|
OOPSE-1.0 |
| 6403 |
|
|
|
| 6404 |
gezelter |
2199 |
2004-12-04 14:29 tim |
| 6405 |
tim |
2102 |
|
| 6406 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
| 6407 |
|
|
|
| 6408 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
| 6409 |
tim |
2102 |
|
| 6410 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
| 6411 |
|
|
|
| 6412 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
| 6413 |
tim |
2102 |
|
| 6414 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
| 6415 |
|
|
|
| 6416 |
gezelter |
2199 |
2004-12-04 00:24 tim |
| 6417 |
tim |
2102 |
|
| 6418 |
|
|
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
| 6419 |
|
|
integrators/Integrator.hpp, |
| 6420 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
| 6421 |
|
|
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
| 6422 |
|
|
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
| 6423 |
|
|
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
| 6424 |
|
|
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
| 6425 |
|
|
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
| 6426 |
|
|
|
| 6427 |
gezelter |
2199 |
2004-12-03 19:01 tim |
| 6428 |
tim |
2102 |
|
| 6429 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
| 6430 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
| 6431 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 6432 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 6433 |
|
|
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
| 6434 |
|
|
energy of NVE is not conserved |
| 6435 |
|
|
|
| 6436 |
gezelter |
2199 |
2004-12-03 17:36 tim |
| 6437 |
tim |
2102 |
|
| 6438 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
| 6439 |
|
|
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
| 6440 |
|
|
|
| 6441 |
gezelter |
2199 |
2004-12-03 16:30 tim |
| 6442 |
tim |
2102 |
|
| 6443 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
| 6444 |
|
|
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
| 6445 |
|
|
integrators/NVE.cpp, primitives/Molecule.cpp, |
| 6446 |
|
|
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
| 6447 |
|
|
primitives/Torsion.hpp: more missing function get implemented |
| 6448 |
|
|
|
| 6449 |
gezelter |
2199 |
2004-12-03 15:30 tim |
| 6450 |
tim |
2102 |
|
| 6451 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
| 6452 |
|
|
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
| 6453 |
|
|
|
| 6454 |
gezelter |
2199 |
2004-12-03 12:59 tim |
| 6455 |
tim |
2102 |
|
| 6456 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
| 6457 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6458 |
|
|
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
| 6459 |
|
|
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
| 6460 |
|
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
| 6461 |
|
|
utils/TypeContainer.hpp: begin to fix bugs |
| 6462 |
|
|
|
| 6463 |
gezelter |
2199 |
2004-12-02 19:26 tim |
| 6464 |
tim |
2102 |
|
| 6465 |
tim |
2116 |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
| 6466 |
|
|
new_design. |
| 6467 |
|
|
|
| 6468 |
gezelter |
2199 |
2004-12-02 19:26 tim |
| 6469 |
tim |
2116 |
|
| 6470 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 6471 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
| 6472 |
|
|
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
| 6473 |
|
|
integrators/IntegratorCreator.cpp, |
| 6474 |
|
|
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
| 6475 |
|
|
io/SectionParserManager.hpp, utils/Makefile, |
| 6476 |
|
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
| 6477 |
|
|
bug in countTokens in StringTokenizer |
| 6478 |
|
|
|
| 6479 |
gezelter |
2199 |
2004-12-02 19:06 tim |
| 6480 |
tim |
2102 |
|
| 6481 |
|
|
* forceFields/newDUFF.frc: minor fix |
| 6482 |
|
|
|
| 6483 |
gezelter |
2199 |
2004-12-02 18:15 tim |
| 6484 |
tim |
2102 |
|
| 6485 |
|
|
* forceFields/newDUFF.frc: new ForceField format |
| 6486 |
|
|
|
| 6487 |
gezelter |
2199 |
2004-12-02 17:15 tim |
| 6488 |
tim |
2102 |
|
| 6489 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 6490 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
| 6491 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
| 6492 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
| 6493 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
| 6494 |
|
|
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
| 6495 |
|
|
integrators/IntegratorCreator.hpp, |
| 6496 |
|
|
integrators/IntegratorFactory.cpp, |
| 6497 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 6498 |
|
|
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
| 6499 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 6500 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 6501 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
| 6502 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 6503 |
|
|
types/Makefile: refine factory pattern to make it initialized |
| 6504 |
|
|
correctly |
| 6505 |
|
|
|
| 6506 |
gezelter |
2199 |
2004-12-02 17:15 tim |
| 6507 |
tim |
2102 |
|
| 6508 |
|
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
| 6509 |
|
|
was initially added on branch new_design. |
| 6510 |
|
|
|
| 6511 |
gezelter |
2199 |
2004-12-02 17:15 tim |
| 6512 |
tim |
2102 |
|
| 6513 |
tim |
2116 |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
| 6514 |
|
|
was initially added on branch new_design. |
| 6515 |
|
|
|
| 6516 |
gezelter |
2199 |
2004-12-02 17:15 tim |
| 6517 |
tim |
2116 |
|
| 6518 |
|
|
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
| 6519 |
|
|
was initially added on branch new_design. |
| 6520 |
|
|
|
| 6521 |
gezelter |
2199 |
2004-12-02 17:15 tim |
| 6522 |
tim |
2116 |
|
| 6523 |
|
|
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
| 6524 |
|
|
was initially added on branch new_design. |
| 6525 |
|
|
|
| 6526 |
gezelter |
2199 |
2004-12-02 11:53 tim |
| 6527 |
tim |
2116 |
|
| 6528 |
tim |
2102 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
| 6529 |
|
|
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
| 6530 |
|
|
|
| 6531 |
gezelter |
2199 |
2004-12-02 11:04 tim |
| 6532 |
tim |
2102 |
|
| 6533 |
|
|
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
| 6534 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 6535 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6536 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6537 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
| 6538 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 6539 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6540 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 6541 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 6542 |
|
|
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
| 6543 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
| 6544 |
|
|
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
| 6545 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 6546 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 6547 |
|
|
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
| 6548 |
|
|
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
| 6549 |
|
|
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
| 6550 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 6551 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 6552 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
| 6553 |
|
|
have two linking problem |
| 6554 |
|
|
|
| 6555 |
gezelter |
2199 |
2004-12-02 00:17 tim |
| 6556 |
tim |
2102 |
|
| 6557 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 6558 |
|
|
applications/simpleBuilder/Lattice.cpp, |
| 6559 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 6560 |
|
|
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
| 6561 |
|
|
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
| 6562 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
| 6563 |
|
|
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
| 6564 |
|
|
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
| 6565 |
|
|
visitors/ZconsVisitor.cpp: change endl to std::endl |
| 6566 |
|
|
|
| 6567 |
gezelter |
2199 |
2004-12-02 00:14 tim |
| 6568 |
tim |
2102 |
|
| 6569 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
| 6570 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
| 6571 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
| 6572 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 6573 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 6574 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6575 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6576 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
| 6577 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
| 6578 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
| 6579 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
| 6580 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 6581 |
|
|
visitors/RigidBodyVisitor.hpp: minor fix |
| 6582 |
|
|
|
| 6583 |
gezelter |
2199 |
2004-12-02 00:09 tim |
| 6584 |
tim |
2102 |
|
| 6585 |
|
|
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
| 6586 |
|
|
remove StreamTokenizer |
| 6587 |
|
|
|
| 6588 |
gezelter |
2199 |
2004-12-02 00:06 tim |
| 6589 |
tim |
2102 |
|
| 6590 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
| 6591 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
| 6592 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
| 6593 |
|
|
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
| 6594 |
|
|
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
| 6595 |
|
|
namespace std in .cpp file |
| 6596 |
|
|
|
| 6597 |
gezelter |
2199 |
2004-12-02 00:04 tim |
| 6598 |
tim |
2102 |
|
| 6599 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
| 6600 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
| 6601 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
| 6602 |
|
|
applications/simpleBuilder/Lattice.cpp, |
| 6603 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 6604 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6605 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6606 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
| 6607 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
| 6608 |
|
|
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
| 6609 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
| 6610 |
|
|
minimizers/MinimizerParameterSet.hpp, |
| 6611 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
| 6612 |
|
|
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
| 6613 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
| 6614 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 6615 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 6616 |
|
|
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
| 6617 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 6618 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
| 6619 |
|
|
qulified name prefix std |
| 6620 |
|
|
|
| 6621 |
gezelter |
2199 |
2004-12-01 23:55 tim |
| 6622 |
tim |
2102 |
|
| 6623 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
| 6624 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
| 6625 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
| 6626 |
|
|
applications/simpleBuilder/Lattice.hpp, |
| 6627 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 6628 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
| 6629 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
| 6630 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
| 6631 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
| 6632 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
| 6633 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
| 6634 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 6635 |
|
|
visitors/RigidBodyVisitor.hpp: replace string by std::string |
| 6636 |
|
|
|
| 6637 |
gezelter |
2199 |
2004-12-01 22:12 tim |
| 6638 |
tim |
2102 |
|
| 6639 |
|
|
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
| 6640 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
| 6641 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
| 6642 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
| 6643 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
| 6644 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
| 6645 |
|
|
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
| 6646 |
|
|
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
| 6647 |
|
|
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
| 6648 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
| 6649 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
| 6650 |
|
|
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
| 6651 |
|
|
src/utils/Makefile, src/utils/StringUtils.cpp, |
| 6652 |
|
|
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
| 6653 |
|
|
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
| 6654 |
|
|
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
| 6655 |
|
|
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
| 6656 |
|
|
header files |
| 6657 |
|
|
|
| 6658 |
gezelter |
2199 |
2004-12-01 21:23 tim |
| 6659 |
tim |
2102 |
|
| 6660 |
|
|
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
| 6661 |
|
|
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
| 6662 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
| 6663 |
|
|
begin to fix linking problem |
| 6664 |
|
|
|
| 6665 |
gezelter |
2199 |
2004-12-01 21:08 tim |
| 6666 |
tim |
2102 |
|
| 6667 |
|
|
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
| 6668 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
| 6669 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
| 6670 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
| 6671 |
|
|
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
| 6672 |
|
|
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
| 6673 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
| 6674 |
|
|
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
| 6675 |
|
|
still has some linking problem |
| 6676 |
|
|
|
| 6677 |
gezelter |
2199 |
2004-12-01 19:26 tim |
| 6678 |
tim |
2102 |
|
| 6679 |
|
|
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
| 6680 |
|
|
utils/OOPSEConstant.hpp: NVT get built |
| 6681 |
|
|
|
| 6682 |
gezelter |
2199 |
2004-12-01 19:09 tim |
| 6683 |
tim |
2102 |
|
| 6684 |
tim |
2116 |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
| 6685 |
|
|
branch new_design. |
| 6686 |
tim |
2102 |
|
| 6687 |
gezelter |
2199 |
2004-12-01 19:09 tim |
| 6688 |
tim |
2102 |
|
| 6689 |
tim |
2116 |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
| 6690 |
|
|
branch new_design. |
| 6691 |
|
|
|
| 6692 |
gezelter |
2199 |
2004-12-01 19:09 tim |
| 6693 |
tim |
2116 |
|
| 6694 |
tim |
2102 |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
| 6695 |
|
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 6696 |
|
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
| 6697 |
|
|
integrators/Integrator.hpp, integrators/Makefile, |
| 6698 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, |
| 6699 |
|
|
integrators/RotationAlgorithm.hpp, |
| 6700 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 6701 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
| 6702 |
|
|
get built |
| 6703 |
|
|
|
| 6704 |
gezelter |
2199 |
2004-12-01 19:09 tim |
| 6705 |
tim |
2102 |
|
| 6706 |
tim |
2116 |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
| 6707 |
|
|
was initially added on branch new_design. |
| 6708 |
tim |
2102 |
|
| 6709 |
gezelter |
2199 |
2004-12-01 17:45 tim |
| 6710 |
tim |
2102 |
|
| 6711 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
| 6712 |
|
|
integrators/IntegratorFactory.cpp, |
| 6713 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
| 6714 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 6715 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 6716 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
| 6717 |
|
|
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
| 6718 |
|
|
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
| 6719 |
|
|
|
| 6720 |
gezelter |
2199 |
2004-12-01 17:45 tim |
| 6721 |
tim |
2102 |
|
| 6722 |
|
|
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
| 6723 |
|
|
branch new_design. |
| 6724 |
|
|
|
| 6725 |
gezelter |
2199 |
2004-12-01 15:05 tim |
| 6726 |
tim |
2102 |
|
| 6727 |
|
|
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
| 6728 |
|
|
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
| 6729 |
|
|
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
| 6730 |
|
|
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
| 6731 |
|
|
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 6732 |
|
|
visitors/ZconsVisitor.hpp: visitors get built |
| 6733 |
|
|
|
| 6734 |
gezelter |
2199 |
2004-12-01 14:32 chrisfen |
| 6735 |
tim |
2102 |
|
| 6736 |
|
|
* samples/water/tip3p_ice/tp3.md: fixed a sample |
| 6737 |
|
|
|
| 6738 |
gezelter |
2199 |
2004-12-01 14:10 tim |
| 6739 |
tim |
2102 |
|
| 6740 |
|
|
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
| 6741 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 6742 |
|
|
src/types/AtomType.hpp, src/utils/Utility.hpp, |
| 6743 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 6744 |
|
|
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
| 6745 |
|
|
spell check |
| 6746 |
|
|
|
| 6747 |
gezelter |
2199 |
2004-12-01 13:42 tim |
| 6748 |
tim |
2102 |
|
| 6749 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
| 6750 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 6751 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
| 6752 |
|
|
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
| 6753 |
|
|
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
| 6754 |
|
|
and constraint, other directories get built |
| 6755 |
|
|
|
| 6756 |
gezelter |
2199 |
2004-12-01 12:38 tim |
| 6757 |
tim |
2102 |
|
| 6758 |
|
|
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
| 6759 |
|
|
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
| 6760 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 6761 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
| 6762 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 6763 |
|
|
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
| 6764 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
| 6765 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 6766 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
| 6767 |
|
|
refactory AtomType |
| 6768 |
|
|
|
| 6769 |
gezelter |
2199 |
2004-11-30 22:11 tim |
| 6770 |
tim |
2102 |
|
| 6771 |
|
|
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
| 6772 |
|
|
|
| 6773 |
gezelter |
2199 |
2004-11-30 21:30 tim |
| 6774 |
tim |
2102 |
|
| 6775 |
|
|
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
| 6776 |
|
|
NumericConstant |
| 6777 |
|
|
|
| 6778 |
gezelter |
2199 |
2004-11-30 21:24 tim |
| 6779 |
tim |
2102 |
|
| 6780 |
|
|
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
| 6781 |
|
|
primitives/RigidBody.cpp: minor fix |
| 6782 |
|
|
|
| 6783 |
gezelter |
2199 |
2004-11-30 18:14 tim |
| 6784 |
tim |
2102 |
|
| 6785 |
|
|
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
| 6786 |
|
|
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
| 6787 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
| 6788 |
|
|
get built, next is integrator |
| 6789 |
|
|
|
| 6790 |
gezelter |
2199 |
2004-11-30 17:43 tim |
| 6791 |
tim |
2102 |
|
| 6792 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 6793 |
|
|
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
| 6794 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6795 |
|
|
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
| 6796 |
|
|
utils/StringUtils.hpp: brains get built |
| 6797 |
|
|
|
| 6798 |
gezelter |
2199 |
2004-11-30 15:50 tim |
| 6799 |
tim |
2102 |
|
| 6800 |
|
|
* src/: brains/ForceManager.cpp, brains/Makefile, |
| 6801 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 6802 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 6803 |
|
|
utils/StringUtils.hpp: brains get built, io is next |
| 6804 |
|
|
|
| 6805 |
gezelter |
2199 |
2004-11-30 14:58 tim |
| 6806 |
tim |
2102 |
|
| 6807 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 6808 |
|
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 6809 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
| 6810 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 6811 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 6812 |
|
|
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
| 6813 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
| 6814 |
|
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
| 6815 |
|
|
|
| 6816 |
gezelter |
2199 |
2004-11-30 14:58 tim |
| 6817 |
tim |
2102 |
|
| 6818 |
tim |
2116 |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
| 6819 |
|
|
added on branch new_design. |
| 6820 |
|
|
|
| 6821 |
gezelter |
2199 |
2004-11-30 12:54 tim |
| 6822 |
tim |
2116 |
|
| 6823 |
tim |
2102 |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
| 6824 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
| 6825 |
|
|
utils/LocalIndexManager.hpp: more get fixed |
| 6826 |
|
|
|
| 6827 |
gezelter |
2199 |
2004-11-30 00:03 tim |
| 6828 |
tim |
2102 |
|
| 6829 |
tim |
2116 |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
| 6830 |
|
|
initially added on branch new_design. |
| 6831 |
|
|
|
| 6832 |
gezelter |
2199 |
2004-11-30 00:03 tim |
| 6833 |
tim |
2116 |
|
| 6834 |
tim |
2102 |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
| 6835 |
|
|
LocalndexManager.hpp to LocalIndexManager.hpp |
| 6836 |
|
|
|
| 6837 |
gezelter |
2199 |
2004-11-29 23:43 tim |
| 6838 |
tim |
2102 |
|
| 6839 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
| 6840 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 6841 |
|
|
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
| 6842 |
|
|
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
| 6843 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 6844 |
|
|
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
| 6845 |
|
|
|
| 6846 |
gezelter |
2199 |
2004-11-29 23:14 tim |
| 6847 |
tim |
2102 |
|
| 6848 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
| 6849 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 6850 |
|
|
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
| 6851 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
| 6852 |
|
|
fixed |
| 6853 |
|
|
|
| 6854 |
gezelter |
2199 |
2004-11-29 22:49 tim |
| 6855 |
tim |
2102 |
|
| 6856 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
| 6857 |
|
|
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
| 6858 |
|
|
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
| 6859 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
| 6860 |
|
|
types/QuarticTorsionType.hpp: minor fixed |
| 6861 |
|
|
|
| 6862 |
gezelter |
2199 |
2004-11-29 22:32 tim |
| 6863 |
tim |
2102 |
|
| 6864 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
| 6865 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 6866 |
|
|
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
| 6867 |
|
|
embedded |
| 6868 |
|
|
|
| 6869 |
gezelter |
2199 |
2004-11-29 16:42 tim |
| 6870 |
tim |
2102 |
|
| 6871 |
|
|
* test/math/: Makefile, PolynomialTestCase.cpp, |
| 6872 |
|
|
PolynomialTestCase.hpp: add PolynomialTestCase |
| 6873 |
|
|
|
| 6874 |
gezelter |
2199 |
2004-11-29 16:42 tim |
| 6875 |
tim |
2102 |
|
| 6876 |
|
|
* src/math/Polynomial.hpp: Polynomial passes unit test |
| 6877 |
|
|
|
| 6878 |
gezelter |
2199 |
2004-11-29 15:03 tim |
| 6879 |
tim |
2102 |
|
| 6880 |
|
|
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
| 6881 |
|
|
QuarticTorsion.hpp to QuarticTorsionType.hpp |
| 6882 |
|
|
|
| 6883 |
gezelter |
2199 |
2004-11-29 15:03 tim |
| 6884 |
tim |
2102 |
|
| 6885 |
|
|
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
| 6886 |
|
|
initially added on branch new_design. |
| 6887 |
|
|
|
| 6888 |
gezelter |
2199 |
2004-11-29 14:56 tim |
| 6889 |
tim |
2102 |
|
| 6890 |
|
|
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
| 6891 |
|
|
initially added on branch new_design. |
| 6892 |
|
|
|
| 6893 |
gezelter |
2199 |
2004-11-29 14:56 tim |
| 6894 |
tim |
2102 |
|
| 6895 |
|
|
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
| 6896 |
|
|
CubicTorsionType and QuarticTorsionType |
| 6897 |
|
|
|
| 6898 |
gezelter |
2199 |
2004-11-29 14:56 tim |
| 6899 |
tim |
2102 |
|
| 6900 |
|
|
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
| 6901 |
|
|
initially added on branch new_design. |
| 6902 |
|
|
|
| 6903 |
gezelter |
2199 |
2004-11-29 13:00 tim |
| 6904 |
tim |
2102 |
|
| 6905 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
| 6906 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 6907 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
| 6908 |
|
|
fixed |
| 6909 |
|
|
|
| 6910 |
gezelter |
2199 |
2004-11-29 12:59 tim |
| 6911 |
tim |
2102 |
|
| 6912 |
|
|
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
| 6913 |
|
|
new_design. |
| 6914 |
|
|
|
| 6915 |
gezelter |
2199 |
2004-11-29 12:59 tim |
| 6916 |
tim |
2102 |
|
| 6917 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
| 6918 |
|
|
Algorithm for std::string |
| 6919 |
|
|
|
| 6920 |
gezelter |
2199 |
2004-11-29 10:52 tim |
| 6921 |
tim |
2102 |
|
| 6922 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
| 6923 |
|
|
some useless files |
| 6924 |
|
|
|
| 6925 |
gezelter |
2199 |
2004-11-29 10:50 tim |
| 6926 |
tim |
2102 |
|
| 6927 |
|
|
* src/io/: BondTypesSectionParser.cpp, |
| 6928 |
|
|
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
| 6929 |
|
|
ElectrostaticAtomTypesSectionParser.cpp, |
| 6930 |
|
|
HarmonicBondTypesSectionParser.cpp, |
| 6931 |
|
|
HarmonicBondTypesSectionParser.hpp, |
| 6932 |
|
|
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
| 6933 |
|
|
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
| 6934 |
|
|
StickyAtomTypesSectionParser.hpp: more files get fixed |
| 6935 |
|
|
|
| 6936 |
gezelter |
2199 |
2004-11-29 10:27 tim |
| 6937 |
tim |
2102 |
|
| 6938 |
|
|
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
| 6939 |
|
|
DirectionalAtomTypesSectionParser.cpp, |
| 6940 |
|
|
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
| 6941 |
|
|
Makefile, SectionParser.cpp, SectionParser.hpp, |
| 6942 |
|
|
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
| 6943 |
|
|
built |
| 6944 |
|
|
|
| 6945 |
gezelter |
2199 |
2004-11-29 09:49 tim |
| 6946 |
tim |
2102 |
|
| 6947 |
|
|
* src/types/UreyBradleyBendType.hpp: types get built |
| 6948 |
|
|
|
| 6949 |
gezelter |
2199 |
2004-11-29 09:40 tim |
| 6950 |
tim |
2102 |
|
| 6951 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
| 6952 |
|
|
types get built |
| 6953 |
|
|
|
| 6954 |
gezelter |
2199 |
2004-11-25 21:13 tim |
| 6955 |
tim |
2102 |
|
| 6956 |
|
|
* src/: UseTheForce/ForceField.hpp, |
| 6957 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
| 6958 |
|
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
| 6959 |
|
|
files |
| 6960 |
|
|
|
| 6961 |
gezelter |
2199 |
2004-11-25 15:18 tim |
| 6962 |
tim |
2102 |
|
| 6963 |
tim |
2116 |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
| 6964 |
|
|
initially added on branch new_design. |
| 6965 |
|
|
|
| 6966 |
gezelter |
2199 |
2004-11-25 15:18 tim |
| 6967 |
tim |
2116 |
|
| 6968 |
tim |
2102 |
* src/: io/AtomTypesSectionParser.cpp, |
| 6969 |
|
|
io/BondTypesSectionParser.cpp, |
| 6970 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 6971 |
|
|
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
| 6972 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
| 6973 |
|
|
files |
| 6974 |
|
|
|
| 6975 |
gezelter |
2199 |
2004-11-25 15:18 tim |
| 6976 |
tim |
2102 |
|
| 6977 |
|
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
| 6978 |
|
|
initially added on branch new_design. |
| 6979 |
|
|
|
| 6980 |
gezelter |
2199 |
2004-11-24 17:12 tim |
| 6981 |
tim |
2102 |
|
| 6982 |
|
|
* src/: io/AtomTypesSectionParser.cpp, |
| 6983 |
|
|
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
| 6984 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 6985 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 6986 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
| 6987 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
| 6988 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
| 6989 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 6990 |
|
|
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
| 6991 |
|
|
io/EAMAtomTypesSectionParser.hpp, |
| 6992 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 6993 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
| 6994 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
| 6995 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
| 6996 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
| 6997 |
|
|
io/SectionParser.hpp, io/SectionParserManager.hpp, |
| 6998 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
| 6999 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
| 7000 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 7001 |
|
|
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
| 7002 |
|
|
|
| 7003 |
gezelter |
2199 |
2004-11-24 16:33 tim |
| 7004 |
tim |
2102 |
|
| 7005 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
| 7006 |
|
|
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
| 7007 |
|
|
LJFF.cpp, Makefile: UseTheForce get built |
| 7008 |
|
|
|
| 7009 |
gezelter |
2199 |
2004-11-24 15:55 tim |
| 7010 |
tim |
2102 |
|
| 7011 |
|
|
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
| 7012 |
|
|
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
| 7013 |
|
|
primitives/Makefile, primitives/Molecule.cpp, |
| 7014 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 7015 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
| 7016 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
| 7017 |
|
|
primitives/UreyBradleyBend.hpp: types and primitives get built |
| 7018 |
|
|
|
| 7019 |
gezelter |
2199 |
2004-11-24 14:49 tim |
| 7020 |
tim |
2102 |
|
| 7021 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 7022 |
|
|
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
| 7023 |
|
|
StringTokenizerTestCase |
| 7024 |
|
|
|
| 7025 |
gezelter |
2199 |
2004-11-24 14:49 tim |
| 7026 |
tim |
2102 |
|
| 7027 |
|
|
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
| 7028 |
|
|
StringTokenizer.hpp: StringTokenizer passes unit test |
| 7029 |
|
|
|
| 7030 |
gezelter |
2199 |
2004-11-24 13:20 tim |
| 7031 |
tim |
2102 |
|
| 7032 |
|
|
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
| 7033 |
|
|
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
| 7034 |
|
|
change Makefile |
| 7035 |
|
|
|
| 7036 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
| 7037 |
tim |
2102 |
|
| 7038 |
|
|
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
| 7039 |
|
|
fine |
| 7040 |
|
|
|
| 7041 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
| 7042 |
tim |
2102 |
|
| 7043 |
|
|
* src/integrators/Integrator.cpp: improved restraints |
| 7044 |
|
|
|
| 7045 |
gezelter |
2199 |
2004-11-24 13:05 chrisfen |
| 7046 |
tim |
2102 |
|
| 7047 |
|
|
* samples/water/tip3p_ice/tp3.md: oops... |
| 7048 |
|
|
|
| 7049 |
gezelter |
2199 |
2004-11-24 12:42 tim |
| 7050 |
tim |
1779 |
|
| 7051 |
|
|
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
| 7052 |
|
|
brains/DataStorage.hpp, brains/SimCreator.cpp, |
| 7053 |
|
|
brains/SimCreator.hpp, integrators/Integrator.hpp, |
| 7054 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 7055 |
|
|
primitives/DirectionalAtom.cpp: add SetForceManager method to |
| 7056 |
|
|
integrator |
| 7057 |
|
|
|
| 7058 |
gezelter |
2199 |
2004-11-23 18:12 tim |
| 7059 |
tim |
1779 |
|
| 7060 |
|
|
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
| 7061 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
| 7062 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
| 7063 |
|
|
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
| 7064 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
| 7065 |
|
|
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
| 7066 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 7067 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
| 7068 |
|
|
types/UreyBradleyBendType.hpp: refactory NPT integrator |
| 7069 |
|
|
|
| 7070 |
gezelter |
2199 |
2004-11-23 17:50 chrisfen |
| 7071 |
tim |
1779 |
|
| 7072 |
|
|
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
| 7073 |
|
|
Restraints should work in parallel now |
| 7074 |
|
|
|
| 7075 |
gezelter |
2199 |
2004-11-23 17:48 chrisfen |
| 7076 |
tim |
1779 |
|
| 7077 |
|
|
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 7078 |
|
|
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 7079 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
| 7080 |
|
|
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
| 7081 |
|
|
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
| 7082 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
| 7083 |
|
|
to restraints |
| 7084 |
|
|
|
| 7085 |
gezelter |
2199 |
2004-11-23 17:47 chrisfen |
| 7086 |
tim |
1779 |
|
| 7087 |
|
|
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
| 7088 |
|
|
return to the original on next commit |
| 7089 |
|
|
|
| 7090 |
gezelter |
2199 |
2004-11-23 12:53 tim |
| 7091 |
tim |
1779 |
|
| 7092 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 7093 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 7094 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 7095 |
|
|
io/ChargeAtomTypesSectionParser.cpp, |
| 7096 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
| 7097 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
| 7098 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
| 7099 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 7100 |
|
|
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
| 7101 |
|
|
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
| 7102 |
|
|
|
| 7103 |
gezelter |
2199 |
2004-11-23 12:53 tim |
| 7104 |
tim |
1779 |
|
| 7105 |
|
|
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
| 7106 |
|
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
| 7107 |
|
|
branch new_design. |
| 7108 |
|
|
|
| 7109 |
gezelter |
2199 |
2004-11-23 12:53 tim |
| 7110 |
tim |
1779 |
|
| 7111 |
tim |
2116 |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
| 7112 |
|
|
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
| 7113 |
|
|
branch new_design. |
| 7114 |
tim |
1779 |
|
| 7115 |
gezelter |
2199 |
2004-11-23 01:03 tim |
| 7116 |
tim |
1779 |
|
| 7117 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
| 7118 |
|
|
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
| 7119 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
| 7120 |
|
|
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
| 7121 |
|
|
|
| 7122 |
gezelter |
2199 |
2004-11-23 01:03 tim |
| 7123 |
tim |
1779 |
|
| 7124 |
tim |
2116 |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
| 7125 |
|
|
was initially added on branch new_design. |
| 7126 |
|
|
|
| 7127 |
gezelter |
2199 |
2004-11-23 01:03 tim |
| 7128 |
tim |
2116 |
|
| 7129 |
tim |
1779 |
* src/io/EAMAtomTypesSectionParser.hpp: file |
| 7130 |
|
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
| 7131 |
|
|
new_design. |
| 7132 |
|
|
|
| 7133 |
gezelter |
2199 |
2004-11-23 01:03 tim |
| 7134 |
tim |
1779 |
|
| 7135 |
tim |
2116 |
* src/io/EAMAtomTypesSectionParser.cpp: file |
| 7136 |
|
|
EAMAtomTypesSectionParser.cpp was initially added on branch |
| 7137 |
|
|
new_design. |
| 7138 |
tim |
1779 |
|
| 7139 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7140 |
tim |
1779 |
|
| 7141 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.hpp: file |
| 7142 |
|
|
TorsionTypesSectionParser.hpp was initially added on branch |
| 7143 |
tim |
1779 |
new_design. |
| 7144 |
|
|
|
| 7145 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7146 |
tim |
1779 |
|
| 7147 |
|
|
* src/io/BendTypesSectionParser.hpp: file |
| 7148 |
|
|
BendTypesSectionParser.hpp was initially added on branch |
| 7149 |
|
|
new_design. |
| 7150 |
|
|
|
| 7151 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7152 |
tim |
1779 |
|
| 7153 |
|
|
* src/io/BondTypesSectionParser.hpp: file |
| 7154 |
|
|
BondTypesSectionParser.hpp was initially added on branch |
| 7155 |
|
|
new_design. |
| 7156 |
|
|
|
| 7157 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7158 |
tim |
1779 |
|
| 7159 |
tim |
2116 |
* src/io/BondTypesSectionParser.cpp: file |
| 7160 |
|
|
BondTypesSectionParser.cpp was initially added on branch |
| 7161 |
tim |
1779 |
new_design. |
| 7162 |
|
|
|
| 7163 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7164 |
tim |
1779 |
|
| 7165 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.cpp: file |
| 7166 |
|
|
TorsionTypesSectionParser.cpp was initially added on branch |
| 7167 |
tim |
1779 |
new_design. |
| 7168 |
|
|
|
| 7169 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7170 |
tim |
1779 |
|
| 7171 |
|
|
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
| 7172 |
|
|
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
| 7173 |
|
|
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
| 7174 |
|
|
BondTypesSectionParser, BendTypesSectionParser and |
| 7175 |
|
|
TorsionTypeSectionParser |
| 7176 |
|
|
|
| 7177 |
gezelter |
2199 |
2004-11-22 23:35 tim |
| 7178 |
tim |
1779 |
|
| 7179 |
tim |
2116 |
* src/io/BendTypesSectionParser.cpp: file |
| 7180 |
|
|
BendTypesSectionParser.cpp was initially added on branch |
| 7181 |
|
|
new_design. |
| 7182 |
|
|
|
| 7183 |
gezelter |
2199 |
2004-11-22 18:04 tim |
| 7184 |
tim |
2116 |
|
| 7185 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
| 7186 |
|
|
DUFF and EAM |
| 7187 |
|
|
|
| 7188 |
gezelter |
2199 |
2004-11-22 18:02 tim |
| 7189 |
tim |
1779 |
|
| 7190 |
tim |
2116 |
* src/io/: DirectionalAtomTypesParser.hpp, |
| 7191 |
|
|
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
| 7192 |
|
|
|
| 7193 |
gezelter |
2199 |
2004-11-22 18:02 tim |
| 7194 |
tim |
2116 |
|
| 7195 |
tim |
1779 |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
| 7196 |
|
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
| 7197 |
|
|
new_design. |
| 7198 |
|
|
|
| 7199 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7200 |
tim |
1779 |
|
| 7201 |
tim |
2116 |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
| 7202 |
|
|
DipoleAtomTypesSectionParser.hpp was initially added on branch |
| 7203 |
|
|
new_design. |
| 7204 |
tim |
1779 |
|
| 7205 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7206 |
tim |
1779 |
|
| 7207 |
tim |
2116 |
* src/io/AtomTypesSectionParser.hpp: file |
| 7208 |
|
|
AtomTypesSectionParser.hpp was initially added on branch |
| 7209 |
tim |
1779 |
new_design. |
| 7210 |
|
|
|
| 7211 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7212 |
tim |
1779 |
|
| 7213 |
|
|
* src/io/HarmonicBondTypesSectionParser.hpp: file |
| 7214 |
|
|
HarmonicBondTypesSectionParser.hpp was initially added on branch |
| 7215 |
|
|
new_design. |
| 7216 |
|
|
|
| 7217 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7218 |
tim |
1779 |
|
| 7219 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.cpp: file |
| 7220 |
|
|
StickyAtomTypesSectionParser.cpp was initially added on branch |
| 7221 |
tim |
1779 |
new_design. |
| 7222 |
|
|
|
| 7223 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7224 |
tim |
1779 |
|
| 7225 |
tim |
2116 |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
| 7226 |
|
|
LennardJonesAtomTypesSectionParser.hpp was initially added on |
| 7227 |
|
|
branch new_design. |
| 7228 |
|
|
|
| 7229 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7230 |
tim |
2116 |
|
| 7231 |
|
|
* src/io/HarmonicBondTypesSectionParser.cpp: file |
| 7232 |
|
|
HarmonicBondTypesSectionParser.cpp was initially added on branch |
| 7233 |
|
|
new_design. |
| 7234 |
|
|
|
| 7235 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7236 |
tim |
2116 |
|
| 7237 |
tim |
2102 |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
| 7238 |
|
|
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
| 7239 |
|
|
new_design. |
| 7240 |
|
|
|
| 7241 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7242 |
tim |
2102 |
|
| 7243 |
tim |
2116 |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
| 7244 |
|
|
was initially added on branch new_design. |
| 7245 |
|
|
|
| 7246 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7247 |
tim |
2116 |
|
| 7248 |
|
|
* src/io/AtomTypesSectionParser.cpp: file |
| 7249 |
|
|
AtomTypesSectionParser.cpp was initially added on branch |
| 7250 |
|
|
new_design. |
| 7251 |
|
|
|
| 7252 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7253 |
tim |
2116 |
|
| 7254 |
|
|
* src/io/ChargeAtomTypesSectionParser.cpp: file |
| 7255 |
|
|
ChargeAtomTypesSectionParser.cpp was initially added on branch |
| 7256 |
|
|
new_design. |
| 7257 |
|
|
|
| 7258 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7259 |
tim |
2116 |
|
| 7260 |
|
|
* src/io/DipoleAtomTypesSectionParser.cpp: file |
| 7261 |
|
|
DipoleAtomTypesSectionParser.cpp was initially added on branch |
| 7262 |
|
|
new_design. |
| 7263 |
|
|
|
| 7264 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7265 |
tim |
2116 |
|
| 7266 |
tim |
2102 |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
| 7267 |
|
|
LennardJonesAtomTypesSectionParser.cpp was initially added on |
| 7268 |
tim |
1779 |
branch new_design. |
| 7269 |
|
|
|
| 7270 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7271 |
tim |
1779 |
|
| 7272 |
tim |
2116 |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
| 7273 |
|
|
ChargeAtomTypesSectionParser.hpp was initially added on branch |
| 7274 |
tim |
1779 |
new_design. |
| 7275 |
|
|
|
| 7276 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7277 |
tim |
1779 |
|
| 7278 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.hpp: file |
| 7279 |
|
|
StickyAtomTypesSectionParser.hpp was initially added on branch |
| 7280 |
|
|
new_design. |
| 7281 |
|
|
|
| 7282 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7283 |
tim |
2116 |
|
| 7284 |
|
|
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
| 7285 |
|
|
added on branch new_design. |
| 7286 |
|
|
|
| 7287 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7288 |
tim |
2116 |
|
| 7289 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 7290 |
|
|
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
| 7291 |
|
|
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 7292 |
|
|
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
| 7293 |
|
|
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 7294 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
| 7295 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
| 7296 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
| 7297 |
|
|
io/DirectionalAtomTypesParser.hpp, |
| 7298 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
| 7299 |
|
|
io/HarmonicBondTypesSectionParser.cpp, |
| 7300 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
| 7301 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
| 7302 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 7303 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 7304 |
|
|
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
| 7305 |
|
|
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
| 7306 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
| 7307 |
|
|
utils/GenericData.hpp: adding section parsers |
| 7308 |
|
|
|
| 7309 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7310 |
tim |
2102 |
|
| 7311 |
tim |
2116 |
* src/io/DirectionalAtomTypesParser.hpp: file |
| 7312 |
|
|
DirectionalAtomTypesParser.hpp was initially added on branch |
| 7313 |
tim |
1779 |
new_design. |
| 7314 |
|
|
|
| 7315 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7316 |
tim |
1779 |
|
| 7317 |
tim |
2102 |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
| 7318 |
tim |
1779 |
was initially added on branch new_design. |
| 7319 |
|
|
|
| 7320 |
gezelter |
2199 |
2004-11-22 15:55 tim |
| 7321 |
tim |
1779 |
|
| 7322 |
tim |
2116 |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
| 7323 |
|
|
added on branch new_design. |
| 7324 |
tim |
1779 |
|
| 7325 |
gezelter |
2199 |
2004-11-19 17:12 tim |
| 7326 |
tim |
1779 |
|
| 7327 |
tim |
2116 |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
| 7328 |
tim |
1779 |
added on branch new_design. |
| 7329 |
|
|
|
| 7330 |
gezelter |
2199 |
2004-11-19 17:12 tim |
| 7331 |
tim |
1779 |
|
| 7332 |
|
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
| 7333 |
|
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
| 7334 |
|
|
types/FixedBondType.hpp: remove more useless files |
| 7335 |
|
|
|
| 7336 |
gezelter |
2199 |
2004-11-19 16:47 tim |
| 7337 |
tim |
2102 |
|
| 7338 |
tim |
1779 |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
| 7339 |
|
|
integrators/Integrator.cpp, applications/Makedepend: remove more |
| 7340 |
|
|
useless files |
| 7341 |
|
|
|
| 7342 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7343 |
tim |
1779 |
|
| 7344 |
tim |
2116 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 7345 |
|
|
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
| 7346 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
| 7347 |
|
|
integrators/NVT.hpp: refactory integrator |
| 7348 |
|
|
|
| 7349 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7350 |
tim |
2116 |
|
| 7351 |
tim |
1779 |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
| 7352 |
|
|
branch new_design. |
| 7353 |
|
|
|
| 7354 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7355 |
tim |
1779 |
|
| 7356 |
tim |
2116 |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
| 7357 |
|
|
branch new_design. |
| 7358 |
tim |
1779 |
|
| 7359 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7360 |
tim |
1779 |
|
| 7361 |
|
|
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
| 7362 |
|
|
branch new_design. |
| 7363 |
|
|
|
| 7364 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7365 |
tim |
1779 |
|
| 7366 |
tim |
2116 |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
| 7367 |
|
|
on branch new_design. |
| 7368 |
tim |
1779 |
|
| 7369 |
gezelter |
2199 |
2004-11-19 16:38 tim |
| 7370 |
tim |
1779 |
|
| 7371 |
tim |
2116 |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
| 7372 |
tim |
1779 |
branch new_design. |
| 7373 |
|
|
|
| 7374 |
gezelter |
2199 |
2004-11-19 15:37 tim |
| 7375 |
tim |
2102 |
|
| 7376 |
tim |
2116 |
* forceFields/newDUFF.frc: new DUFF forcefield |
| 7377 |
tim |
2102 |
|
| 7378 |
gezelter |
2199 |
2004-11-19 15:23 tim |
| 7379 |
tim |
1779 |
|
| 7380 |
tim |
2116 |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
| 7381 |
|
|
branch new_design. |
| 7382 |
tim |
1779 |
|
| 7383 |
gezelter |
2199 |
2004-11-19 15:23 tim |
| 7384 |
tim |
1779 |
|
| 7385 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
| 7386 |
|
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
| 7387 |
|
|
utils/TypeContainer.hpp: add EAM |
| 7388 |
|
|
|
| 7389 |
gezelter |
2199 |
2004-11-19 15:23 tim |
| 7390 |
tim |
1779 |
|
| 7391 |
|
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
| 7392 |
|
|
branch new_design. |
| 7393 |
|
|
|
| 7394 |
gezelter |
2199 |
2004-11-19 13:02 tim |
| 7395 |
tim |
2102 |
|
| 7396 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
| 7397 |
|
|
error checking |
| 7398 |
|
|
|
| 7399 |
gezelter |
2199 |
2004-11-19 12:56 tim |
| 7400 |
tim |
1779 |
|
| 7401 |
tim |
2116 |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
| 7402 |
tim |
1779 |
was initially added on branch new_design. |
| 7403 |
|
|
|
| 7404 |
gezelter |
2199 |
2004-11-19 12:56 tim |
| 7405 |
tim |
1779 |
|
| 7406 |
tim |
2116 |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
| 7407 |
tim |
1779 |
was initially added on branch new_design. |
| 7408 |
|
|
|
| 7409 |
gezelter |
2199 |
2004-11-19 12:56 tim |
| 7410 |
tim |
1779 |
|
| 7411 |
|
|
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
| 7412 |
|
|
added on branch new_design. |
| 7413 |
|
|
|
| 7414 |
gezelter |
2199 |
2004-11-19 12:56 tim |
| 7415 |
tim |
1779 |
|
| 7416 |
|
|
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
| 7417 |
|
|
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
| 7418 |
|
|
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
| 7419 |
|
|
integrators/IntegratorFactory.cpp, |
| 7420 |
|
|
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
| 7421 |
|
|
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
| 7422 |
|
|
utils/StringTokenizer.cpp: DUFF is almost done except error |
| 7423 |
|
|
checking |
| 7424 |
|
|
|
| 7425 |
gezelter |
2199 |
2004-11-18 19:11 tim |
| 7426 |
tim |
1779 |
|
| 7427 |
|
|
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
| 7428 |
|
|
|
| 7429 |
gezelter |
2199 |
2004-11-18 18:26 tim |
| 7430 |
tim |
1779 |
|
| 7431 |
tim |
2116 |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
| 7432 |
|
|
initially added on branch new_design. |
| 7433 |
|
|
|
| 7434 |
gezelter |
2199 |
2004-11-18 18:26 tim |
| 7435 |
tim |
2116 |
|
| 7436 |
tim |
1779 |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
| 7437 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 7438 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
| 7439 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
| 7440 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 7441 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 7442 |
|
|
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
| 7443 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
| 7444 |
|
|
DUFF parser |
| 7445 |
|
|
|
| 7446 |
gezelter |
2199 |
2004-11-18 16:42 tim |
| 7447 |
tim |
2102 |
|
| 7448 |
tim |
1779 |
* forceFields/newDUFF.frc: adding new format DUFF force field |
| 7449 |
|
|
|
| 7450 |
gezelter |
2199 |
2004-11-18 10:57 chrisfen |
| 7451 |
tim |
1779 |
|
| 7452 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
| 7453 |
|
|
slowed down the force loop |
| 7454 |
|
|
|
| 7455 |
gezelter |
2199 |
2004-11-18 00:42 tim |
| 7456 |
tim |
1779 |
|
| 7457 |
tim |
2116 |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
| 7458 |
tim |
1779 |
initially added on branch new_design. |
| 7459 |
|
|
|
| 7460 |
gezelter |
2199 |
2004-11-18 00:42 tim |
| 7461 |
tim |
1779 |
|
| 7462 |
tim |
2116 |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
| 7463 |
tim |
1779 |
initially added on branch new_design. |
| 7464 |
|
|
|
| 7465 |
gezelter |
2199 |
2004-11-18 00:42 tim |
| 7466 |
tim |
1779 |
|
| 7467 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
| 7468 |
|
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
| 7469 |
|
|
utils/NumericConstant.hpp: Adding NumericConstant class |
| 7470 |
|
|
|
| 7471 |
gezelter |
2199 |
2004-11-17 23:16 tim |
| 7472 |
tim |
1779 |
|
| 7473 |
|
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
| 7474 |
|
|
UseTheForce/ForceFields.hpp: remove more junk files |
| 7475 |
|
|
|
| 7476 |
gezelter |
2199 |
2004-11-17 23:12 tim |
| 7477 |
tim |
1779 |
|
| 7478 |
|
|
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
| 7479 |
|
|
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
| 7480 |
|
|
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
| 7481 |
|
|
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
| 7482 |
|
|
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
| 7483 |
|
|
primitives/TorsionExtensions.cpp: remove some junk files |
| 7484 |
|
|
|
| 7485 |
gezelter |
2199 |
2004-11-17 23:07 tim |
| 7486 |
tim |
1779 |
|
| 7487 |
|
|
* src/primitives/BendExtensions.cpp: remove some junk files |
| 7488 |
|
|
|
| 7489 |
gezelter |
2199 |
2004-11-17 23:04 tim |
| 7490 |
tim |
1779 |
|
| 7491 |
|
|
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
| 7492 |
|
|
QuadraticBondType.hpp: refine QudraticBond |
| 7493 |
|
|
|
| 7494 |
gezelter |
2199 |
2004-11-17 22:57 tim |
| 7495 |
tim |
1779 |
|
| 7496 |
|
|
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
| 7497 |
|
|
|
| 7498 |
gezelter |
2199 |
2004-11-17 22:57 tim |
| 7499 |
tim |
1779 |
|
| 7500 |
|
|
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
| 7501 |
|
|
initially added on branch new_design. |
| 7502 |
|
|
|
| 7503 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7504 |
tim |
1779 |
|
| 7505 |
tim |
2116 |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
| 7506 |
|
|
was initially added on branch new_design. |
| 7507 |
|
|
|
| 7508 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7509 |
tim |
2116 |
|
| 7510 |
tim |
1779 |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
| 7511 |
|
|
added on branch new_design. |
| 7512 |
|
|
|
| 7513 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7514 |
tim |
1779 |
|
| 7515 |
tim |
2116 |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
| 7516 |
|
|
added on branch new_design. |
| 7517 |
|
|
|
| 7518 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7519 |
tim |
2116 |
|
| 7520 |
tim |
1779 |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
| 7521 |
|
|
initially added on branch new_design. |
| 7522 |
|
|
|
| 7523 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7524 |
tim |
1779 |
|
| 7525 |
tim |
2116 |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
| 7526 |
tim |
1779 |
initially added on branch new_design. |
| 7527 |
|
|
|
| 7528 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7529 |
tim |
1779 |
|
| 7530 |
tim |
2116 |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
| 7531 |
tim |
1779 |
initially added on branch new_design. |
| 7532 |
|
|
|
| 7533 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7534 |
tim |
1779 |
|
| 7535 |
|
|
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
| 7536 |
|
|
added on branch new_design. |
| 7537 |
|
|
|
| 7538 |
gezelter |
2199 |
2004-11-17 16:47 tim |
| 7539 |
tim |
1779 |
|
| 7540 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
| 7541 |
|
|
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
| 7542 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
| 7543 |
|
|
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
| 7544 |
|
|
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
| 7545 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
| 7546 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 7547 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
| 7548 |
|
|
UreyBradleyBend and GhostBend |
| 7549 |
|
|
|
| 7550 |
gezelter |
2199 |
2004-11-17 13:58 tim |
| 7551 |
tim |
2102 |
|
| 7552 |
tim |
1779 |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
| 7553 |
|
|
was initially added on branch new_design. |
| 7554 |
|
|
|
| 7555 |
gezelter |
2199 |
2004-11-17 13:58 tim |
| 7556 |
tim |
1779 |
|
| 7557 |
|
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
| 7558 |
|
|
was initially added on branch new_design. |
| 7559 |
|
|
|
| 7560 |
gezelter |
2199 |
2004-11-17 13:58 tim |
| 7561 |
tim |
1779 |
|
| 7562 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
| 7563 |
|
|
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
| 7564 |
|
|
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
| 7565 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
| 7566 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
| 7567 |
|
|
stuff and Chebyshev Polynomial |
| 7568 |
|
|
|
| 7569 |
gezelter |
2199 |
2004-11-17 13:58 tim |
| 7570 |
tim |
1779 |
|
| 7571 |
tim |
2116 |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
| 7572 |
tim |
1779 |
initially added on branch new_design. |
| 7573 |
|
|
|
| 7574 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7575 |
tim |
1779 |
|
| 7576 |
tim |
2116 |
* src/types/PolynomialTorsionType.hpp: file |
| 7577 |
|
|
PolynomialTorsionType.hpp was initially added on branch new_design. |
| 7578 |
tim |
1779 |
|
| 7579 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7580 |
tim |
1779 |
|
| 7581 |
|
|
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
| 7582 |
|
|
initially added on branch new_design. |
| 7583 |
|
|
|
| 7584 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7585 |
tim |
1779 |
|
| 7586 |
|
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
| 7587 |
|
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
| 7588 |
|
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
| 7589 |
|
|
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
| 7590 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
| 7591 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 7592 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
| 7593 |
|
|
utils/StringTokenizer.hpp: add PolynomialBondType, |
| 7594 |
|
|
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
| 7595 |
|
|
CharmmTorsionType. Need to refine the design and add document for |
| 7596 |
|
|
them |
| 7597 |
|
|
|
| 7598 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7599 |
tim |
1779 |
|
| 7600 |
tim |
2116 |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
| 7601 |
|
|
initially added on branch new_design. |
| 7602 |
|
|
|
| 7603 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7604 |
tim |
2116 |
|
| 7605 |
|
|
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
| 7606 |
|
|
initially added on branch new_design. |
| 7607 |
|
|
|
| 7608 |
gezelter |
2199 |
2004-11-17 01:37 tim |
| 7609 |
tim |
2116 |
|
| 7610 |
|
|
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
| 7611 |
|
|
initially added on branch new_design. |
| 7612 |
|
|
|
| 7613 |
gezelter |
2199 |
2004-11-16 20:11 tim |
| 7614 |
tim |
2116 |
|
| 7615 |
tim |
1779 |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
| 7616 |
|
|
TorsionType.hpp: add PolynomialBondType |
| 7617 |
|
|
|
| 7618 |
gezelter |
2199 |
2004-11-16 20:11 tim |
| 7619 |
tim |
1779 |
|
| 7620 |
|
|
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
| 7621 |
|
|
initially added on branch new_design. |
| 7622 |
|
|
|
| 7623 |
gezelter |
2199 |
2004-11-16 18:20 tim |
| 7624 |
tim |
1779 |
|
| 7625 |
|
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
| 7626 |
|
|
on branch new_design. |
| 7627 |
|
|
|
| 7628 |
gezelter |
2199 |
2004-11-16 18:20 tim |
| 7629 |
tim |
1779 |
|
| 7630 |
tim |
2116 |
* src/math/Polynomial.hpp: Adding Polynomial class |
| 7631 |
tim |
1779 |
|
| 7632 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
| 7633 |
tim |
1779 |
|
| 7634 |
|
|
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
| 7635 |
|
|
added on branch new_design. |
| 7636 |
|
|
|
| 7637 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
| 7638 |
tim |
1779 |
|
| 7639 |
tim |
2116 |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
| 7640 |
|
|
initially added on branch new_design. |
| 7641 |
|
|
|
| 7642 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
| 7643 |
tim |
2116 |
|
| 7644 |
tim |
1779 |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
| 7645 |
|
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
| 7646 |
|
|
|
| 7647 |
gezelter |
2199 |
2004-11-16 15:36 tim |
| 7648 |
tim |
1779 |
|
| 7649 |
|
|
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
| 7650 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
| 7651 |
|
|
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
| 7652 |
|
|
TorsionType |
| 7653 |
|
|
|
| 7654 |
gezelter |
2199 |
2004-11-15 21:07 tim |
| 7655 |
tim |
1779 |
|
| 7656 |
tim |
2116 |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
| 7657 |
|
|
branch new_design. |
| 7658 |
|
|
|
| 7659 |
gezelter |
2199 |
2004-11-15 21:07 tim |
| 7660 |
tim |
2116 |
|
| 7661 |
tim |
1779 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 7662 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
| 7663 |
|
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
| 7664 |
|
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
| 7665 |
|
|
|
| 7666 |
gezelter |
2199 |
2004-11-15 18:00 tim |
| 7667 |
tim |
1779 |
|
| 7668 |
tim |
2116 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 7669 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
| 7670 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
| 7671 |
|
|
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
| 7672 |
|
|
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
| 7673 |
tim |
1779 |
|
| 7674 |
gezelter |
2199 |
2004-11-15 18:00 tim |
| 7675 |
tim |
1779 |
|
| 7676 |
|
|
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
| 7677 |
|
|
was initially added on branch new_design. |
| 7678 |
|
|
|
| 7679 |
gezelter |
2199 |
2004-11-15 18:00 tim |
| 7680 |
tim |
1779 |
|
| 7681 |
tim |
2116 |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
| 7682 |
|
|
was initially added on branch new_design. |
| 7683 |
|
|
|
| 7684 |
gezelter |
2199 |
2004-11-15 18:00 tim |
| 7685 |
tim |
2116 |
|
| 7686 |
tim |
2102 |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
| 7687 |
|
|
branch new_design. |
| 7688 |
tim |
1779 |
|
| 7689 |
gezelter |
2199 |
2004-11-15 13:02 tim |
| 7690 |
tim |
1779 |
|
| 7691 |
tim |
2116 |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
| 7692 |
|
|
initially added on branch new_design. |
| 7693 |
tim |
1779 |
|
| 7694 |
gezelter |
2199 |
2004-11-15 13:02 tim |
| 7695 |
tim |
1779 |
|
| 7696 |
|
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
| 7697 |
|
|
branch new_design. |
| 7698 |
|
|
|
| 7699 |
gezelter |
2199 |
2004-11-15 13:02 tim |
| 7700 |
tim |
1779 |
|
| 7701 |
|
|
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
| 7702 |
|
|
branch new_design. |
| 7703 |
|
|
|
| 7704 |
gezelter |
2199 |
2004-11-15 13:02 tim |
| 7705 |
tim |
1779 |
|
| 7706 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 7707 |
|
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 7708 |
|
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
| 7709 |
|
|
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
| 7710 |
|
|
DumpWriter.Next Step is LJFF and integrators |
| 7711 |
|
|
|
| 7712 |
gezelter |
2199 |
2004-11-13 00:08 tim |
| 7713 |
tim |
1779 |
|
| 7714 |
|
|
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 7715 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 7716 |
|
|
brains/SimInfo.hpp, primitives/Molecule.cpp, |
| 7717 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
| 7718 |
|
|
refactory, refactory |
| 7719 |
|
|
|
| 7720 |
gezelter |
2199 |
2004-11-12 17:43 tim |
| 7721 |
tim |
1779 |
|
| 7722 |
|
|
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
| 7723 |
|
|
StringTokenizer.cpp: bug fix in hasMoreTokens |
| 7724 |
|
|
|
| 7725 |
gezelter |
2199 |
2004-11-12 17:28 tim |
| 7726 |
tim |
1779 |
|
| 7727 |
|
|
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
| 7728 |
|
|
initially added on branch new_design. |
| 7729 |
|
|
|
| 7730 |
gezelter |
2199 |
2004-11-12 17:28 tim |
| 7731 |
tim |
1779 |
|
| 7732 |
|
|
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
| 7733 |
|
|
StringUtils, a c-style strtok like class, need unit test |
| 7734 |
|
|
|
| 7735 |
gezelter |
2199 |
2004-11-12 12:40 tim |
| 7736 |
tim |
1779 |
|
| 7737 |
|
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 7738 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 7739 |
|
|
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
| 7740 |
|
|
|
| 7741 |
gezelter |
2199 |
2004-11-12 02:05 tim |
| 7742 |
tim |
1779 |
|
| 7743 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 7744 |
|
|
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
| 7745 |
|
|
MoleculeCreator forget to create CutoffGroups for free atoms |
| 7746 |
|
|
|
| 7747 |
gezelter |
2199 |
2004-11-12 01:19 tim |
| 7748 |
tim |
1779 |
|
| 7749 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 7750 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 7751 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
| 7752 |
|
|
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
| 7753 |
|
|
OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 7754 |
|
|
|
| 7755 |
gezelter |
2199 |
2004-11-11 16:48 chrisfen |
| 7756 |
tim |
1779 |
|
| 7757 |
|
|
* samples/water/tip3p_ice/tp3.md: working sample |
| 7758 |
|
|
|
| 7759 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
| 7760 |
tim |
1779 |
|
| 7761 |
|
|
* src/restraints/Restraints.cpp: working towards parallel |
| 7762 |
|
|
restraints |
| 7763 |
|
|
|
| 7764 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
| 7765 |
tim |
1779 |
|
| 7766 |
|
|
* src/integrators/Integrator.cpp: Commented out some write |
| 7767 |
|
|
statements |
| 7768 |
|
|
|
| 7769 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
| 7770 |
tim |
1779 |
|
| 7771 |
|
|
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
| 7772 |
|
|
write statements |
| 7773 |
|
|
|
| 7774 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
| 7775 |
tim |
1779 |
|
| 7776 |
|
|
* samples/water/tip3p_ice/tp3.md: Fun with ice |
| 7777 |
|
|
|
| 7778 |
gezelter |
2199 |
2004-11-11 11:41 tim |
| 7779 |
tim |
1779 |
|
| 7780 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 7781 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 7782 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
| 7783 |
|
|
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
| 7784 |
|
|
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
| 7785 |
|
|
useless mpiSimulation |
| 7786 |
|
|
|
| 7787 |
gezelter |
2199 |
2004-11-11 11:41 tim |
| 7788 |
tim |
1779 |
|
| 7789 |
|
|
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
| 7790 |
|
|
branch new_design. |
| 7791 |
|
|
|
| 7792 |
gezelter |
2199 |
2004-11-10 17:50 tim |
| 7793 |
tim |
1779 |
|
| 7794 |
|
|
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
| 7795 |
|
|
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
| 7796 |
|
|
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
| 7797 |
|
|
|
| 7798 |
gezelter |
2199 |
2004-11-10 17:01 tim |
| 7799 |
tim |
1779 |
|
| 7800 |
|
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 7801 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
| 7802 |
|
|
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 7803 |
|
|
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
| 7804 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 7805 |
|
|
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
| 7806 |
|
|
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
| 7807 |
|
|
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
| 7808 |
|
|
File will be removed) (3) ForceField (at least LJ) and BondType, |
| 7809 |
|
|
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
| 7810 |
|
|
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
| 7811 |
|
|
|
| 7812 |
gezelter |
2199 |
2004-11-10 09:52 tim |
| 7813 |
tim |
1779 |
|
| 7814 |
|
|
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
| 7815 |
|
|
configurable StatWriter |
| 7816 |
|
|
|
| 7817 |
gezelter |
2199 |
2004-11-10 09:52 tim |
| 7818 |
tim |
1779 |
|
| 7819 |
|
|
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
| 7820 |
|
|
branch new_design. |
| 7821 |
|
|
|
| 7822 |
gezelter |
2199 |
2004-11-09 21:58 tim |
| 7823 |
tim |
1779 |
|
| 7824 |
|
|
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
| 7825 |
|
|
in progress |
| 7826 |
|
|
|
| 7827 |
gezelter |
2199 |
2004-11-09 18:11 tim |
| 7828 |
tim |
1779 |
|
| 7829 |
tim |
2116 |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
| 7830 |
|
|
added on branch new_design. |
| 7831 |
|
|
|
| 7832 |
gezelter |
2199 |
2004-11-09 18:11 tim |
| 7833 |
tim |
2116 |
|
| 7834 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: file |
| 7835 |
|
|
VelocityVerletIntegrator.cpp was initially added on branch |
| 7836 |
|
|
new_design. |
| 7837 |
|
|
|
| 7838 |
gezelter |
2199 |
2004-11-09 18:11 tim |
| 7839 |
tim |
2116 |
|
| 7840 |
tim |
1779 |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
| 7841 |
|
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 7842 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
| 7843 |
|
|
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
| 7844 |
|
|
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
| 7845 |
|
|
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
| 7846 |
|
|
|
| 7847 |
gezelter |
2199 |
2004-11-09 18:11 tim |
| 7848 |
tim |
1779 |
|
| 7849 |
|
|
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
| 7850 |
|
|
added on branch new_design. |
| 7851 |
|
|
|
| 7852 |
gezelter |
2199 |
2004-11-09 18:11 tim |
| 7853 |
tim |
1779 |
|
| 7854 |
|
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
| 7855 |
|
|
branch new_design. |
| 7856 |
|
|
|
| 7857 |
gezelter |
2199 |
2004-11-08 20:08 tim |
| 7858 |
tim |
2102 |
|
| 7859 |
tim |
1779 |
* src/integrators/VelocityVerletIntegrator.hpp: file |
| 7860 |
|
|
VelocityVerletIntegrator.hpp was initially added on branch |
| 7861 |
|
|
new_design. |
| 7862 |
|
|
|
| 7863 |
gezelter |
2199 |
2004-11-08 20:08 tim |
| 7864 |
tim |
1779 |
|
| 7865 |
tim |
2116 |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
| 7866 |
|
|
branch new_design. |
| 7867 |
|
|
|
| 7868 |
gezelter |
2199 |
2004-11-08 20:08 tim |
| 7869 |
tim |
2116 |
|
| 7870 |
tim |
1779 |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
| 7871 |
|
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
| 7872 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 7873 |
|
|
utils/TypeContainer.hpp: More to break |
| 7874 |
|
|
|
| 7875 |
gezelter |
2199 |
2004-11-06 00:21 tim |
| 7876 |
tim |
2102 |
|
| 7877 |
tim |
1779 |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
| 7878 |
|
|
added on branch new_design. |
| 7879 |
|
|
|
| 7880 |
gezelter |
2199 |
2004-11-06 00:21 tim |
| 7881 |
tim |
1779 |
|
| 7882 |
|
|
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
| 7883 |
|
|
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
| 7884 |
|
|
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
| 7885 |
|
|
ForceField and TypeContainer classes |
| 7886 |
|
|
|
| 7887 |
gezelter |
2199 |
2004-11-05 18:38 tim |
| 7888 |
tim |
1779 |
|
| 7889 |
tim |
2116 |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
| 7890 |
|
|
initially added on branch new_design. |
| 7891 |
|
|
|
| 7892 |
gezelter |
2199 |
2004-11-05 18:38 tim |
| 7893 |
tim |
2116 |
|
| 7894 |
tim |
1779 |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
| 7895 |
|
|
initially added on branch new_design. |
| 7896 |
|
|
|
| 7897 |
gezelter |
2199 |
2004-11-05 18:38 tim |
| 7898 |
tim |
1779 |
|
| 7899 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 7900 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 7901 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 7902 |
|
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
| 7903 |
|
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
| 7904 |
|
|
|
| 7905 |
gezelter |
2199 |
2004-11-05 16:45 chrisfen |
| 7906 |
tim |
2102 |
|
| 7907 |
tim |
1779 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 7908 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
| 7909 |
|
|
linear visitor |
| 7910 |
|
|
|
| 7911 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
| 7912 |
tim |
1779 |
|
| 7913 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
| 7914 |
|
|
debugging process |
| 7915 |
|
|
|
| 7916 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
| 7917 |
tim |
1779 |
|
| 7918 |
|
|
* make/Makefile.in: included visitors and minimizer |
| 7919 |
|
|
|
| 7920 |
gezelter |
2199 |
2004-11-05 16:03 chrisfen |
| 7921 |
tim |
1779 |
|
| 7922 |
|
|
* ChangeLog: new changes |
| 7923 |
|
|
|
| 7924 |
gezelter |
2199 |
2004-11-04 21:56 tim |
| 7925 |
tim |
1701 |
|
| 7926 |
chrisfen |
1714 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
| 7927 |
|
|
primitives/Molecule.hpp: Pain...... |
| 7928 |
tim |
1712 |
|
| 7929 |
gezelter |
2199 |
2004-11-04 15:55 tim |
| 7930 |
chrisfen |
1714 |
|
| 7931 |
|
|
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
| 7932 |
|
|
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
| 7933 |
|
|
src/brains/Stats.hpp: time to break SimSetup |
| 7934 |
|
|
|
| 7935 |
gezelter |
2199 |
2004-11-04 15:51 gezelter |
| 7936 |
chrisfen |
1714 |
|
| 7937 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
| 7938 |
|
|
classes in progress |
| 7939 |
|
|
|
| 7940 |
gezelter |
2199 |
2004-11-04 14:48 tim |
| 7941 |
tim |
1712 |
|
| 7942 |
|
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
| 7943 |
tim |
1701 |
branch new_design. |
| 7944 |
|
|
|
| 7945 |
gezelter |
2199 |
2004-11-04 14:48 tim |
| 7946 |
tim |
1712 |
|
| 7947 |
|
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
| 7948 |
|
|
branch new_design. |
| 7949 |
|
|
|
| 7950 |
gezelter |
2199 |
2004-11-04 14:48 tim |
| 7951 |
tim |
1712 |
|
| 7952 |
tim |
2116 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 7953 |
|
|
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 7954 |
|
|
class |
| 7955 |
|
|
|
| 7956 |
gezelter |
2199 |
2004-11-04 11:22 gezelter |
| 7957 |
tim |
2116 |
|
| 7958 |
tim |
1712 |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 7959 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
| 7960 |
|
|
linearAxis are virtual in StuntDouble, but are implemented by |
| 7961 |
|
|
DirectionalAtom and RigidBody In StuntDouble, they should return |
| 7962 |
|
|
false and "-1" but there should be logic to figure them out in the |
| 7963 |
|
|
other two classes |
| 7964 |
|
|
|
| 7965 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
| 7966 |
tim |
1712 |
|
| 7967 |
|
|
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
| 7968 |
|
|
remember what I did |
| 7969 |
|
|
|
| 7970 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
| 7971 |
tim |
1712 |
|
| 7972 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
| 7973 |
|
|
|
| 7974 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
| 7975 |
tim |
1712 |
|
| 7976 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
| 7977 |
|
|
in the entry_plug so that it only is set if the atoms really are in |
| 7978 |
|
|
the simulation |
| 7979 |
|
|
|
| 7980 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
| 7981 |
tim |
1712 |
|
| 7982 |
|
|
* samples/water/ssd/ssd.md: testing force fields |
| 7983 |
|
|
|
| 7984 |
gezelter |
2199 |
2004-11-04 11:19 gezelter |
| 7985 |
tim |
1712 |
|
| 7986 |
|
|
* samples/shape/linear.in: testing shapes |
| 7987 |
|
|
|
| 7988 |
gezelter |
2199 |
2004-11-03 14:56 tim |
| 7989 |
tim |
1712 |
|
| 7990 |
|
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
| 7991 |
|
|
class(similar as SimSetup) |
| 7992 |
|
|
|
| 7993 |
gezelter |
2199 |
2004-11-03 14:56 tim |
| 7994 |
tim |
1712 |
|
| 7995 |
|
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
| 7996 |
|
|
added on branch new_design. |
| 7997 |
|
|
|
| 7998 |
gezelter |
2199 |
2004-11-03 14:56 tim |
| 7999 |
chrisfen |
1714 |
|
| 8000 |
|
|
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
| 8001 |
|
|
added on branch new_design. |
| 8002 |
|
|
|
| 8003 |
gezelter |
2199 |
2004-11-03 13:00 tim |
| 8004 |
tim |
1712 |
|
| 8005 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8006 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
| 8007 |
|
|
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
| 8008 |
|
|
brains/DataStorage.hpp, primitives/Atom.hpp, |
| 8009 |
|
|
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
| 8010 |
|
|
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
| 8011 |
|
|
compiled. Still a long way to go ...... |
| 8012 |
|
|
|
| 8013 |
gezelter |
2199 |
2004-11-03 11:08 tim |
| 8014 |
tim |
1712 |
|
| 8015 |
|
|
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
| 8016 |
|
|
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
| 8017 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
| 8018 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
| 8019 |
|
|
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
| 8020 |
|
|
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
| 8021 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
| 8022 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
| 8023 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
| 8024 |
|
|
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
| 8025 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
| 8026 |
|
|
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
| 8027 |
|
|
|
| 8028 |
gezelter |
2199 |
2004-11-02 17:41 tim |
| 8029 |
tim |
1712 |
|
| 8030 |
tim |
2116 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 8031 |
|
|
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 8032 |
|
|
Need unit test |
| 8033 |
chrisfen |
1714 |
|
| 8034 |
gezelter |
2199 |
2004-11-02 17:41 tim |
| 8035 |
chrisfen |
1714 |
|
| 8036 |
tim |
1712 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
| 8037 |
|
|
initially added on branch new_design. |
| 8038 |
|
|
|
| 8039 |
gezelter |
2199 |
2004-11-02 17:41 tim |
| 8040 |
tim |
1712 |
|
| 8041 |
tim |
2116 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
| 8042 |
|
|
branch new_design. |
| 8043 |
tim |
1712 |
|
| 8044 |
gezelter |
2199 |
2004-11-02 11:59 tim |
| 8045 |
tim |
1712 |
|
| 8046 |
tim |
2116 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 8047 |
|
|
branch new_design. |
| 8048 |
|
|
|
| 8049 |
gezelter |
2199 |
2004-11-02 11:59 tim |
| 8050 |
tim |
2116 |
|
| 8051 |
tim |
2102 |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 8052 |
|
|
SimSnapshotManager.hpp: SimModel in progress |
| 8053 |
tim |
1712 |
|
| 8054 |
gezelter |
2199 |
2004-11-02 10:28 chrisfen |
| 8055 |
tim |
1701 |
|
| 8056 |
|
|
* src/: UseTheForce/DarkSide/shapes.F90, |
| 8057 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
| 8058 |
|
|
looks like it's working |
| 8059 |
|
|
|
| 8060 |
gezelter |
2199 |
2004-11-02 10:27 tim |
| 8061 |
tim |
1701 |
|
| 8062 |
tim |
2116 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 8063 |
|
|
functions for dealing with memory issue |
| 8064 |
|
|
|
| 8065 |
gezelter |
2199 |
2004-11-02 10:27 tim |
| 8066 |
tim |
2116 |
|
| 8067 |
tim |
2102 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 8068 |
|
|
added on branch new_design. |
| 8069 |
tim |
1701 |
|
| 8070 |
gezelter |
2199 |
2004-11-02 10:23 tim |
| 8071 |
tim |
1701 |
|
| 8072 |
|
|
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
| 8073 |
|
|
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
| 8074 |
|
|
SimModel(something similar as SimInfo) |
| 8075 |
|
|
|
| 8076 |
gezelter |
2199 |
2004-11-01 17:52 tim |
| 8077 |
tim |
1701 |
|
| 8078 |
|
|
* src/: applications/simpleBuilder/MoLocator.hpp, |
| 8079 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 8080 |
|
|
brains/DataStorage.hpp, brains/ForceFields.cpp, |
| 8081 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
| 8082 |
|
|
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
| 8083 |
|
|
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
| 8084 |
|
|
math/SquareMatrix3.hpp, math/Vector3.hpp, |
| 8085 |
|
|
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
| 8086 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 8087 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 8088 |
|
|
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
| 8089 |
|
|
restraints/Restraints.cpp, types/TorsionType.hpp, |
| 8090 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
| 8091 |
|
|
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
| 8092 |
|
|
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
| 8093 |
|
|
RigidBody and StuntDouble classes get compiled |
| 8094 |
|
|
|
| 8095 |
gezelter |
2199 |
2004-11-01 16:40 tim |
| 8096 |
tim |
1701 |
|
| 8097 |
tim |
2116 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 8098 |
|
|
on branch new_design. |
| 8099 |
|
|
|
| 8100 |
gezelter |
2199 |
2004-11-01 16:40 tim |
| 8101 |
tim |
2116 |
|
| 8102 |
tim |
2102 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 8103 |
|
|
branch new_design. |
| 8104 |
tim |
1701 |
|
| 8105 |
gezelter |
2199 |
2004-11-01 16:40 tim |
| 8106 |
tim |
1701 |
|
| 8107 |
|
|
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
| 8108 |
|
|
branch new_design. |
| 8109 |
|
|
|
| 8110 |
gezelter |
2199 |
2004-11-01 16:40 tim |
| 8111 |
tim |
1701 |
|
| 8112 |
tim |
2116 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 8113 |
|
|
version of Bond, Bend and Torsion. |
| 8114 |
tim |
1701 |
|
| 8115 |
gezelter |
2199 |
2004-11-01 16:37 tim |
| 8116 |
tim |
1701 |
|
| 8117 |
|
|
* src/types/BendType.hpp: file BendType.hpp was initially added on |
| 8118 |
|
|
branch new_design. |
| 8119 |
|
|
|
| 8120 |
gezelter |
2199 |
2004-11-01 16:37 tim |
| 8121 |
tim |
1701 |
|
| 8122 |
tim |
2116 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 8123 |
|
|
BondType, BendType, TorsionType |
| 8124 |
tim |
1701 |
|
| 8125 |
gezelter |
2199 |
2004-11-01 16:37 tim |
| 8126 |
tim |
1701 |
|
| 8127 |
|
|
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
| 8128 |
|
|
added on branch new_design. |
| 8129 |
|
|
|
| 8130 |
gezelter |
2199 |
2004-11-01 16:37 tim |
| 8131 |
tim |
1701 |
|
| 8132 |
tim |
2116 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 8133 |
|
|
branch new_design. |
| 8134 |
tim |
1701 |
|
| 8135 |
gezelter |
2199 |
2004-11-01 15:15 tim |
| 8136 |
tim |
1701 |
|
| 8137 |
|
|
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 8138 |
|
|
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 8139 |
|
|
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
| 8140 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
| 8141 |
|
|
break, break and break..... |
| 8142 |
|
|
|
| 8143 |
gezelter |
2199 |
2004-11-01 14:57 tim |
| 8144 |
tim |
1701 |
|
| 8145 |
|
|
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
| 8146 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
| 8147 |
|
|
StuntDouble.hpp: these core classes get compiled |
| 8148 |
|
|
|
| 8149 |
chrisfen |
2762 |
2004-10-29 18:37 tim |
| 8150 |
tim |
1701 |
|
| 8151 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
| 8152 |
|
|
class |
| 8153 |
|
|
|
| 8154 |
chrisfen |
2762 |
2004-10-29 18:28 chrisfen |
| 8155 |
tim |
1701 |
|
| 8156 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
| 8157 |
|
|
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
| 8158 |
|
|
types/ShapeAtomType.cpp: still debugging |
| 8159 |
|
|
|
| 8160 |
chrisfen |
2762 |
2004-10-29 18:28 chrisfen |
| 8161 |
tim |
1701 |
|
| 8162 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
| 8163 |
|
|
shapes rcut calculator added |
| 8164 |
|
|
|
| 8165 |
chrisfen |
2762 |
2004-10-29 18:27 chrisfen |
| 8166 |
tim |
1701 |
|
| 8167 |
|
|
* samples/shape/linear.md: shorter run |
| 8168 |
|
|
|
| 8169 |
chrisfen |
2762 |
2004-10-29 16:54 tim |
| 8170 |
tim |
1701 |
|
| 8171 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
| 8172 |
|
|
|
| 8173 |
chrisfen |
2762 |
2004-10-29 12:22 tim |
| 8174 |
tim |
1701 |
|
| 8175 |
|
|
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
| 8176 |
|
|
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
| 8177 |
|
|
some deprecated files |
| 8178 |
|
|
|
| 8179 |
chrisfen |
2762 |
2004-10-29 12:20 tim |
| 8180 |
tim |
1701 |
|
| 8181 |
|
|
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
| 8182 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
| 8183 |
|
|
More painful reconstruction is coming !!! |
| 8184 |
|
|
|
| 8185 |
chrisfen |
2762 |
2004-10-28 18:34 tim |
| 8186 |
tim |
1701 |
|
| 8187 |
|
|
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
| 8188 |
|
|
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
| 8189 |
|
|
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
| 8190 |
|
|
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
| 8191 |
|
|
DirectionalAtom and RigidBody |
| 8192 |
|
|
|
| 8193 |
chrisfen |
2762 |
2004-10-28 18:26 tim |
| 8194 |
tim |
1701 |
|
| 8195 |
|
|
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
| 8196 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
| 8197 |
|
|
src/applications/simpleBuilder/Vector3d.hpp, |
| 8198 |
|
|
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
| 8199 |
|
|
remove old Vector3d.hpp from application/simpleBuilder |
| 8200 |
|
|
|
| 8201 |
chrisfen |
2762 |
2004-10-28 17:42 tim |
| 8202 |
tim |
1701 |
|
| 8203 |
|
|
* src/utils/next_combination.hpp: Minor change in next_combination |
| 8204 |
|
|
|
| 8205 |
chrisfen |
2762 |
2004-10-28 17:28 tim |
| 8206 |
tim |
1681 |
|
| 8207 |
|
|
* src/utils/next_combination.hpp, |
| 8208 |
|
|
test/utils/NextCombinationTestCase.cpp, |
| 8209 |
|
|
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
| 8210 |
|
|
|
| 8211 |
chrisfen |
2762 |
2004-10-28 17:11 tim |
| 8212 |
tim |
1681 |
|
| 8213 |
|
|
* src/utils/next_combination.hpp: change documentation of |
| 8214 |
|
|
next_combination.hpp |
| 8215 |
|
|
|
| 8216 |
chrisfen |
2762 |
2004-10-28 16:41 tim |
| 8217 |
tim |
1681 |
|
| 8218 |
|
|
* ChangeLog, src/utils/next_combination.hpp, |
| 8219 |
|
|
test/utils/NextCombinationTestCase.cpp, |
| 8220 |
|
|
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
| 8221 |
|
|
|
| 8222 |
chrisfen |
2762 |
2004-10-28 16:01 tim |
| 8223 |
tim |
1681 |
|
| 8224 |
|
|
* src/utils/next_combination.hpp: adding replace wildcard function |
| 8225 |
|
|
|
| 8226 |
chrisfen |
2762 |
2004-10-28 15:33 tim |
| 8227 |
tim |
1681 |
|
| 8228 |
|
|
* src/utils/next_combination.hpp: Minor change |
| 8229 |
|
|
|
| 8230 |
chrisfen |
2762 |
2004-10-28 15:06 tim |
| 8231 |
tim |
1677 |
|
| 8232 |
|
|
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
| 8233 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
| 8234 |
|
|
src/utils/next_combination.hpp, test/utils/Makefile, |
| 8235 |
|
|
test/utils/NextCombinationTestCase.cpp, |
| 8236 |
|
|
test/utils/ReplaceWildCardTestCase.cpp, |
| 8237 |
|
|
test/utils/next_combination.hpp: STL next_permutation like |
| 8238 |
|
|
next_combination is working |
| 8239 |
|
|
|
| 8240 |
chrisfen |
2762 |
2004-10-28 13:22 chrisfen |
| 8241 |
tim |
1677 |
|
| 8242 |
|
|
* src/UseTheForce/WATER.cpp: fix of setDipoles |
| 8243 |
|
|
|
| 8244 |
chrisfen |
2762 |
2004-10-28 13:20 gezelter |
| 8245 |
tim |
1677 |
|
| 8246 |
|
|
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
| 8247 |
|
|
shapeFile |
| 8248 |
|
|
|
| 8249 |
chrisfen |
2762 |
2004-10-28 13:20 gezelter |
| 8250 |
tim |
1677 |
|
| 8251 |
|
|
* samples/shape/linear.md: forgot the orientation line |
| 8252 |
|
|
|
| 8253 |
chrisfen |
2762 |
2004-10-28 12:56 gezelter |
| 8254 |
tim |
1677 |
|
| 8255 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8256 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 8257 |
|
|
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
| 8258 |
|
|
declaration foo |
| 8259 |
|
|
|
| 8260 |
chrisfen |
2762 |
2004-10-28 12:55 gezelter |
| 8261 |
tim |
1677 |
|
| 8262 |
|
|
* samples/lipid/5x5.md: uncommented .in line |
| 8263 |
|
|
|
| 8264 |
chrisfen |
2762 |
2004-10-28 11:42 tim |
| 8265 |
tim |
1677 |
|
| 8266 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
| 8267 |
|
|
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
| 8268 |
|
|
in progress |
| 8269 |
|
|
|
| 8270 |
chrisfen |
2762 |
2004-10-28 11:15 tim |
| 8271 |
tim |
1677 |
|
| 8272 |
|
|
* test/utils/: NextCombinationTestCase.cpp, |
| 8273 |
|
|
NextCombinationTestCase.hpp: adding next_combination test case |
| 8274 |
|
|
|
| 8275 |
chrisfen |
2762 |
2004-10-28 11:02 tim |
| 8276 |
tim |
1677 |
|
| 8277 |
|
|
* test/utils/next_combination.hpp: STL Compatible combination |
| 8278 |
|
|
sequence generator |
| 8279 |
|
|
|
| 8280 |
chrisfen |
2762 |
2004-10-28 02:23 tim |
| 8281 |
tim |
1677 |
|
| 8282 |
|
|
* test/utils/: GenerateCombination.hpp, |
| 8283 |
|
|
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
| 8284 |
|
|
|
| 8285 |
chrisfen |
2762 |
2004-10-28 02:16 tim |
| 8286 |
tim |
1677 |
|
| 8287 |
|
|
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
| 8288 |
|
|
next_combination function. |
| 8289 |
|
|
|
| 8290 |
chrisfen |
2762 |
2004-10-27 23:27 tim |
| 8291 |
tim |
1677 |
|
| 8292 |
|
|
* test/utils/ReplaceWildCard.hpp: no message |
| 8293 |
|
|
|
| 8294 |
chrisfen |
2762 |
2004-10-27 23:14 tim |
| 8295 |
tim |
1677 |
|
| 8296 |
|
|
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
| 8297 |
|
|
ReplaceWildCard(recursive version) is working, need refactoring. An |
| 8298 |
|
|
iterative version is on the way |
| 8299 |
|
|
|
| 8300 |
chrisfen |
2762 |
2004-10-27 22:28 tim |
| 8301 |
tim |
1677 |
|
| 8302 |
|
|
* test/utils/: Makefile, ReplaceWildCard.hpp, |
| 8303 |
|
|
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
| 8304 |
|
|
|
| 8305 |
chrisfen |
2762 |
2004-10-27 22:08 tim |
| 8306 |
tim |
1677 |
|
| 8307 |
|
|
* test/utils/: ReplaceWildCardTestCase.cpp, |
| 8308 |
|
|
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
| 8309 |
|
|
|
| 8310 |
chrisfen |
2762 |
2004-10-27 19:17 tim |
| 8311 |
tim |
1677 |
|
| 8312 |
|
|
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
| 8313 |
|
|
test |
| 8314 |
|
|
|
| 8315 |
chrisfen |
2762 |
2004-10-27 02:25 tim |
| 8316 |
tim |
1677 |
|
| 8317 |
|
|
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
| 8318 |
|
|
char matching is on the way |
| 8319 |
|
|
|
| 8320 |
chrisfen |
2762 |
2004-10-27 02:07 tim |
| 8321 |
tim |
1677 |
|
| 8322 |
|
|
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
| 8323 |
|
|
|
| 8324 |
chrisfen |
2762 |
2004-10-26 23:00 gezelter |
| 8325 |
tim |
1674 |
|
| 8326 |
|
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
| 8327 |
|
|
|
| 8328 |
chrisfen |
2762 |
2004-10-26 22:20 gezelter |
| 8329 |
tim |
1674 |
|
| 8330 |
|
|
* src/UseTheForce/ForceFields.hpp: subclass foo |
| 8331 |
|
|
|
| 8332 |
chrisfen |
2762 |
2004-10-26 22:16 gezelter |
| 8333 |
tim |
1674 |
|
| 8334 |
|
|
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
| 8335 |
|
|
string conversion |
| 8336 |
|
|
|
| 8337 |
chrisfen |
2762 |
2004-10-26 20:01 gezelter |
| 8338 |
tim |
1674 |
|
| 8339 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8340 |
|
|
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
| 8341 |
|
|
brains/SimSetup.hpp: char* -> string |
| 8342 |
|
|
|
| 8343 |
chrisfen |
2762 |
2004-10-26 18:25 gezelter |
| 8344 |
tim |
1674 |
|
| 8345 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
| 8346 |
|
|
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
| 8347 |
|
|
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
| 8348 |
|
|
isXXX |
| 8349 |
|
|
|
| 8350 |
chrisfen |
2762 |
2004-10-26 18:25 gezelter |
| 8351 |
tim |
1674 |
|
| 8352 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 8353 |
|
|
define name collision |
| 8354 |
|
|
|
| 8355 |
chrisfen |
2762 |
2004-10-26 18:24 gezelter |
| 8356 |
tim |
1674 |
|
| 8357 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8358 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
| 8359 |
|
|
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
| 8360 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 8361 |
|
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
| 8362 |
|
|
forcefield refactoring for shapes |
| 8363 |
|
|
|
| 8364 |
chrisfen |
2762 |
2004-10-26 18:24 gezelter |
| 8365 |
tim |
1677 |
|
| 8366 |
|
|
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
| 8367 |
|
|
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
| 8368 |
|
|
linear.md, linear.shape, toluene.shape: adding sample shape |
| 8369 |
|
|
directory |
| 8370 |
|
|
|
| 8371 |
chrisfen |
2762 |
2004-10-26 18:19 tim |
| 8372 |
tim |
1674 |
|
| 8373 |
|
|
* ChangeLog, src/brains/DataStorage.cpp, |
| 8374 |
|
|
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
| 8375 |
|
|
test/brains/DataStorageTestCase.cpp, |
| 8376 |
|
|
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
| 8377 |
|
|
DataStorage passes unit test |
| 8378 |
|
|
|
| 8379 |
chrisfen |
2762 |
2004-10-26 14:03 chrisfen |
| 8380 |
tim |
1674 |
|
| 8381 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
| 8382 |
|
|
Changes to help advance shapes |
| 8383 |
|
|
|
| 8384 |
chrisfen |
2762 |
2004-10-26 14:02 chrisfen |
| 8385 |
tim |
1674 |
|
| 8386 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
| 8387 |
|
|
Shapes force field reader |
| 8388 |
|
|
|
| 8389 |
chrisfen |
2762 |
2004-10-26 13:28 tim |
| 8390 |
tim |
1674 |
|
| 8391 |
|
|
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
| 8392 |
|
|
SnapshotTestCase in progress |
| 8393 |
|
|
|
| 8394 |
chrisfen |
2762 |
2004-10-25 18:46 tim |
| 8395 |
tim |
1648 |
|
| 8396 |
|
|
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 8397 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 8398 |
|
|
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
| 8399 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
| 8400 |
|
|
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
| 8401 |
|
|
and Vector classes |
| 8402 |
|
|
|
| 8403 |
chrisfen |
2762 |
2004-10-25 13:03 tim |
| 8404 |
tim |
1644 |
|
| 8405 |
|
|
* ChangeLog, src/utils/GenericFactory.hpp, |
| 8406 |
|
|
test/utils/GenericFactoryTestCase.cpp, |
| 8407 |
|
|
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
| 8408 |
|
|
GenericFactory Test Case. GenericFactory now can bed used to creat |
| 8409 |
|
|
ForcefieldFactory and IntegratorFactory etc. |
| 8410 |
|
|
|
| 8411 |
chrisfen |
2762 |
2004-10-25 00:08 tim |
| 8412 |
tim |
1644 |
|
| 8413 |
|
|
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
| 8414 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
| 8415 |
|
|
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
| 8416 |
|
|
get reconstructed |
| 8417 |
|
|
|
| 8418 |
chrisfen |
2762 |
2004-10-24 03:55 tim |
| 8419 |
tim |
1644 |
|
| 8420 |
|
|
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
| 8421 |
|
|
|
| 8422 |
chrisfen |
2762 |
2004-10-23 19:09 tim |
| 8423 |
tim |
1644 |
|
| 8424 |
|
|
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
| 8425 |
|
|
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
| 8426 |
|
|
RigidBody.cpp: Refactoring in progress |
| 8427 |
|
|
|
| 8428 |
chrisfen |
2762 |
2004-10-22 19:09 tim |
| 8429 |
tim |
1643 |
|
| 8430 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
| 8431 |
|
|
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
| 8432 |
|
|
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
| 8433 |
|
|
test/brains/StuntDouble.hpp: more work in Snapshot |
| 8434 |
|
|
|
| 8435 |
chrisfen |
2762 |
2004-10-22 18:59 chrisfen |
| 8436 |
tim |
1643 |
|
| 8437 |
|
|
* src/: UseTheForce/LJFF.cpp, |
| 8438 |
|
|
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
| 8439 |
|
|
god! It runs and conserves energy! |
| 8440 |
|
|
|
| 8441 |
chrisfen |
2762 |
2004-10-22 18:54 chrisfen |
| 8442 |
tim |
1643 |
|
| 8443 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
| 8444 |
|
|
|
| 8445 |
chrisfen |
2762 |
2004-10-22 18:53 chrisfen |
| 8446 |
tim |
1643 |
|
| 8447 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8448 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 8449 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 8450 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
| 8451 |
|
|
breakey |
| 8452 |
|
|
|
| 8453 |
chrisfen |
2762 |
2004-10-22 18:53 chrisfen |
| 8454 |
tim |
1643 |
|
| 8455 |
|
|
* make/Makefile.in: compiler flags |
| 8456 |
|
|
|
| 8457 |
chrisfen |
2762 |
2004-10-22 17:20 gezelter |
| 8458 |
tim |
1643 |
|
| 8459 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8460 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
| 8461 |
|
|
brains/fSimulation.h, types/AtomType.hpp, |
| 8462 |
|
|
types/DirectionalAtomType.hpp: fixey fixey |
| 8463 |
|
|
|
| 8464 |
chrisfen |
2762 |
2004-10-22 16:22 gezelter |
| 8465 |
tim |
1643 |
|
| 8466 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
| 8467 |
|
|
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
| 8468 |
|
|
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
| 8469 |
|
|
fortran files and c/Fortran interfaces |
| 8470 |
|
|
|
| 8471 |
chrisfen |
2762 |
2004-10-22 16:21 gezelter |
| 8472 |
tim |
1643 |
|
| 8473 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
| 8474 |
|
|
DirectionalAtomType.hpp, Makefile: More on AtomType and |
| 8475 |
|
|
DirectionalAtomType |
| 8476 |
|
|
|
| 8477 |
chrisfen |
2762 |
2004-10-22 10:47 gezelter |
| 8478 |
tim |
1639 |
|
| 8479 |
|
|
* src/types/AtomType.hpp: Adding AtomType |
| 8480 |
|
|
|
| 8481 |
chrisfen |
2762 |
2004-10-21 17:31 tim |
| 8482 |
tim |
1639 |
|
| 8483 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
| 8484 |
|
|
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
| 8485 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 8486 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
| 8487 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
| 8488 |
|
|
Snapshot and SnapshotManager in progress |
| 8489 |
|
|
|
| 8490 |
chrisfen |
2762 |
2004-10-21 17:30 tim |
| 8491 |
tim |
1639 |
|
| 8492 |
|
|
* test/brains/: BrainsTest.cpp, Makefile, |
| 8493 |
|
|
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
| 8494 |
|
|
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
| 8495 |
|
|
Snapshot and snapshotManager. |
| 8496 |
|
|
|
| 8497 |
chrisfen |
2762 |
2004-10-21 16:15 gezelter |
| 8498 |
tim |
1630 |
|
| 8499 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8500 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 8501 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
| 8502 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
| 8503 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
| 8504 |
|
|
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
| 8505 |
|
|
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
| 8506 |
|
|
Fixey Fixey. |
| 8507 |
|
|
|
| 8508 |
chrisfen |
2762 |
2004-10-21 12:32 tim |
| 8509 |
tim |
1630 |
|
| 8510 |
|
|
* src/utils/GenericData.cpp, src/utils/Makefile, |
| 8511 |
|
|
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
| 8512 |
|
|
|
| 8513 |
chrisfen |
2762 |
2004-10-21 12:24 tim |
| 8514 |
tim |
1630 |
|
| 8515 |
|
|
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
| 8516 |
|
|
|
| 8517 |
chrisfen |
2762 |
2004-10-21 12:22 tim |
| 8518 |
tim |
1630 |
|
| 8519 |
|
|
* ChangeLog, src/brains/SimSetup.cpp, |
| 8520 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
| 8521 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 8522 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 8523 |
|
|
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
| 8524 |
|
|
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
| 8525 |
|
|
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
| 8526 |
|
|
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
| 8527 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
| 8528 |
|
|
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 8529 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
| 8530 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
| 8531 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 8532 |
|
|
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
| 8533 |
|
|
GenericData |
| 8534 |
|
|
|
| 8535 |
chrisfen |
2762 |
2004-10-21 11:25 chuckv |
| 8536 |
tim |
1630 |
|
| 8537 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
| 8538 |
|
|
module. |
| 8539 |
|
|
|
| 8540 |
chrisfen |
2762 |
2004-10-21 11:24 chuckv |
| 8541 |
tim |
1630 |
|
| 8542 |
|
|
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
| 8543 |
|
|
fortran lj module. |
| 8544 |
|
|
|
| 8545 |
chrisfen |
2762 |
2004-10-20 18:54 tim |
| 8546 |
tim |
1625 |
|
| 8547 |
|
|
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
| 8548 |
|
|
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
| 8549 |
|
|
test/utils/PropertyMapTestCase.cpp, |
| 8550 |
|
|
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
| 8551 |
|
|
GenericData and PropertyMap pass unit test. |
| 8552 |
|
|
|
| 8553 |
chrisfen |
2762 |
2004-10-20 17:52 gezelter |
| 8554 |
tim |
1622 |
|
| 8555 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
| 8556 |
|
|
DarkSide/sticky_interface.h: fixed a fortran name problem |
| 8557 |
|
|
|
| 8558 |
chrisfen |
2762 |
2004-10-20 17:38 tim |
| 8559 |
tim |
1622 |
|
| 8560 |
|
|
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
| 8561 |
|
|
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
| 8562 |
|
|
UtilTest, UtilTest.cpp: adding generic data test case |
| 8563 |
|
|
|
| 8564 |
chrisfen |
2762 |
2004-10-20 17:16 chuckv |
| 8565 |
tim |
1622 |
|
| 8566 |
|
|
* configure, ac-tools/aclocal.m4, |
| 8567 |
|
|
src/UseTheForce/DarkSide/Makefile, |
| 8568 |
|
|
src/UseTheForce/DarkSide/mpiSimulation.F90, |
| 8569 |
|
|
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 8570 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
| 8571 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 8572 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
| 8573 |
|
|
Fortran/C++ interface de-obfuscation project appears to be |
| 8574 |
|
|
complete! Woo hoo! |
| 8575 |
|
|
|
| 8576 |
chrisfen |
2762 |
2004-10-20 16:47 chuckv |
| 8577 |
tim |
1622 |
|
| 8578 |
|
|
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 8579 |
|
|
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
| 8580 |
|
|
continues |
| 8581 |
|
|
|
| 8582 |
chrisfen |
2762 |
2004-10-20 16:46 chuckv |
| 8583 |
tim |
1622 |
|
| 8584 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 8585 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 8586 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
| 8587 |
|
|
UseTheForce/doForces_interface.h, |
| 8588 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
| 8589 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
| 8590 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
| 8591 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
| 8592 |
|
|
UseTheForce/DarkSide/mpiSimulation_interface.h, |
| 8593 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
| 8594 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
| 8595 |
|
|
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
| 8596 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
| 8597 |
|
|
de-obfuscation project (It is a very long story) |
| 8598 |
|
|
|
| 8599 |
chrisfen |
2762 |
2004-10-20 14:07 tim |
| 8600 |
tim |
1622 |
|
| 8601 |
|
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
| 8602 |
|
|
test/math/SquareMatrix3TestCase.cpp, |
| 8603 |
|
|
test/math/SquareMatrixTestCase.cpp, |
| 8604 |
|
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
| 8605 |
|
|
|
| 8606 |
chrisfen |
2762 |
2004-10-20 01:52 tim |
| 8607 |
tim |
1616 |
|
| 8608 |
|
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
| 8609 |
|
|
SnapshotManager in design phase |
| 8610 |
|
|
|
| 8611 |
chrisfen |
2762 |
2004-10-20 00:54 gezelter |
| 8612 |
tim |
1616 |
|
| 8613 |
|
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
| 8614 |
|
|
problem prevented linking |
| 8615 |
|
|
|
| 8616 |
chrisfen |
2762 |
2004-10-20 00:54 gezelter |
| 8617 |
tim |
1616 |
|
| 8618 |
|
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
| 8619 |
|
|
|
| 8620 |
chrisfen |
2762 |
2004-10-20 00:26 gezelter |
| 8621 |
tim |
1616 |
|
| 8622 |
|
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
| 8623 |
|
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
| 8624 |
|
|
more fortran name mangling |
| 8625 |
|
|
|
| 8626 |
chrisfen |
2762 |
2004-10-20 00:23 gezelter |
| 8627 |
tim |
1616 |
|
| 8628 |
|
|
* src/profiling/timing.F90: yet more fortran renaming |
| 8629 |
|
|
|
| 8630 |
chrisfen |
2762 |
2004-10-20 00:19 gezelter |
| 8631 |
tim |
1616 |
|
| 8632 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
| 8633 |
|
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
| 8634 |
|
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
| 8635 |
|
|
wrappers.F90: Fortran name cleanup continues |
| 8636 |
|
|
|
| 8637 |
chrisfen |
2762 |
2004-10-20 00:12 gezelter |
| 8638 |
tim |
1616 |
|
| 8639 |
|
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
| 8640 |
|
|
broken fortran stuff |
| 8641 |
|
|
|
| 8642 |
chrisfen |
2762 |
2004-10-20 00:02 gezelter |
| 8643 |
tim |
1616 |
|
| 8644 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
| 8645 |
|
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
| 8646 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 8647 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 8648 |
|
|
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
| 8649 |
|
|
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
| 8650 |
|
|
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
| 8651 |
|
|
mpiSimulation_interface.h, mpiSimulation_module.F90, |
| 8652 |
|
|
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
| 8653 |
|
|
shapes_interface.h, shapes_module.h, simulation.F90, |
| 8654 |
|
|
simulation_interface.h, simulation_module.F90, |
| 8655 |
|
|
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
| 8656 |
|
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
| 8657 |
|
|
name sanity on the fortran side |
| 8658 |
|
|
|
| 8659 |
chrisfen |
2762 |
2004-10-19 20:18 tim |
| 8660 |
tim |
1616 |
|
| 8661 |
|
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
| 8662 |
|
|
|
| 8663 |
chrisfen |
2762 |
2004-10-19 19:01 tim |
| 8664 |
tim |
1616 |
|
| 8665 |
|
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 8666 |
|
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
| 8667 |
|
|
except diagonalize(), all of functions in math library pass the |
| 8668 |
|
|
test |
| 8669 |
|
|
|
| 8670 |
chrisfen |
2762 |
2004-10-19 18:43 chuckv |
| 8671 |
tim |
1616 |
|
| 8672 |
|
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
| 8673 |
|
|
C-fortran interface functions. |
| 8674 |
|
|
|
| 8675 |
chrisfen |
2762 |
2004-10-19 18:37 chuckv |
| 8676 |
tim |
1616 |
|
| 8677 |
|
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
| 8678 |
|
|
eam_module_inteface.h, gb_module_interface.h, |
| 8679 |
|
|
mpisimulation_module_interface.h, simulation_module_interface.h, |
| 8680 |
|
|
sticky_pair_module_interface.h: Added correct prototypes for |
| 8681 |
|
|
C-fortran interface functions. |
| 8682 |
|
|
|
| 8683 |
chrisfen |
2762 |
2004-10-19 17:28 tim |
| 8684 |
tim |
1616 |
|
| 8685 |
|
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
| 8686 |
|
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
| 8687 |
|
|
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
| 8688 |
|
|
test/math/RectMatrixTestCase.cpp, |
| 8689 |
|
|
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
| 8690 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
| 8691 |
|
|
bugs get fixed at math library |
| 8692 |
|
|
|
| 8693 |
chrisfen |
2762 |
2004-10-19 16:43 chuckv |
| 8694 |
tim |
1616 |
|
| 8695 |
|
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
| 8696 |
|
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
| 8697 |
|
|
DarkSide/mpisimulation_module_interface.h, |
| 8698 |
|
|
DarkSide/simulation_module_interface.h, |
| 8699 |
|
|
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
| 8700 |
|
|
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
| 8701 |
|
|
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
| 8702 |
|
|
DarkSide/simulation_module.F90, do_Forces.F90, |
| 8703 |
|
|
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
| 8704 |
|
|
notifycutoffs_module_interface.h: Added new files for fortran |
| 8705 |
|
|
interface. |
| 8706 |
|
|
|
| 8707 |
chrisfen |
2762 |
2004-10-19 16:43 gezelter |
| 8708 |
tim |
1616 |
|
| 8709 |
|
|
* src/UseTheForce/Makefile: regressing |
| 8710 |
|
|
|
| 8711 |
chrisfen |
2762 |
2004-10-19 16:40 gezelter |
| 8712 |
tim |
1616 |
|
| 8713 |
|
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
| 8714 |
|
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
| 8715 |
|
|
working on shapes for portability |
| 8716 |
|
|
|
| 8717 |
chrisfen |
2762 |
2004-10-19 16:40 gezelter |
| 8718 |
tim |
1616 |
|
| 8719 |
|
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
| 8720 |
|
|
|
| 8721 |
chrisfen |
2762 |
2004-10-19 14:21 chrisfen |
| 8722 |
tim |
1616 |
|
| 8723 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
| 8724 |
|
|
findBegin |
| 8725 |
|
|
|
| 8726 |
chrisfen |
2762 |
2004-10-19 00:34 tim |
| 8727 |
tim |
1603 |
|
| 8728 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
| 8729 |
|
|
are fixed in Vector class |
| 8730 |
|
|
|
| 8731 |
chrisfen |
2762 |
2004-10-19 00:28 tim |
| 8732 |
tim |
1603 |
|
| 8733 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
| 8734 |
|
|
some bugs in RectMatrixTestCase |
| 8735 |
|
|
|
| 8736 |
chrisfen |
2762 |
2004-10-19 00:21 tim |
| 8737 |
tim |
1603 |
|
| 8738 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
| 8739 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
| 8740 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
| 8741 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
| 8742 |
|
|
|
| 8743 |
chrisfen |
2762 |
2004-10-18 19:13 tim |
| 8744 |
tim |
1603 |
|
| 8745 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
| 8746 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 8747 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 8748 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
| 8749 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
| 8750 |
|
|
tests on math library |
| 8751 |
|
|
|
| 8752 |
chrisfen |
2762 |
2004-10-18 17:03 tim |
| 8753 |
tim |
1603 |
|
| 8754 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
| 8755 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
| 8756 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
| 8757 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
| 8758 |
|
|
more testing units |
| 8759 |
|
|
|
| 8760 |
chrisfen |
2762 |
2004-10-18 13:07 tim |
| 8761 |
tim |
1603 |
|
| 8762 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
| 8763 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
| 8764 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
| 8765 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
| 8766 |
|
|
|
| 8767 |
chrisfen |
2762 |
2004-10-18 12:30 gezelter |
| 8768 |
tim |
1603 |
|
| 8769 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 8770 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
| 8771 |
|
|
\phi) |
| 8772 |
|
|
|
| 8773 |
chrisfen |
2762 |
2004-10-18 12:29 gezelter |
| 8774 |
tim |
1603 |
|
| 8775 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
| 8776 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
| 8777 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
| 8778 |
|
|
Shapes into OOPSE |
| 8779 |
|
|
|
| 8780 |
chrisfen |
2762 |
2004-10-18 11:21 gezelter |
| 8781 |
tim |
1603 |
|
| 8782 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
| 8783 |
|
|
|
| 8784 |
chrisfen |
2762 |
2004-10-18 01:23 tim |
| 8785 |
tim |
1603 |
|
| 8786 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
| 8787 |
|
|
|
| 8788 |
chrisfen |
2762 |
2004-10-18 01:23 tim |
| 8789 |
tim |
1603 |
|
| 8790 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
| 8791 |
|
|
test case |
| 8792 |
|
|
|
| 8793 |
chrisfen |
2762 |
2004-10-16 21:19 tim |
| 8794 |
tim |
1594 |
|
| 8795 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
| 8796 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
| 8797 |
|
|
progress |
| 8798 |
|
|
|
| 8799 |
chrisfen |
2762 |
2004-10-15 21:31 tim |
| 8800 |
tim |
1594 |
|
| 8801 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
| 8802 |
|
|
|
| 8803 |
chrisfen |
2762 |
2004-10-15 17:11 tim |
| 8804 |
tim |
1594 |
|
| 8805 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
| 8806 |
|
|
IfstrstreamTestCase.hpp: adding test file |
| 8807 |
|
|
|
| 8808 |
chrisfen |
2762 |
2004-10-15 17:10 tim |
| 8809 |
tim |
1594 |
|
| 8810 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
| 8811 |
|
|
|
| 8812 |
chrisfen |
2762 |
2004-10-15 16:42 tim |
| 8813 |
tim |
1594 |
|
| 8814 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
| 8815 |
|
|
|
| 8816 |
chrisfen |
2762 |
2004-10-15 16:35 tim |
| 8817 |
tim |
1594 |
|
| 8818 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
| 8819 |
|
|
|
| 8820 |
chrisfen |
2762 |
2004-10-15 16:34 tim |
| 8821 |
tim |
1594 |
|
| 8822 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
| 8823 |
|
|
namespace oopse |
| 8824 |
|
|
|
| 8825 |
chrisfen |
2762 |
2004-10-15 15:38 chuckv |
| 8826 |
tim |
1594 |
|
| 8827 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
| 8828 |
|
|
XLF and XLC. |
| 8829 |
|
|
|
| 8830 |
chrisfen |
2762 |
2004-10-15 14:28 tim |
| 8831 |
tim |
1594 |
|
| 8832 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
| 8833 |
|
|
adding ifstrstream test case |
| 8834 |
|
|
|
| 8835 |
chrisfen |
2762 |
2004-10-15 14:20 tim |
| 8836 |
tim |
1594 |
|
| 8837 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
| 8838 |
|
|
|
| 8839 |
chrisfen |
2762 |
2004-10-15 14:18 tim |
| 8840 |
tim |
1594 |
|
| 8841 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
| 8842 |
|
|
|
| 8843 |
chrisfen |
2762 |
2004-10-15 14:17 tim |
| 8844 |
tim |
1594 |
|
| 8845 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
| 8846 |
|
|
|
| 8847 |
chrisfen |
2762 |
2004-10-15 14:16 tim |
| 8848 |
tim |
1594 |
|
| 8849 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 8850 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
| 8851 |
|
|
|
| 8852 |
chrisfen |
2762 |
2004-10-15 11:37 tim |
| 8853 |
tim |
1594 |
|
| 8854 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
| 8855 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
| 8856 |
|
|
|
| 8857 |
chrisfen |
2762 |
2004-10-15 11:20 tim |
| 8858 |
tim |
1594 |
|
| 8859 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
| 8860 |
|
|
|
| 8861 |
chrisfen |
2762 |
2004-10-15 11:19 tim |
| 8862 |
tim |
1594 |
|
| 8863 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
| 8864 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 8865 |
|
|
SquareMatrixTestCase class |
| 8866 |
|
|
|
| 8867 |
chrisfen |
2762 |
2004-10-15 03:52 tim |
| 8868 |
tim |
1594 |
|
| 8869 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
| 8870 |
|
|
|
| 8871 |
chrisfen |
2762 |
2004-10-14 19:28 tim |
| 8872 |
tim |
1594 |
|
| 8873 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 8874 |
|
|
Vector.hpp: math library in progress |
| 8875 |
|
|
|
| 8876 |
chrisfen |
2762 |
2004-10-14 19:27 tim |
| 8877 |
tim |
1594 |
|
| 8878 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
| 8879 |
|
|
|
| 8880 |
chrisfen |
2762 |
2004-10-13 19:53 tim |
| 8881 |
tim |
1594 |
|
| 8882 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
| 8883 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
| 8884 |
|
|
|
| 8885 |
chrisfen |
2762 |
2004-10-13 18:28 tim |
| 8886 |
tim |
1594 |
|
| 8887 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
| 8888 |
|
|
class |
| 8889 |
|
|
|
| 8890 |
chrisfen |
2762 |
2004-10-13 18:27 tim |
| 8891 |
tim |
1594 |
|
| 8892 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
| 8893 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
| 8894 |
|
|
|
| 8895 |
chrisfen |
2762 |
2004-10-13 18:24 tim |
| 8896 |
tim |
1594 |
|
| 8897 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
| 8898 |
|
|
|
| 8899 |
chrisfen |
2762 |
2004-10-13 02:51 tim |
| 8900 |
tim |
1594 |
|
| 8901 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
| 8902 |
|
|
Vector3.hpp: refactory vector and matrix classes |
| 8903 |
|
|
|
| 8904 |
chrisfen |
2762 |
2004-10-13 02:50 tim |
| 8905 |
tim |
1594 |
|
| 8906 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
| 8907 |
|
|
|
| 8908 |
chrisfen |
2762 |
2004-10-12 19:57 tim |
| 8909 |
tim |
1594 |
|
| 8910 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
| 8911 |
|
|
Matrix3x3d.hpp |
| 8912 |
|
|
|
| 8913 |
chrisfen |
2762 |
2004-10-12 15:08 tim |
| 8914 |
tim |
1594 |
|
| 8915 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
| 8916 |
|
|
|
| 8917 |
chrisfen |
2762 |
2004-10-11 18:15 tim |
| 8918 |
tim |
1594 |
|
| 8919 |
|
|
* src/: constraints/AbstractClasses.hpp, |
| 8920 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 8921 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
| 8922 |
|
|
|
| 8923 |
chrisfen |
2762 |
2004-10-11 17:54 tim |
| 8924 |
tim |
1594 |
|
| 8925 |
|
|
* scripts/filepp: fix a bug in filepp |
| 8926 |
|
|
|
| 8927 |
chrisfen |
2762 |
2004-10-11 17:13 tim |
| 8928 |
tim |
1594 |
|
| 8929 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
| 8930 |
|
|
of compilers |
| 8931 |
|
|
|
| 8932 |
chrisfen |
2762 |
2004-10-11 17:10 tim |
| 8933 |
tim |
1594 |
|
| 8934 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
| 8935 |
|
|
c/c++ now |
| 8936 |
|
|
|
| 8937 |
chrisfen |
2762 |
2004-10-11 14:40 tim |
| 8938 |
tim |
1594 |
|
| 8939 |
|
|
* make/Makefile.in: remove -module from F90Options |
| 8940 |
|
|
|
| 8941 |
chrisfen |
2762 |
2004-10-11 14:01 tim |
| 8942 |
tim |
1594 |
|
| 8943 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
| 8944 |
|
|
target directory |
| 8945 |
|
|
|
| 8946 |
chrisfen |
2762 |
2004-10-11 11:43 gezelter |
| 8947 |
tim |
1594 |
|
| 8948 |
|
|
* make/Makefile.in: fixed makefile.in |
| 8949 |
|
|
|
| 8950 |
chrisfen |
2762 |
2004-10-11 10:51 tim |
| 8951 |
tim |
1594 |
|
| 8952 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 8953 |
|
|
machine |
| 8954 |
|
|
|
| 8955 |
chrisfen |
2762 |
2004-10-11 10:26 tim |
| 8956 |
tim |
1594 |
|
| 8957 |
|
|
* forceFields/Makefile: add Makefile |
| 8958 |
|
|
|
| 8959 |
chrisfen |
2762 |
2004-10-11 10:23 tim |
| 8960 |
tim |
1594 |
|
| 8961 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 8962 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 8963 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 8964 |
|
|
directory |
| 8965 |
|
|
|
| 8966 |
chrisfen |
2762 |
2004-10-11 10:23 tim |
| 8967 |
tim |
1594 |
|
| 8968 |
gezelter |
2199 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 8969 |
|
|
Makefile |
| 8970 |
tim |
1594 |
|
| 8971 |
chrisfen |
2762 |
2004-10-09 02:01 tim |
| 8972 |
tim |
1594 |
|
| 8973 |
gezelter |
2199 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 8974 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 8975 |
|
|
Remove some Makefile.in |
| 8976 |
|
|
|
| 8977 |
chrisfen |
2762 |
2004-10-08 19:15 tim |
| 8978 |
gezelter |
2199 |
|
| 8979 |
tim |
1594 |
* make/Makefile.in: [no log message] |
| 8980 |
|
|
|
| 8981 |
chrisfen |
2762 |
2004-10-08 18:51 tim |
| 8982 |
tim |
1594 |
|
| 8983 |
|
|
* make/Makefile.in: fix make install |
| 8984 |
|
|
|
| 8985 |
chrisfen |
2762 |
2004-10-08 18:10 tim |
| 8986 |
tim |
1594 |
|
| 8987 |
|
|
* make/Makefile.in: adding make install |
| 8988 |
|
|
|
| 8989 |
chrisfen |
2762 |
2004-10-08 18:04 tim |
| 8990 |
tim |
1594 |
|
| 8991 |
gezelter |
2199 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 8992 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 8993 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 8994 |
tim |
1594 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 8995 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
| 8996 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 8997 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 8998 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
| 8999 |
|
|
|
| 9000 |
chrisfen |
2762 |
2004-10-06 19:03 gezelter |
| 9001 |
tim |
1594 |
|
| 9002 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
| 9003 |
|
|
stuff |
| 9004 |
|
|
|
| 9005 |
chrisfen |
2762 |
2004-10-06 19:03 gezelter |
| 9006 |
tim |
1594 |
|
| 9007 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 9008 |
|
|
make/Doxyfile, src/applications/getopt.c, |
| 9009 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 9010 |
|
|
build fixes |
| 9011 |
|
|
|
| 9012 |
chrisfen |
2762 |
2004-10-06 18:20 tim |
| 9013 |
tim |
1594 |
|
| 9014 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
| 9015 |
|
|
|
| 9016 |
chrisfen |
2762 |
2004-10-06 18:19 tim |
| 9017 |
tim |
1594 |
|
| 9018 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
| 9019 |
|
|
and suffix |
| 9020 |
|
|
|
| 9021 |
chrisfen |
2762 |
2004-10-06 17:27 gezelter |
| 9022 |
tim |
1594 |
|
| 9023 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 9024 |
|
|
OOPSE-2.0 directory structure yet |
| 9025 |
|
|
|
| 9026 |
chrisfen |
2762 |
2004-10-06 17:27 gezelter |
| 9027 |
tim |
1594 |
|
| 9028 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
| 9029 |
|
|
|
| 9030 |
chrisfen |
2762 |
2004-10-06 17:22 gezelter |
| 9031 |
gezelter |
1490 |
|
| 9032 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 9033 |
|
|
make/Makefile.in: cleaning up build process |
| 9034 |
gezelter |
1490 |
|
| 9035 |
chrisfen |
2762 |
2004-10-06 16:01 chrisfen |
| 9036 |
tim |
1594 |
|
| 9037 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
| 9038 |
|
|
restraints more intelligent - no longer gives uninformative seg |
| 9039 |
|
|
faults |
| 9040 |
|
|
|
| 9041 |
chrisfen |
2762 |
2004-10-06 15:55 gezelter |
| 9042 |
tim |
1594 |
|
| 9043 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
| 9044 |
|
|
|
| 9045 |
chrisfen |
2762 |
2004-10-06 15:51 gezelter |
| 9046 |
gezelter |
1490 |
|
| 9047 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 9048 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 9049 |
gezelter |
1490 |
|
| 9050 |
chrisfen |
2762 |
2004-10-06 14:53 tim |
| 9051 |
tim |
1594 |
|
| 9052 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
| 9053 |
|
|
|
| 9054 |
chrisfen |
2762 |
2004-10-06 14:18 tim |
| 9055 |
tim |
1594 |
|
| 9056 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
| 9057 |
|
|
combine all of the static libraries to a big library |
| 9058 |
|
|
|
| 9059 |
chrisfen |
2762 |
2004-10-05 18:57 tim |
| 9060 |
tim |
1594 |
|
| 9061 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
| 9062 |
|
|
|
| 9063 |
chrisfen |
2762 |
2004-10-05 15:37 tim |
| 9064 |
tim |
1594 |
|
| 9065 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
| 9066 |
|
|
UseTheForce/mpiSimulation_module.F90, |
| 9067 |
|
|
UseTheForce/DarkSide/Makefile, |
| 9068 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 9069 |
|
|
mpiSimulation_module to DarkSide |
| 9070 |
|
|
|
| 9071 |
chrisfen |
2762 |
2004-10-05 15:35 tim |
| 9072 |
tim |
1594 |
|
| 9073 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
| 9074 |
|
|
library instead of shared library |
| 9075 |
|
|
|
| 9076 |
chrisfen |
2762 |
2004-10-05 10:14 tim |
| 9077 |
tim |
1594 |
|
| 9078 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 9079 |
|
|
to filepp |
| 9080 |
|
|
|
| 9081 |
chrisfen |
2762 |
2004-10-04 16:56 tim |
| 9082 |
tim |
1594 |
|
| 9083 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
| 9084 |
|
|
|
| 9085 |
chrisfen |
2762 |
2004-10-04 12:24 gezelter |
| 9086 |
tim |
1594 |
|
| 9087 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
| 9088 |
|
|
|
| 9089 |
chrisfen |
2762 |
2004-10-04 12:06 gezelter |
| 9090 |
tim |
1594 |
|
| 9091 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
| 9092 |
|
|
|
| 9093 |
chrisfen |
2762 |
2004-10-04 11:27 gezelter |
| 9094 |
tim |
1594 |
|
| 9095 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
| 9096 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 9097 |
|
|
shapes |
| 9098 |
|
|
|
| 9099 |
chrisfen |
2762 |
2004-10-02 00:40 tim |
| 9100 |
tim |
1594 |
|
| 9101 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 9102 |
|
|
|
| 9103 |
chrisfen |
2762 |
2004-10-02 00:22 tim |
| 9104 |
tim |
1594 |
|
| 9105 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 9106 |
|
|
|
| 9107 |
chrisfen |
2762 |
2004-10-01 17:59 tim |
| 9108 |
tim |
1594 |
|
| 9109 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 9110 |
|
|
|
| 9111 |
chrisfen |
2762 |
2004-10-01 17:22 gezelter |
| 9112 |
gezelter |
1490 |
|
| 9113 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 9114 |
|
|
few minor build changes |
| 9115 |
gezelter |
1490 |
|
| 9116 |
chrisfen |
2762 |
2004-10-01 17:11 tim |
| 9117 |
tim |
1594 |
|
| 9118 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
| 9119 |
|
|
|
| 9120 |
chrisfen |
2762 |
2004-09-30 11:41 tim |
| 9121 |
tim |
1594 |
|
| 9122 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 9123 |
|
|
remove object files belong to current package. turn off silent |
| 9124 |
|
|
mode |
| 9125 |
|
|
|
| 9126 |
chrisfen |
2762 |
2004-09-29 17:55 tim |
| 9127 |
tim |
1594 |
|
| 9128 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
| 9129 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 9130 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 9131 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 9132 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
| 9133 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 9134 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
| 9135 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
| 9136 |
|
|
|
| 9137 |
chrisfen |
2762 |
2004-09-29 17:54 tim |
| 9138 |
tim |
1594 |
|
| 9139 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
| 9140 |
|
|
script |
| 9141 |
|
|
|
| 9142 |
chrisfen |
2762 |
2004-09-29 17:32 tim |
| 9143 |
tim |
1594 |
|
| 9144 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
| 9145 |
|
|
|
| 9146 |
chrisfen |
2762 |
2004-09-29 14:37 tim |
| 9147 |
tim |
1594 |
|
| 9148 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 9149 |
|
|
|
| 9150 |
chrisfen |
2762 |
2004-09-29 13:57 gezelter |
| 9151 |
gezelter |
1490 |
|
| 9152 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
| 9153 |
gezelter |
1490 |
|
| 9154 |
chrisfen |
2762 |
2004-09-29 13:56 gezelter |
| 9155 |
tim |
1594 |
|
| 9156 |
chrisfen |
2727 |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
| 9157 |
|
|
make stuff |
| 9158 |
tim |
1594 |
|
| 9159 |
chrisfen |
2762 |
2004-09-29 13:46 tim |
| 9160 |
gezelter |
1490 |
|
| 9161 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
| 9162 |
gezelter |
1490 |
|
| 9163 |
chrisfen |
2762 |
2004-09-29 13:12 tim |
| 9164 |
tim |
1594 |
|
| 9165 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 9166 |
|
|
|
| 9167 |
chrisfen |
2762 |
2004-09-29 11:58 gezelter |
| 9168 |
gezelter |
1490 |
|
| 9169 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
| 9170 |
gezelter |
1490 |
|
| 9171 |
chrisfen |
2762 |
2004-09-29 11:00 tim |
| 9172 |
tim |
1594 |
|
| 9173 |
|
|
* make/Makefile: add print statment to rules |
| 9174 |
|
|
|
| 9175 |
chrisfen |
2762 |
2004-09-29 10:59 tim |
| 9176 |
tim |
1594 |
|
| 9177 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 9178 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 9179 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
| 9180 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 9181 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 9182 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 9183 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 9184 |
|
|
|
| 9185 |
chrisfen |
2762 |
2004-09-28 22:55 tim |
| 9186 |
tim |
1594 |
|
| 9187 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 9188 |
|
|
which cause headache in bulding libutils |
| 9189 |
|
|
|
| 9190 |
chrisfen |
2762 |
2004-09-28 19:24 tim |
| 9191 |
tim |
1594 |
|
| 9192 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 9193 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 9194 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 9195 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 9196 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 9197 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 9198 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 9199 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 9200 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 9201 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 9202 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 9203 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 9204 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 9205 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 9206 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 9207 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 9208 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 9209 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 9210 |
|
|
change directory structure of application. Every executable file is |
| 9211 |
|
|
replaced in seperate directory |
| 9212 |
|
|
|
| 9213 |
chrisfen |
2762 |
2004-09-28 18:15 gezelter |
| 9214 |
tim |
1594 |
|
| 9215 |
|
|
* lib/dummy: Keep that lib around, please. |
| 9216 |
|
|
|
| 9217 |
chrisfen |
2762 |
2004-09-28 18:14 gezelter |
| 9218 |
gezelter |
1490 |
|
| 9219 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 9220 |
|
|
starting a configure version |
| 9221 |
gezelter |
1490 |
|
| 9222 |
chrisfen |
2762 |
2004-09-28 17:08 tim |
| 9223 |
tim |
1594 |
|
| 9224 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 9225 |
|
|
UseTheForce/DarkSide/Makefile, |
| 9226 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 9227 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 9228 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 9229 |
|
|
around to solve dependency problem |
| 9230 |
|
|
|
| 9231 |
chrisfen |
2762 |
2004-09-28 16:43 tim |
| 9232 |
gezelter |
1490 |
|
| 9233 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 9234 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 9235 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
| 9236 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 9237 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 9238 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 9239 |
|
|
src/utils/Makefile: [no log message] |
| 9240 |
gezelter |
1490 |
|
| 9241 |
chrisfen |
2762 |
2004-09-28 16:41 tim |
| 9242 |
tim |
1594 |
|
| 9243 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 9244 |
|
|
problem |
| 9245 |
|
|
|
| 9246 |
chrisfen |
2762 |
2004-09-28 12:13 tim |
| 9247 |
tim |
1594 |
|
| 9248 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 9249 |
|
|
src/io/Makefile: add yacc and lex rules |
| 9250 |
|
|
|
| 9251 |
chrisfen |
2762 |
2004-09-27 16:24 tim |
| 9252 |
tim |
1594 |
|
| 9253 |
|
|
* make/Makefile: adding include path to F90Options |
| 9254 |
|
|
|
| 9255 |
chrisfen |
2762 |
2004-09-27 16:13 tim |
| 9256 |
tim |
1594 |
|
| 9257 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
| 9258 |
|
|
|
| 9259 |
chrisfen |
2762 |
2004-09-24 12:27 tim |
| 9260 |
tim |
1594 |
|
| 9261 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 9262 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 9263 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 9264 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 9265 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 9266 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 9267 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 9268 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 9269 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
| 9270 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 9271 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 9272 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 9273 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 9274 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 9275 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 9276 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 9277 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 9278 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 9279 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 9280 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 9281 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 9282 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 9283 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 9284 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 9285 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 9286 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 9287 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 9288 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 9289 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 9290 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 9291 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 9292 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 9293 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 9294 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
| 9295 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 9296 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 9297 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 9298 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 9299 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 9300 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 9301 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 9302 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 9303 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 9304 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 9305 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 9306 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 9307 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 9308 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 9309 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 9310 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 9311 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 9312 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 9313 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 9314 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 9315 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 9316 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 9317 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 9318 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 9319 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
| 9320 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 9321 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 9322 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 9323 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 9324 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
| 9325 |
|
|
|
| 9326 |
chrisfen |
2762 |
2004-09-24 00:16 gezelter |
| 9327 |
gezelter |
1490 |
|
| 9328 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 9329 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 9330 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 9331 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 9332 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 9333 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 9334 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 9335 |
|
|
src/UseTheForce/fForceField.h, |
| 9336 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 9337 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
| 9338 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
| 9339 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
| 9340 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
| 9341 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 9342 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
| 9343 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 9344 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
| 9345 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 9346 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 9347 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 9348 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
| 9349 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
| 9350 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 9351 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 9352 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
| 9353 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 9354 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 9355 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
| 9356 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 9357 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 9358 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 9359 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 9360 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 9361 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 9362 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 9363 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 9364 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 9365 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 9366 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 9367 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 9368 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 9369 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 9370 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 9371 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 9372 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
| 9373 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 9374 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 9375 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 9376 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 9377 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 9378 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 9379 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 9380 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 9381 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 9382 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 9383 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 9384 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 9385 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 9386 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 9387 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 9388 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 9389 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 9390 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 9391 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 9392 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 9393 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
| 9394 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 9395 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 9396 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 9397 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 9398 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 9399 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 9400 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 9401 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 9402 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 9403 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 9404 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 9405 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 9406 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 9407 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 9408 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
| 9409 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 9410 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 9411 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 9412 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 9413 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 9414 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 9415 |
|
|
src/utils/simError.c, src/utils/simError.h, |
| 9416 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 9417 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 9418 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 9419 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 9420 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 9421 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
| 9422 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 9423 |
chrisfen |
2727 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 9424 |
|
|
make/_files/style.css, samples/Makefile.in, |
| 9425 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 9426 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 9427 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 9428 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 9429 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 9430 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 9431 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 9432 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 9433 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 9434 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 9435 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 9436 |
|
|
src/applications/LatticeCreator.cpp, |
| 9437 |
|
|
src/applications/LatticeCreator.hpp, |
| 9438 |
|
|
src/applications/LatticeFactory.cpp, |
| 9439 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 9440 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 9441 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 9442 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
| 9443 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
| 9444 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 9445 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 9446 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 9447 |
|
|
src/applications/simpleBuilder.ggo, |
| 9448 |
|
|
src/applications/simpleBuilderCmd.c, |
| 9449 |
|
|
src/integrators/AbstractClasses.hpp, |
| 9450 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 9451 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 9452 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 9453 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 9454 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 9455 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 9456 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 9457 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 9458 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 9459 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 9460 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 9461 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 9462 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 9463 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 9464 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 9465 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 9466 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 9467 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 9468 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 9469 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 9470 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 9471 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 9472 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
| 9473 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 9474 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 9475 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 9476 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 9477 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 9478 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 9479 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 9480 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 9481 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 9482 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 9483 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 9484 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 9485 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 9486 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 9487 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 9488 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 9489 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 9490 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 9491 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 9492 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 9493 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 9494 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 9495 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 9496 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 9497 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 9498 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 9499 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 9500 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 9501 |
gezelter |
1490 |
|
| 9502 |
chrisfen |
2762 |
2004-09-24 00:16 gezelter |
| 9503 |
gezelter |
1490 |
|
| 9504 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 9505 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 9506 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 9507 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 9508 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 9509 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 9510 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 9511 |
|
|
src/UseTheForce/fForceField.h, |
| 9512 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
| 9513 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
| 9514 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
| 9515 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
| 9516 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
| 9517 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 9518 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
| 9519 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 9520 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
| 9521 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 9522 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 9523 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 9524 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
| 9525 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
| 9526 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 9527 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 9528 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
| 9529 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
| 9530 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 9531 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
| 9532 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 9533 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 9534 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 9535 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 9536 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 9537 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 9538 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 9539 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 9540 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 9541 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 9542 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 9543 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 9544 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 9545 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 9546 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 9547 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 9548 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
| 9549 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 9550 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 9551 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 9552 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 9553 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 9554 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 9555 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 9556 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 9557 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 9558 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 9559 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 9560 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 9561 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 9562 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 9563 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 9564 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 9565 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 9566 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 9567 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 9568 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 9569 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
| 9570 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 9571 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 9572 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 9573 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 9574 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 9575 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 9576 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 9577 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 9578 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 9579 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 9580 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 9581 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 9582 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 9583 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 9584 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
| 9585 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 9586 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 9587 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 9588 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 9589 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 9590 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 9591 |
|
|
src/utils/simError.c, src/utils/simError.h, |
| 9592 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 9593 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 9594 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 9595 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 9596 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 9597 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
| 9598 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 9599 |
chrisfen |
2727 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 9600 |
|
|
make/_files/style.css, samples/Makefile.in, |
| 9601 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 9602 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 9603 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 9604 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 9605 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 9606 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 9607 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 9608 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 9609 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 9610 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 9611 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 9612 |
|
|
src/applications/LatticeCreator.cpp, |
| 9613 |
|
|
src/applications/LatticeCreator.hpp, |
| 9614 |
|
|
src/applications/LatticeFactory.cpp, |
| 9615 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 9616 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 9617 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 9618 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
| 9619 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
| 9620 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 9621 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 9622 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 9623 |
|
|
src/applications/simpleBuilder.ggo, |
| 9624 |
|
|
src/applications/simpleBuilderCmd.c, |
| 9625 |
|
|
src/integrators/AbstractClasses.hpp, |
| 9626 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 9627 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 9628 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 9629 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 9630 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 9631 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 9632 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 9633 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 9634 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 9635 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 9636 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 9637 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 9638 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 9639 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 9640 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 9641 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 9642 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 9643 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 9644 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 9645 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 9646 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 9647 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 9648 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
| 9649 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 9650 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 9651 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 9652 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 9653 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 9654 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 9655 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 9656 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 9657 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 9658 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 9659 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 9660 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 9661 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 9662 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 9663 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 9664 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 9665 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 9666 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 9667 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 9668 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 9669 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 9670 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 9671 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 9672 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 9673 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 9674 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 9675 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 9676 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
| 9677 |
gezelter |
1490 |
|
