| 1 |
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2005-05-28 19:16 tim |
| 2 |
< |
|
| 3 |
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* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
| 4 |
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AtomNameVisitor |
| 5 |
< |
|
| 6 |
< |
2005-05-28 19:09 tim |
| 7 |
< |
|
| 8 |
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* src/integrators/Integrator.cpp: dding resetIntegrator |
| 9 |
< |
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| 10 |
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2005-05-28 19:06 tim |
| 11 |
< |
|
| 12 |
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* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
| 13 |
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NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
| 14 |
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VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
| 15 |
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resetIntegrator |
| 16 |
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| 17 |
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2005-05-27 16:11 tim |
| 18 |
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| 19 |
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* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
| 20 |
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Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
| 21 |
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SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
| 22 |
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StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
| 23 |
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StaticProps |
| 24 |
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| 25 |
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2005-05-26 23:41 tim |
| 26 |
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| 27 |
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* src/: applications/staticProps/Makefile, |
| 28 |
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applications/staticProps/P2OrderParameter.cpp, |
| 29 |
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applications/staticProps/P2OrderParameter.hpp, |
| 30 |
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applications/staticProps/StaticProps.cpp, |
| 31 |
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applications/staticProps/StaticProps.ggo, |
| 32 |
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applications/staticProps/StaticPropsCmd.c, |
| 33 |
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applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
| 34 |
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utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
| 35 |
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|
| 36 |
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2005-05-26 17:45 tim |
| 37 |
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| 38 |
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 39 |
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applications/dump2Xyz/Dump2XYZCmd.c, |
| 40 |
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applications/dump2Xyz/Dump2XYZCmd.h, |
| 41 |
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applications/staticProps/Makefile, |
| 42 |
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applications/staticProps/P2OrderParameter.cpp, |
| 43 |
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applications/staticProps/P2OrderParameter.hpp, |
| 44 |
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applications/staticProps/RadialDistrFunc.cpp, |
| 45 |
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applications/staticProps/RadialDistrFunc.hpp, |
| 46 |
< |
applications/staticProps/StaticAnalyser.hpp, |
| 47 |
< |
applications/staticProps/StaticProps.cpp, |
| 48 |
< |
applications/staticProps/StaticProps.ggo, |
| 49 |
< |
applications/staticProps/StaticPropsCmd.c, |
| 50 |
< |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
| 51 |
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visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
| 52 |
< |
AtomNameVisitor to convert atom name to its base name; |
| 53 |
< |
wrappingvisitor now wrap back to the center of the mass; adding |
| 54 |
< |
P2OrderParameter into StaticProps |
| 55 |
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|
| 56 |
< |
2005-05-22 16:36 chuckv |
| 57 |
< |
|
| 58 |
< |
* samples/metals/nanorod/Au_nanoparticle_FCC.md, |
| 59 |
< |
src/applications/nanoRodBuilder/Geometry.cpp, |
| 60 |
< |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 61 |
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src/applications/nanoRodBuilder/GeometryFactory.cpp, |
| 62 |
< |
src/applications/nanoRodBuilder/GeometryFactory.hpp, |
| 63 |
< |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 64 |
< |
src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
| 65 |
< |
tensor. |
| 66 |
< |
|
| 67 |
< |
2005-05-22 16:05 tim |
| 68 |
< |
|
| 69 |
< |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 70 |
< |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 71 |
< |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
| 72 |
< |
printPressureTensor |
| 73 |
< |
|
| 74 |
< |
2005-05-20 14:27 tim |
| 75 |
< |
|
| 76 |
< |
* src/integrators/NPrT.cpp: NPrT in progress |
| 77 |
< |
|
| 78 |
< |
2005-05-20 11:01 tim |
| 79 |
< |
|
| 80 |
< |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
| 81 |
< |
utils/OOPSEConstant.hpp: NPrT in progress |
| 82 |
< |
|
| 83 |
< |
2005-05-19 16:31 tim |
| 84 |
< |
|
| 85 |
< |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
| 86 |
< |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
| 87 |
< |
io/Globals.hpp: NPAT is working |
| 88 |
< |
|
| 89 |
< |
2005-05-19 10:49 tim |
| 90 |
< |
|
| 91 |
< |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
| 92 |
< |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
| 93 |
< |
|
| 94 |
< |
2005-05-18 23:28 tim |
| 95 |
< |
|
| 96 |
< |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
| 97 |
< |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
| 98 |
< |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
| 99 |
< |
|
| 100 |
< |
2005-05-18 14:06 chrisfen |
| 101 |
< |
|
| 102 |
< |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
| 103 |
< |
some tap changes |
| 104 |
< |
|
| 105 |
< |
2005-05-18 13:31 chrisfen |
| 106 |
< |
|
| 107 |
< |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 108 |
< |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
| 109 |
< |
in the first solvation shell for tap |
| 110 |
< |
|
| 111 |
< |
2005-05-18 07:35 chrisfen |
| 112 |
< |
|
| 113 |
< |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
| 114 |
< |
for testing purposes |
| 115 |
< |
|
| 116 |
< |
2005-05-17 17:35 chrisfen |
| 117 |
< |
|
| 118 |
< |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
| 119 |
< |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
| 120 |
< |
src/UseTheForce/doForces.F90, |
| 121 |
< |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 122 |
< |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 123 |
< |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
| 124 |
< |
correcting changes to the previous merge that were not caught |
| 125 |
< |
|
| 126 |
< |
2005-05-16 23:20 chuckv |
| 127 |
< |
|
| 128 |
< |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
| 129 |
< |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
| 130 |
< |
build. |
| 131 |
< |
|
| 132 |
< |
2005-05-16 22:46 kdaily |
| 133 |
< |
|
| 134 |
< |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
| 135 |
< |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
| 136 |
< |
|
| 137 |
< |
2005-05-16 21:08 kdaily |
| 138 |
< |
|
| 139 |
< |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
| 140 |
< |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
| 141 |
< |
src/types/DirectionalAtomType.cpp, |
| 142 |
< |
src/types/DirectionalAtomType.hpp: added gb |
| 143 |
< |
|
| 144 |
< |
2005-05-13 15:36 chrisfen |
| 145 |
< |
|
| 146 |
< |
* forceFields/DUFF2.frc: Better tap |
| 147 |
< |
|
| 148 |
< |
2005-05-12 14:43 chrisfen |
| 149 |
< |
|
| 150 |
< |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
| 151 |
< |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
| 152 |
< |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 153 |
< |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
| 154 |
< |
Need to parametrize. |
| 155 |
< |
|
| 156 |
< |
2005-05-11 18:15 chuckv |
| 157 |
< |
|
| 158 |
< |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
| 159 |
< |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
| 160 |
< |
build issues under ifc7. |
| 161 |
< |
|
| 162 |
< |
2005-05-09 17:07 chuckv |
| 163 |
< |
|
| 164 |
< |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
| 165 |
< |
builder changes. |
| 166 |
< |
|
| 167 |
< |
2005-05-05 10:06 chrisfen |
| 168 |
< |
|
| 169 |
< |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
| 170 |
< |
to TAP |
| 171 |
< |
|
| 172 |
< |
2005-05-05 09:47 chrisfen |
| 173 |
< |
|
| 174 |
< |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
| 175 |
< |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
| 176 |
< |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
| 177 |
< |
src/UseTheForce/DarkSide/atype.F90, |
| 178 |
< |
src/UseTheForce/DarkSide/atype_interface.F90, |
| 179 |
< |
src/UseTheForce/DarkSide/simulation.F90, |
| 180 |
< |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
| 181 |
< |
src/brains/fSimulation.h, src/io/Makefile, |
| 182 |
< |
src/io/StickyAtomTypesSectionParser.cpp, |
| 183 |
< |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
| 184 |
< |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
| 185 |
< |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
| 186 |
< |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
| 187 |
< |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
| 188 |
< |
not parametrized, but OOPSE will now let me run it... |
| 189 |
< |
|
| 190 |
< |
2005-05-03 17:55 chuckv |
| 191 |
< |
|
| 192 |
< |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 193 |
< |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
| 194 |
< |
Adding support for generic geometry to nanorodbuilder. |
| 195 |
< |
|
| 196 |
< |
2005-05-03 12:55 chuckv |
| 197 |
< |
|
| 198 |
< |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 199 |
< |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
| 200 |
< |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
| 201 |
< |
|
| 202 |
< |
2005-04-29 14:16 gezelter |
| 203 |
< |
|
| 204 |
< |
* make/Makefile.in: [no log message] |
| 205 |
< |
|
| 206 |
< |
2005-04-29 11:26 chrisfen |
| 207 |
< |
|
| 208 |
< |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
| 209 |
< |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
| 210 |
< |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
| 211 |
< |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
| 212 |
< |
samples/water/tip4p/water.md: Added TIP4P-Ew |
| 213 |
< |
|
| 214 |
< |
2005-04-27 19:24 chuckv |
| 215 |
< |
|
| 216 |
< |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 217 |
< |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
| 218 |
< |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
| 219 |
< |
nanoRodBuilder.... |
| 220 |
< |
|
| 221 |
< |
2005-04-27 15:13 chrisfen |
| 222 |
< |
|
| 223 |
< |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
| 224 |
< |
src/UseTheForce/DarkSide/atype.F90, |
| 225 |
< |
src/UseTheForce/DarkSide/shapes.F90, |
| 226 |
< |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 227 |
< |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
| 228 |
< |
write statements and am closer to a working shapes |
| 229 |
< |
|
| 230 |
< |
2005-04-22 16:57 chuckv |
| 231 |
< |
|
| 232 |
< |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
| 233 |
< |
|
| 234 |
< |
2005-04-22 16:52 tim |
| 235 |
< |
|
| 236 |
< |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
| 237 |
< |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
| 238 |
< |
problem of c++ |
| 239 |
< |
|
| 240 |
< |
2005-04-21 09:12 chrisfen |
| 241 |
< |
|
| 242 |
< |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
| 243 |
< |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
| 244 |
< |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
| 245 |
< |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
| 246 |
< |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
| 247 |
< |
src/UseTheForce/DarkSide/shapes.F90, |
| 248 |
< |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 249 |
< |
src/UseTheForce/DarkSide/shapes_interface.h, |
| 250 |
< |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
| 251 |
< |
src/io/Makefile, src/io/SectionParser.cpp, |
| 252 |
< |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 253 |
< |
src/io/ShapeAtomTypesSectionParser.cpp, |
| 254 |
< |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
| 255 |
< |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
| 256 |
< |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
| 257 |
< |
bounds overwrite (I think...). At least the parser loads the |
| 258 |
< |
forcefield fine... |
| 259 |
< |
|
| 260 |
< |
2005-04-18 10:44 chrisfen |
| 261 |
< |
|
| 262 |
< |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
| 263 |
< |
Mac (capitalization confusion of filenames) |
| 264 |
< |
|
| 265 |
< |
2005-04-17 22:50 chrisfen |
| 266 |
< |
|
| 267 |
< |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
| 268 |
< |
UseTheForce/Shapes_FF.cpp, |
| 269 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
| 270 |
< |
io/ShapeAtomTypesSectionParser.cpp, |
| 271 |
< |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
| 272 |
< |
|
| 273 |
< |
2005-04-15 17:43 gezelter |
| 274 |
< |
|
| 275 |
< |
* README: gmake in case people forget |
| 276 |
< |
|
| 277 |
< |
2005-04-15 17:40 gezelter |
| 278 |
< |
|
| 279 |
< |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
| 280 |
< |
banner. Vanity. |
| 281 |
< |
|
| 282 |
< |
2005-04-15 17:22 gezelter |
| 283 |
< |
|
| 284 |
< |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
| 285 |
< |
in banner (and version numbers in config.h) |
| 286 |
< |
|
| 287 |
< |
2005-04-15 17:22 gezelter |
| 288 |
< |
|
| 289 |
< |
* ChangeLog, LICENSE, README: Documentation changes |
| 290 |
< |
|
| 291 |
< |
2005-04-15 17:03 gezelter |
| 292 |
< |
|
| 293 |
< |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 294 |
< |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
| 295 |
< |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 296 |
< |
UseTheForce/ForceFieldCreator.hpp, |
| 297 |
< |
UseTheForce/ForceFieldFactory.cpp, |
| 298 |
< |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 299 |
< |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
| 300 |
< |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
| 301 |
< |
UseTheForce/notifyCutoffs.F90, |
| 302 |
< |
UseTheForce/notifyCutoffs_interface.F90, |
| 303 |
< |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 304 |
< |
UseTheForce/DarkSide/atype.F90, |
| 305 |
< |
UseTheForce/DarkSide/atype_interface.F90, |
| 306 |
< |
UseTheForce/DarkSide/eam.F90, |
| 307 |
< |
UseTheForce/DarkSide/eam_interface.F90, |
| 308 |
< |
UseTheForce/DarkSide/eam_interface.h, |
| 309 |
< |
UseTheForce/DarkSide/electrostatic.F90, |
| 310 |
< |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 311 |
< |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 312 |
< |
UseTheForce/DarkSide/force_globals.F90, |
| 313 |
< |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 314 |
< |
UseTheForce/DarkSide/lj_interface.F90, |
| 315 |
< |
UseTheForce/DarkSide/lj_interface.h, |
| 316 |
< |
UseTheForce/DarkSide/neighborLists.F90, |
| 317 |
< |
UseTheForce/DarkSide/reactionField.F90, |
| 318 |
< |
UseTheForce/DarkSide/shapes.F90, |
| 319 |
< |
UseTheForce/DarkSide/shapes_interface.F90, |
| 320 |
< |
UseTheForce/DarkSide/shapes_interface.h, |
| 321 |
< |
UseTheForce/DarkSide/simParallel.F90, |
| 322 |
< |
UseTheForce/DarkSide/simParallel_interface.F90, |
| 323 |
< |
UseTheForce/DarkSide/simParallel_interface.h, |
| 324 |
< |
UseTheForce/DarkSide/simulation.F90, |
| 325 |
< |
UseTheForce/DarkSide/simulation_interface.F90, |
| 326 |
< |
UseTheForce/DarkSide/simulation_interface.h, |
| 327 |
< |
UseTheForce/DarkSide/sticky.F90, |
| 328 |
< |
UseTheForce/DarkSide/sticky_interface.F90, |
| 329 |
< |
UseTheForce/DarkSide/sticky_interface.h, |
| 330 |
< |
UseTheForce/DarkSide/switcheroo.F90, |
| 331 |
< |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 332 |
< |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 333 |
< |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 334 |
< |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
| 335 |
< |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
| 336 |
< |
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 337 |
< |
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 338 |
< |
applications/dynamicProps/DynamicProps.cpp, |
| 339 |
< |
applications/dynamicProps/DynamicPropsCmd.c, |
| 340 |
< |
applications/dynamicProps/DynamicPropsCmd.h, |
| 341 |
< |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
| 342 |
< |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
| 343 |
< |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
| 344 |
< |
applications/dynamicProps/RCorrFunc.cpp, |
| 345 |
< |
applications/dynamicProps/RCorrFunc.hpp, |
| 346 |
< |
applications/dynamicProps/TimeCorrFunc.cpp, |
| 347 |
< |
applications/dynamicProps/TimeCorrFunc.hpp, |
| 348 |
< |
applications/dynamicProps/VCorrFunc.cpp, |
| 349 |
< |
applications/dynamicProps/VCorrFunc.hpp, |
| 350 |
< |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 351 |
< |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 352 |
< |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 353 |
< |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 354 |
< |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
| 355 |
< |
applications/oopse/oopse.cpp, |
| 356 |
< |
applications/simpleBuilder/simpleBuilder.cpp, |
| 357 |
< |
applications/simpleBuilder/simpleBuilderCmd.c, |
| 358 |
< |
applications/simpleBuilder/simpleBuilderCmd.h, |
| 359 |
< |
applications/staticProps/GofAngle2.cpp, |
| 360 |
< |
applications/staticProps/GofAngle2.hpp, |
| 361 |
< |
applications/staticProps/GofR.cpp, |
| 362 |
< |
applications/staticProps/GofR.hpp, |
| 363 |
< |
applications/staticProps/GofRAngle.cpp, |
| 364 |
< |
applications/staticProps/GofRAngle.hpp, |
| 365 |
< |
applications/staticProps/GofXyz.cpp, |
| 366 |
< |
applications/staticProps/GofXyz.hpp, |
| 367 |
< |
applications/staticProps/RadialDistrFunc.cpp, |
| 368 |
< |
applications/staticProps/RadialDistrFunc.hpp, |
| 369 |
< |
applications/staticProps/StaticProps.cpp, |
| 370 |
< |
applications/staticProps/StaticPropsCmd.c, |
| 371 |
< |
applications/staticProps/StaticPropsCmd.h, |
| 372 |
< |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 373 |
< |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 374 |
< |
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 375 |
< |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
| 376 |
< |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
| 377 |
< |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 378 |
< |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 379 |
< |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
| 380 |
< |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 381 |
< |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 382 |
< |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
| 383 |
< |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
| 384 |
< |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
| 385 |
< |
constraints/ZconstraintForceManager.cpp, |
| 386 |
< |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 387 |
< |
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 388 |
< |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 389 |
< |
integrators/IntegratorFactory.cpp, |
| 390 |
< |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 391 |
< |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 392 |
< |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 393 |
< |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 394 |
< |
integrators/NVT.cpp, integrators/NVT.hpp, |
| 395 |
< |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 396 |
< |
integrators/Velocitizer.hpp, |
| 397 |
< |
integrators/VelocityVerletIntegrator.cpp, |
| 398 |
< |
integrators/VelocityVerletIntegrator.hpp, |
| 399 |
< |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 400 |
< |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 401 |
< |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 402 |
< |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 403 |
< |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 404 |
< |
io/ChargeAtomTypesSectionParser.hpp, |
| 405 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
| 406 |
< |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 407 |
< |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 408 |
< |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 409 |
< |
io/Globals.cpp, io/Globals.hpp, |
| 410 |
< |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 411 |
< |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 412 |
< |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
| 413 |
< |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
| 414 |
< |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
| 415 |
< |
io/SectionParser.cpp, io/SectionParser.hpp, |
| 416 |
< |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 417 |
< |
io/StatWriter.cpp, io/StatWriter.hpp, |
| 418 |
< |
io/StickyAtomTypesSectionParser.cpp, |
| 419 |
< |
io/StickyAtomTypesSectionParser.hpp, |
| 420 |
< |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 421 |
< |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 422 |
< |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
| 423 |
< |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
| 424 |
< |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 425 |
< |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
| 426 |
< |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
| 427 |
< |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 428 |
< |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
| 429 |
< |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
| 430 |
< |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 431 |
< |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 432 |
< |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
| 433 |
< |
math/Quaternion.hpp, math/RandNumGen.hpp, |
| 434 |
< |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 435 |
< |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
| 436 |
< |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
| 437 |
< |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
| 438 |
< |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
| 439 |
< |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
| 440 |
< |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 441 |
< |
minimizers/MinimizerFactory.hpp, |
| 442 |
< |
minimizers/MinimizerParameterSet.cpp, |
| 443 |
< |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 444 |
< |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 445 |
< |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 446 |
< |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 447 |
< |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 448 |
< |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 449 |
< |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 450 |
< |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
| 451 |
< |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 452 |
< |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 453 |
< |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 454 |
< |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 455 |
< |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 456 |
< |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 457 |
< |
profiling/timing.F90, restraints/Restraints.cpp, |
| 458 |
< |
restraints/Restraints.hpp, |
| 459 |
< |
restraints/ThermoIntegrationForceManager.cpp, |
| 460 |
< |
restraints/ThermoIntegrationForceManager.hpp, |
| 461 |
< |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 462 |
< |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 463 |
< |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
| 464 |
< |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
| 465 |
< |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 466 |
< |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 467 |
< |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
| 468 |
< |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 469 |
< |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 470 |
< |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 471 |
< |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 472 |
< |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 473 |
< |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 474 |
< |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 475 |
< |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 476 |
< |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
| 477 |
< |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
| 478 |
< |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 479 |
< |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 480 |
< |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
| 481 |
< |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 482 |
< |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
| 483 |
< |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
| 484 |
< |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 485 |
< |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 486 |
< |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 487 |
< |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
| 488 |
< |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
| 489 |
< |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 490 |
< |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 491 |
< |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 492 |
< |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
| 493 |
< |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
| 494 |
< |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 495 |
< |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 496 |
< |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 497 |
< |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
| 498 |
< |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
| 499 |
< |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
| 500 |
< |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
| 501 |
< |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
| 502 |
< |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
| 503 |
< |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
| 504 |
< |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
| 505 |
< |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
| 506 |
< |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 507 |
< |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
| 508 |
< |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
| 509 |
< |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
| 510 |
< |
been drafted to perform our indentation services |
| 511 |
< |
|
| 512 |
< |
2005-04-15 17:03 gezelter |
| 513 |
< |
|
| 514 |
< |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
| 515 |
< |
messages have been added to make users ignore CGAL. |
| 516 |
< |
|
| 517 |
< |
2005-04-15 13:41 tim |
| 518 |
< |
|
| 519 |
< |
* make/Makefile.in: fix make install |
| 520 |
< |
|
| 521 |
< |
2005-04-15 13:41 tim |
| 522 |
< |
|
| 523 |
< |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
| 524 |
< |
add Makefile of samples |
| 525 |
< |
|
| 526 |
< |
2005-04-15 13:33 tim |
| 527 |
< |
|
| 528 |
< |
* samples/: lipid/Makefile, water/dimer/Makefile, |
| 529 |
< |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
| 530 |
< |
installed correctly |
| 531 |
< |
|
| 532 |
< |
2005-04-14 16:41 gezelter |
| 533 |
< |
|
| 534 |
< |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 535 |
< |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
| 536 |
< |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
| 537 |
< |
to use with filepp |
| 538 |
< |
|
| 539 |
< |
2005-04-14 16:20 gezelter |
| 540 |
< |
|
| 541 |
< |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
| 542 |
< |
MoLocator |
| 543 |
< |
|
| 544 |
< |
2005-04-14 14:12 gezelter |
| 545 |
< |
|
| 546 |
< |
* LICENSE: [no log message] |
| 547 |
< |
|
| 548 |
< |
2005-04-14 11:10 chuckv |
| 549 |
< |
|
| 550 |
< |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
| 551 |
< |
nanorodbuilder now exit's when libCGAL is not present. |
| 552 |
< |
|
| 553 |
< |
2005-04-14 10:20 tim |
| 554 |
< |
|
| 555 |
< |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
| 556 |
< |
|
| 557 |
< |
2005-04-13 18:36 chuckv |
| 558 |
< |
|
| 559 |
< |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
| 560 |
< |
interface name for SGI Compiler |
| 561 |
< |
|
| 562 |
< |
2005-04-13 18:29 chrisfen |
| 563 |
< |
|
| 564 |
< |
* samples/water/ssde/ssde.md: oops... bad sample |
| 565 |
< |
|
| 566 |
< |
2005-04-13 18:00 chuckv |
| 567 |
< |
|
| 568 |
< |
* src/config.h.in: Change typo in CGAL. |
| 569 |
< |
|
| 570 |
< |
2005-04-13 17:43 tim |
| 571 |
< |
|
| 572 |
< |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
| 573 |
< |
selection/SelectionCompiler.hpp: fix some warning messages |
| 574 |
< |
|
| 575 |
< |
2005-04-13 17:30 gezelter |
| 576 |
< |
|
| 577 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 578 |
< |
make/Makefile.in, src/config.h.in, |
| 579 |
< |
src/applications/nanoRodBuilder/Makefile, |
| 580 |
< |
src/applications/nanoRodBuilder/Makefile.in, |
| 581 |
< |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
| 582 |
< |
checks |
| 583 |
< |
|
| 584 |
< |
2005-04-13 15:36 chuckv |
| 585 |
< |
|
| 586 |
< |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
| 587 |
< |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
| 588 |
< |
DarkSide/electrostatic_interface.F90, |
| 589 |
< |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
| 590 |
< |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
| 591 |
< |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
| 592 |
< |
destroy methods for Fortran modules. |
| 593 |
< |
|
| 594 |
< |
2005-04-13 15:17 chuckv |
| 595 |
< |
|
| 596 |
< |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
| 597 |
< |
shapes_interface.h: Added destroy method to clean up memory |
| 598 |
< |
|
| 599 |
< |
2005-04-13 13:41 tim |
| 600 |
< |
|
| 601 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 602 |
< |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 603 |
< |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
| 604 |
< |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
| 605 |
< |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
| 606 |
< |
fixed |
| 607 |
< |
|
| 608 |
< |
2005-04-12 17:44 chuckv |
| 609 |
< |
|
| 610 |
< |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
| 611 |
< |
for nanoRodBuilder. |
| 612 |
< |
|
| 613 |
< |
2005-04-12 17:42 tim |
| 614 |
< |
|
| 615 |
< |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
| 616 |
< |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
| 617 |
< |
and simpleBuilder(forget to delete lattice) |
| 618 |
< |
|
| 619 |
< |
2005-04-12 17:33 tim |
| 620 |
< |
|
| 621 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 622 |
< |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
| 623 |
< |
refactory lattice |
| 624 |
< |
|
| 625 |
< |
2005-04-12 17:07 tim |
| 626 |
< |
|
| 627 |
< |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
| 628 |
< |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
| 629 |
< |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
| 630 |
< |
LatticeFactory and LatticeCreator |
| 631 |
< |
|
| 632 |
< |
2005-04-12 16:58 tim |
| 633 |
< |
|
| 634 |
< |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 635 |
< |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
| 636 |
< |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 637 |
< |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
| 638 |
< |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
| 639 |
< |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
| 640 |
< |
|
| 641 |
< |
2005-04-12 16:28 gezelter |
| 642 |
< |
|
| 643 |
< |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
| 644 |
< |
vector_class.F90: cleaned up vector_class memory leak fix by |
| 645 |
< |
deallocating in reverse order of how we allocated. Also migrated |
| 646 |
< |
MoLocator into utils directory |
| 647 |
< |
|
| 648 |
< |
2005-04-12 16:27 gezelter |
| 649 |
< |
|
| 650 |
< |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
| 651 |
< |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 652 |
< |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
| 653 |
< |
directory |
| 654 |
< |
|
| 655 |
< |
2005-04-12 16:27 gezelter |
| 656 |
< |
|
| 657 |
< |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
| 658 |
< |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
| 659 |
< |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
| 660 |
< |
nanoRodBuilder/LatticeCreator.hpp, |
| 661 |
< |
nanoRodBuilder/LatticeFactory.cpp, |
| 662 |
< |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
| 663 |
< |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
| 664 |
< |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
| 665 |
< |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 666 |
< |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 667 |
< |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 668 |
< |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
| 669 |
< |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
| 670 |
< |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
| 671 |
< |
these files are now redundant |
| 672 |
< |
|
| 673 |
< |
2005-04-12 16:27 gezelter |
| 674 |
< |
|
| 675 |
< |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
| 676 |
< |
atype_interface.h: cleaned up memory leak fix |
| 677 |
< |
|
| 678 |
< |
2005-04-12 16:26 gezelter |
| 679 |
< |
|
| 680 |
< |
* make/Makefile.in: added lattice subdirectory |
| 681 |
< |
|
| 682 |
< |
2005-04-12 15:57 chrisfen |
| 683 |
< |
|
| 684 |
< |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
| 685 |
< |
a space by accident |
| 686 |
< |
|
| 687 |
< |
2005-04-12 15:56 chrisfen |
| 688 |
< |
|
| 689 |
< |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
| 690 |
< |
quadrupole sample |
| 691 |
< |
|
| 692 |
< |
2005-04-12 15:56 chrisfen |
| 693 |
< |
|
| 694 |
< |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
| 695 |
< |
samples |
| 696 |
< |
|
| 697 |
< |
2005-04-12 13:30 tim |
| 698 |
< |
|
| 699 |
< |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
| 700 |
< |
type in fortran side |
| 701 |
< |
|
| 702 |
< |
2005-04-12 12:45 chuckv |
| 703 |
< |
|
| 704 |
< |
* src/utils/vector_class.F90: Further changes to vector_class |
| 705 |
< |
destroy function. |
| 706 |
< |
|
| 707 |
< |
2005-04-12 12:39 chuckv |
| 708 |
< |
|
| 709 |
< |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
| 710 |
< |
vector_class. |
| 711 |
< |
|
| 712 |
< |
2005-04-12 12:12 chuckv |
| 713 |
< |
|
| 714 |
< |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
| 715 |
< |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
| 716 |
< |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
| 717 |
< |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
| 718 |
< |
|
| 719 |
< |
2005-04-12 09:24 chrisfen |
| 720 |
< |
|
| 721 |
< |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
| 722 |
< |
output |
| 723 |
< |
|
| 724 |
< |
2005-04-11 19:29 chuckv |
| 725 |
< |
|
| 726 |
< |
* src/: UseTheForce/DarkSide/atype.F90, |
| 727 |
< |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
| 728 |
< |
|
| 729 |
< |
2005-04-11 19:28 chuckv |
| 730 |
< |
|
| 731 |
< |
* src/utils/vector_class.F90: Added code to delete vector. |
| 732 |
< |
|
| 733 |
< |
2005-04-11 17:03 chuckv |
| 734 |
< |
|
| 735 |
< |
* samples/metals/nanorod/: Au_nanoparticle.md, |
| 736 |
< |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
| 737 |
< |
aren't these here? |
| 1 |
> |
2006-04-20 23:19 chrisfen |
| 2 |
> |
|
| 3 |
> |
* samples/water/spce/spce.md, |
| 4 |
> |
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
| 5 |
> |
|
| 6 |
> |
2006-04-20 17:02 chrisfen |
| 7 |
> |
|
| 8 |
> |
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
| 9 |
> |
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
| 10 |
> |
|
| 11 |
> |
2006-04-20 14:24 gezelter |
| 12 |
> |
|
| 13 |
> |
* samples/metals/EAM/Au_bulk_voter.md, |
| 14 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 15 |
> |
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
| 16 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
| 17 |
> |
src/UseTheForce/DarkSide/eam.F90, |
| 18 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 19 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, |
| 20 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
| 21 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
| 22 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
| 23 |
> |
src/utils/interpolation.F90: Complete rewrite of spline code and |
| 24 |
> |
everything that uses it. |
| 25 |
> |
|
| 26 |
> |
2006-04-17 17:49 gezelter |
| 27 |
> |
|
| 28 |
> |
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
| 29 |
> |
samples/metals/EAM/Au_bulk_voter.md, |
| 30 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 31 |
> |
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
| 32 |
> |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
| 33 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 34 |
> |
src/UseTheForce/DarkSide/interpolation.F90, |
| 35 |
> |
src/UseTheForce/DarkSide/sticky.F90, |
| 36 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, |
| 37 |
> |
src/UseTheForce/DarkSide/switcheroo.F90, |
| 38 |
> |
src/applications/hydrodynamics/Hydro.ggo, |
| 39 |
> |
src/applications/hydrodynamics/HydroCmd.c, |
| 40 |
> |
src/applications/hydrodynamics/HydroCmd.h, |
| 41 |
> |
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
| 42 |
> |
src/utils/interpolation.F90: Many performance improvements |
| 43 |
> |
|
| 44 |
> |
2006-04-15 22:51 chrisfen |
| 45 |
> |
|
| 46 |
> |
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
| 47 |
> |
src/UseTheForce/fSwitchingFunction.h, |
| 48 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 49 |
> |
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
| 50 |
> |
switcheroo |
| 51 |
> |
|
| 52 |
> |
2006-04-15 17:58 chrisfen |
| 53 |
> |
|
| 54 |
> |
* src/utils/Makefile.in: Since status.F90 is used by |
| 55 |
> |
interpolation.F90, the former needs to be listed above the later in |
| 56 |
> |
the Makefile. |
| 57 |
> |
|
| 58 |
> |
2006-04-14 17:59 gezelter |
| 59 |
> |
|
| 60 |
> |
* src/utils/interpolation.F90: changed the interface a bit |
| 61 |
> |
|
| 62 |
> |
2006-04-14 17:49 gezelter |
| 63 |
> |
|
| 64 |
> |
* src/utils/interpolation.F90: added some logical flags |
| 65 |
> |
|
| 66 |
> |
2006-04-14 17:06 chrisfen |
| 67 |
> |
|
| 68 |
> |
* src/utils/interpolation.F90: Wiped the spline with derivatives |
| 69 |
> |
and corrected a boundary comparision error by eliminating the |
| 70 |
> |
check. This algorithm REQUIRES known first derivatives at the |
| 71 |
> |
endpoints. |
| 72 |
> |
|
| 73 |
> |
2006-04-14 16:04 gezelter |
| 74 |
> |
|
| 75 |
> |
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
| 76 |
> |
interpolation module |
| 77 |
> |
|
| 78 |
> |
2006-04-14 15:57 gezelter |
| 79 |
> |
|
| 80 |
> |
* src/utils/interpolation.F90: Heavily modified interpolation |
| 81 |
> |
module, also moved to "utils" |
| 82 |
> |
|
| 83 |
> |
2006-04-12 17:15 chuckv |
| 84 |
> |
|
| 85 |
> |
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
| 86 |
> |
module. |
| 87 |
> |
|
| 88 |
> |
2006-04-11 11:33 gezelter |
| 89 |
> |
|
| 90 |
> |
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
| 91 |
> |
StaticPropsCmd.h: [no log message] |
| 92 |
> |
|
| 93 |
> |
2006-04-03 11:37 chuckv |
| 94 |
> |
|
| 95 |
> |
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
| 96 |
> |
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
| 97 |
> |
simParallel for error reporting. |
| 98 |
> |
|
| 99 |
> |
2006-03-31 13:09 tim |
| 100 |
> |
|
| 101 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
| 102 |
> |
|
| 103 |
> |
2006-03-30 16:08 chuckv |
| 104 |
> |
|
| 105 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
| 106 |
> |
where SCList capacity was not reset to zero on destruction. |
| 107 |
> |
|
| 108 |
> |
2006-03-30 14:37 chuckv |
| 109 |
> |
|
| 110 |
> |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 111 |
> |
More testing of nanoparticleBuilder. |
| 112 |
> |
|
| 113 |
> |
2006-03-29 17:24 chuckv |
| 114 |
> |
|
| 115 |
> |
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
| 116 |
> |
file exists. |
| 117 |
> |
|
| 118 |
> |
2006-03-29 14:17 chuckv |
| 119 |
> |
|
| 120 |
> |
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
| 121 |
> |
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
| 122 |
> |
latticeOrt in shapedlatice and latticebuilder. |
| 123 |
> |
|
| 124 |
> |
2006-03-29 13:11 tim |
| 125 |
> |
|
| 126 |
> |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 127 |
> |
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
| 128 |
> |
in calculating correlation functions |
| 129 |
> |
|
| 130 |
> |
2006-03-29 13:09 tim |
| 131 |
> |
|
| 132 |
> |
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
| 133 |
> |
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
| 134 |
> |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
| 135 |
> |
RoughShell Model is working; (20)Adding a new option into Hydro |
| 136 |
> |
which allows user to generate the beads only |
| 137 |
> |
|
| 138 |
> |
2006-03-27 11:21 chuckv |
| 139 |
> |
|
| 140 |
> |
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
| 141 |
> |
nanoparticle builder. |
| 142 |
> |
|
| 143 |
> |
2006-03-27 11:03 chuckv |
| 144 |
> |
|
| 145 |
> |
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
| 146 |
> |
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
| 147 |
> |
makefile |
| 148 |
> |
|
| 149 |
> |
2006-03-24 15:46 chuckv |
| 150 |
> |
|
| 151 |
> |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 152 |
> |
Debugging changes to nanoparticle builder. |
| 153 |
> |
|
| 154 |
> |
2006-03-24 12:29 tim |
| 155 |
> |
|
| 156 |
> |
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 157 |
> |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 158 |
> |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
| 159 |
> |
|
| 160 |
> |
2006-03-24 11:49 tim |
| 161 |
> |
|
| 162 |
> |
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 163 |
> |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 164 |
> |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
| 165 |
> |
function. The command line option for DynamicProps is now changed. |
| 166 |
> |
--rcorr is for position correlation and --rmsd is for mean square |
| 167 |
> |
displacement. |
| 168 |
> |
|
| 169 |
> |
2006-03-23 10:03 tim |
| 170 |
> |
|
| 171 |
> |
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
| 172 |
> |
AnalyticalModel.hpp, ApproximationModel.cpp, |
| 173 |
> |
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
| 174 |
> |
method |
| 175 |
> |
|
| 176 |
> |
2006-03-23 10:02 tim |
| 177 |
> |
|
| 178 |
> |
* src/io/Globals.hpp: remove a unknown method |
| 179 |
> |
|
| 180 |
> |
2006-03-23 10:00 tim |
| 181 |
> |
|
| 182 |
> |
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
| 183 |
> |
|
| 184 |
> |
2006-03-23 09:59 tim |
| 185 |
> |
|
| 186 |
> |
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
| 187 |
> |
can not be opened for preprocessing |
| 188 |
> |
|
| 189 |
> |
2006-03-22 15:57 chuckv |
| 190 |
> |
|
| 191 |
> |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
| 192 |
> |
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
| 193 |
> |
shaped lattice. |
| 194 |
> |
|
| 195 |
> |
2006-03-21 10:33 tim |
| 196 |
> |
|
| 197 |
> |
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
| 198 |
> |
in calculating hydrodynamics tensor when the radius of beads are |
| 199 |
> |
not the same |
| 200 |
> |
|
| 201 |
> |
2006-03-20 19:26 tim |
| 202 |
> |
|
| 203 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 204 |
> |
applications/hydrodynamics/BeadModel.cpp, |
| 205 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 206 |
> |
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
| 207 |
> |
for ellipsoid |
| 208 |
> |
|
| 209 |
> |
2006-03-20 14:12 tim |
| 210 |
> |
|
| 211 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 212 |
> |
applications/hydrodynamics/Ellipsoid.cpp, |
| 213 |
> |
applications/hydrodynamics/Ellipsoid.hpp, |
| 214 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 215 |
> |
integrators/LDForceManager.cpp: Verify the correctness of |
| 216 |
> |
Ellipsoid's hydrodynamics properties |
| 217 |
> |
|
| 218 |
> |
2006-03-17 18:51 tim |
| 219 |
> |
|
| 220 |
> |
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
| 221 |
> |
version of Hydro is working now. |
| 222 |
> |
|
| 223 |
> |
2006-03-17 18:20 tim |
| 224 |
> |
|
| 225 |
> |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 226 |
> |
applications/hydrodynamics/AnalyticalModel.hpp, |
| 227 |
> |
applications/hydrodynamics/ApproximationModel.cpp, |
| 228 |
> |
applications/hydrodynamics/ApproximationModel.hpp, |
| 229 |
> |
applications/hydrodynamics/BeadModel.hpp, |
| 230 |
> |
applications/hydrodynamics/CompositeShape.cpp, |
| 231 |
> |
applications/hydrodynamics/CompositeShape.hpp, |
| 232 |
> |
applications/hydrodynamics/Ellipsoid.cpp, |
| 233 |
> |
applications/hydrodynamics/Ellipsoid.hpp, |
| 234 |
> |
applications/hydrodynamics/Hydro.cpp, |
| 235 |
> |
applications/hydrodynamics/Hydro.ggo, |
| 236 |
> |
applications/hydrodynamics/HydroCmd.c, |
| 237 |
> |
applications/hydrodynamics/HydroCmd.h, |
| 238 |
> |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 239 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 240 |
> |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 241 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 242 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 243 |
> |
applications/hydrodynamics/Makefile, |
| 244 |
> |
applications/hydrodynamics/RoughShell.cpp, |
| 245 |
> |
applications/hydrodynamics/RoughShell.hpp, |
| 246 |
> |
applications/hydrodynamics/Shape.hpp, |
| 247 |
> |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 248 |
> |
applications/hydrodynamics/ShapeBuilder.hpp, |
| 249 |
> |
applications/hydrodynamics/Spheric.cpp, |
| 250 |
> |
applications/hydrodynamics/Spheric.hpp, |
| 251 |
> |
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 252 |
> |
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 253 |
> |
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
| 254 |
> |
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
| 255 |
> |
utils/HydroProps.hpp: refactor Hydrodynamics module. |
| 256 |
> |
|
| 257 |
> |
2006-03-17 11:10 chuckv |
| 258 |
> |
|
| 259 |
> |
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
| 260 |
> |
Generic Shaped Lattice for oopse. Can overload to get spherical or |
| 261 |
> |
nanorod. |
| 262 |
> |
|
| 263 |
> |
2006-03-16 17:50 tim |
| 264 |
> |
|
| 265 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 266 |
> |
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
| 267 |
> |
LagevinDynamics is working? |
| 268 |
> |
|
| 269 |
> |
2006-03-16 16:52 gezelter |
| 270 |
> |
|
| 271 |
> |
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
| 272 |
> |
problem |
| 273 |
> |
|
| 274 |
> |
2006-03-15 17:08 tim |
| 275 |
> |
|
| 276 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
| 277 |
> |
conversion for diffusion tensor is wrong |
| 278 |
> |
|
| 279 |
> |
2006-03-15 16:28 tim |
| 280 |
> |
|
| 281 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 282 |
> |
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
| 283 |
> |
|
| 284 |
> |
2006-03-15 15:58 tim |
| 285 |
> |
|
| 286 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
| 287 |
> |
the unit in HydrodynamicsModel |
| 288 |
> |
|
| 289 |
> |
2006-03-15 12:35 tim |
| 290 |
> |
|
| 291 |
> |
* src/primitives/RigidBody.cpp: using setFrc in |
| 292 |
> |
RigidBody::calcForcesAndTorques will discard if there are force and |
| 293 |
> |
torque applied in rigid body itself. use addFrc instead. |
| 294 |
> |
|
| 295 |
> |
2006-03-15 10:51 tim |
| 296 |
> |
|
| 297 |
> |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
| 298 |
> |
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
| 299 |
> |
|
| 300 |
> |
2006-03-15 10:50 tim |
| 301 |
> |
|
| 302 |
> |
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
| 303 |
> |
hydrodynamics module into build system |
| 304 |
> |
|
| 305 |
> |
2006-03-14 18:46 tim |
| 306 |
> |
|
| 307 |
> |
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
| 308 |
> |
|
| 309 |
> |
2006-03-13 17:42 tim |
| 310 |
> |
|
| 311 |
> |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 312 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 313 |
> |
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 314 |
> |
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 315 |
> |
brains/Register.cpp, integrators/LDForceManager.cpp, |
| 316 |
> |
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
| 317 |
> |
integrators/LangevinDynamics.hpp, integrators/Makefile, |
| 318 |
> |
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
| 319 |
> |
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
| 320 |
> |
progress |
| 321 |
> |
|
| 322 |
> |
2006-03-07 11:43 gezelter |
| 323 |
> |
|
| 324 |
> |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
| 325 |
> |
double/int bug. Surprised no one ever noticed before... |
| 326 |
> |
|
| 327 |
> |
2006-02-24 16:17 tim |
| 328 |
> |
|
| 329 |
> |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
| 330 |
> |
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
| 331 |
> |
product of Rij |
| 332 |
> |
|
| 333 |
> |
2006-02-23 18:16 tim |
| 334 |
> |
|
| 335 |
> |
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
| 336 |
> |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
| 337 |
> |
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
| 338 |
> |
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
| 339 |
> |
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
| 340 |
> |
StuntDoubleShape.hpp: Bead Model is working |
| 341 |
> |
|
| 342 |
> |
2006-02-22 15:35 tim |
| 343 |
> |
|
| 344 |
> |
* src/: applications/hydrodynamics/Hydro.cpp, |
| 345 |
> |
applications/hydrodynamics/Hydro.ggo, |
| 346 |
> |
applications/hydrodynamics/HydroCmd.c, |
| 347 |
> |
applications/hydrodynamics/HydroCmd.h, |
| 348 |
> |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 349 |
> |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 350 |
> |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 351 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 352 |
> |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 353 |
> |
applications/hydrodynamics/MoleculeShape.cpp, |
| 354 |
> |
applications/hydrodynamics/MoleculeShape.hpp, |
| 355 |
> |
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
| 356 |
> |
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
| 357 |
> |
Module |
| 358 |
> |
|
| 359 |
> |
2006-02-16 17:05 gezelter |
| 360 |
> |
|
| 361 |
> |
* src/brains/Snapshot.cpp: fixed a spelling error |
| 362 |
> |
|
| 363 |
> |
2006-02-16 16:40 gezelter |
| 364 |
> |
|
| 365 |
> |
* src/: UseTheForce/doForces.F90, |
| 366 |
> |
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
| 367 |
> |
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
| 368 |
> |
larger than 1/2 the length of the shortest box dimension. added a |
| 369 |
> |
few fortran utility routines |
| 370 |
> |
|
| 371 |
> |
2006-02-15 15:46 chuckv |
| 372 |
> |
|
| 373 |
> |
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
| 374 |
> |
sphericalNanoparticle.hpp: Changed Names of class files. |
| 375 |
> |
|
| 376 |
> |
2006-02-10 10:45 kdaily |
| 377 |
> |
|
| 378 |
> |
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
| 379 |
> |
message] |
| 380 |
> |
|
| 381 |
> |
2006-02-10 10:12 tim |
| 382 |
> |
|
| 383 |
> |
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
| 384 |
> |
converting integer to double |
| 385 |
> |
|
| 386 |
> |
2006-02-08 13:21 chrisfen |
| 387 |
> |
|
| 388 |
> |
* forceFields/DUFF2.frc: added DPD molecule type parameters |
| 389 |
> |
|
| 390 |
> |
2006-02-07 11:39 tim |
| 391 |
> |
|
| 392 |
> |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 393 |
> |
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
| 394 |
> |
trajectory file during analysis |
| 395 |
> |
|
| 396 |
> |
2006-02-02 12:14 tim |
| 397 |
> |
|
| 398 |
> |
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
| 399 |
> |
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
| 400 |
> |
in AtomStamp where orientation is not set correctly. |
| 401 |
> |
|
| 402 |
> |
2006-02-02 11:49 gezelter |
| 403 |
> |
|
| 404 |
> |
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
| 405 |
> |
contain directional atoms |
| 406 |
> |
|
| 407 |
> |
2006-02-02 10:49 xsun |
| 408 |
> |
|
| 409 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 410 |
> |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
| 411 |
> |
for GBlipid atom type |
| 412 |
> |
|
| 413 |
> |
2006-02-01 21:57 gezelter |
| 414 |
> |
|
| 415 |
> |
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
| 416 |
> |
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
| 417 |
> |
|
| 418 |
> |
2006-02-01 16:06 chrisfen |
| 419 |
> |
|
| 420 |
> |
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
| 421 |
> |
to build |
| 422 |
> |
|
| 423 |
> |
2006-02-01 15:54 chrisfen |
| 424 |
> |
|
| 425 |
> |
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
| 426 |
> |
cutoff radius setting to a more logical procedure - still may |
| 427 |
> |
change... |
| 428 |
> |
|
| 429 |
> |
2006-02-01 12:26 gezelter |
| 430 |
> |
|
| 431 |
> |
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
| 432 |
> |
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
| 433 |
> |
|
| 434 |
> |
2006-01-30 17:25 tim |
| 435 |
> |
|
| 436 |
> |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
| 437 |
> |
applications/dynamicProps/DynamicProps.cpp, |
| 438 |
> |
applications/dynamicProps/DynamicProps.ggo, |
| 439 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
| 440 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
| 441 |
> |
applications/dynamicProps/LegendreCorrFunc.cpp, |
| 442 |
> |
applications/dynamicProps/LegendreCorrFunc.hpp, |
| 443 |
> |
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
| 444 |
> |
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
| 445 |
> |
Adding :LegendrePolynomial |
| 446 |
> |
|
| 447 |
> |
2006-01-19 17:54 chuckv |
| 448 |
> |
|
| 449 |
> |
* src/applications/nanoparticleBuilder/: Makefile, |
| 450 |
> |
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
| 451 |
> |
nanoparticle builder |
| 452 |
> |
|
| 453 |
> |
2006-01-18 16:08 chuckv |
| 454 |
> |
|
| 455 |
> |
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
| 456 |
> |
nanoparticle builder. |
| 457 |
> |
|
| 458 |
> |
2006-01-17 11:16 gezelter |
| 459 |
> |
|
| 460 |
> |
* AUTHORS, README: Cleaning up for 3.0.1 release |
| 461 |
> |
|
| 462 |
> |
2006-01-17 10:50 gezelter |
| 463 |
> |
|
| 464 |
> |
* ChangeLog: Prepping 3.0.1 release |
| 465 |
> |
|
| 466 |
> |
2006-01-17 10:32 gezelter |
| 467 |
> |
|
| 468 |
> |
* src/config.h.in: new version number |
| 469 |
> |
|
| 470 |
> |
2006-01-17 10:32 gezelter |
| 471 |
> |
|
| 472 |
> |
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
| 473 |
> |
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
| 474 |
> |
oopseManual.pdf: Updated Documentation |
| 475 |
> |
|
| 476 |
> |
2006-01-16 18:10 gezelter |
| 477 |
> |
|
| 478 |
> |
* ChangeLog, README: Getting ready for release! |
| 479 |
> |
|
| 480 |
> |
2006-01-16 10:26 gezelter |
| 481 |
> |
|
| 482 |
> |
* configure: Testing commit |
| 483 |
> |
|
| 484 |
> |
2006-01-13 16:57 chuckv |
| 485 |
> |
|
| 486 |
> |
* src/: UseTheForce/SC_FF.cpp, |
| 487 |
> |
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
| 488 |
> |
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
| 489 |
> |
Handled by forceField now. |
| 490 |
> |
|
| 491 |
> |
2006-01-13 14:17 chuckv |
| 492 |
> |
|
| 493 |
> |
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
| 494 |
> |
|
| 495 |
> |
2006-01-13 11:33 gezelter |
| 496 |
> |
|
| 497 |
> |
* Makefile: [no log message] |
| 498 |
> |
|
| 499 |
> |
2006-01-13 11:26 gezelter |
| 500 |
> |
|
| 501 |
> |
* Makefile: testing to make sure GNU make is the make that was used |
| 502 |
> |
to build OOPSE |
| 503 |
> |
|
| 504 |
> |
2006-01-13 10:48 gezelter |
| 505 |
> |
|
| 506 |
> |
* configure, ac-tools/configure.in: changed compiler search order |
| 507 |
> |
|
| 508 |
> |
2006-01-12 19:09 chuckv |
| 509 |
> |
|
| 510 |
> |
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
| 511 |
> |
samples/metals/Sutton-Chen/Au_bulk.in, |
| 512 |
> |
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
| 513 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
| 514 |
> |
units |
| 515 |
> |
|
| 516 |
> |
2006-01-12 16:16 gezelter |
| 517 |
> |
|
| 518 |
> |
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
| 519 |
> |
version info and the copyright date |
| 520 |
> |
|
| 521 |
> |
2006-01-12 15:52 gezelter |
| 522 |
> |
|
| 523 |
> |
* src/config.h.in: added some missing checks for header files |
| 524 |
> |
(particularly zlib.h), used autoheader to help generate config.h.in |
| 525 |
> |
|
| 526 |
> |
2006-01-12 15:51 gezelter |
| 527 |
> |
|
| 528 |
> |
* configure, ac-tools/configure.in: added some missing checks for |
| 529 |
> |
header files (particularly zlib.h) |
| 530 |
> |
|
| 531 |
> |
2006-01-12 15:19 gezelter |
| 532 |
> |
|
| 533 |
> |
* make/Makefile.in: fixed a dependency problem for the Executable |
| 534 |
> |
builds |
| 535 |
> |
|
| 536 |
> |
2006-01-12 15:02 gezelter |
| 537 |
> |
|
| 538 |
> |
* samples/gbljtest/Makefile: Missing Makefile in this sample |
| 539 |
> |
directory |
| 540 |
> |
|
| 541 |
> |
2006-01-12 15:01 gezelter |
| 542 |
> |
|
| 543 |
> |
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
| 544 |
> |
Old makefile.in no longer required |
| 545 |
> |
|
| 546 |
> |
2006-01-12 15:01 gezelter |
| 547 |
> |
|
| 548 |
> |
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
| 549 |
> |
needs to be installed |
| 550 |
> |
|
| 551 |
> |
2006-01-12 14:56 chuckv |
| 552 |
> |
|
| 553 |
> |
* src/io/DumpWriter.cpp: Changed formating. |
| 554 |
> |
|
| 555 |
> |
2006-01-12 11:47 chrisfen |
| 556 |
> |
|
| 557 |
> |
* samples/water/tip4p/tp4.md, |
| 558 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 559 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 560 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 561 |
> |
src/brains/SimInfo.cpp: unifying function name in electrostatics |
| 562 |
> |
|
| 563 |
> |
2006-01-12 11:04 tim |
| 564 |
> |
|
| 565 |
> |
* samples/metals/: EAM/nanoparticle/Makefile, |
| 566 |
> |
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
| 567 |
> |
Sutton-Chen/Makefile: fix make install problem for metals samples |
| 568 |
> |
|
| 569 |
> |
2006-01-12 10:22 tim |
| 570 |
> |
|
| 571 |
> |
* make/Makefile.in: remove samples/metals from install list. |
| 572 |
> |
|
| 573 |
> |
2006-01-12 09:31 tim |
| 574 |
> |
|
| 575 |
> |
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
| 576 |
> |
handle multiple line macro, just convert multiple line macro into |
| 577 |
> |
single line macro. |
| 578 |
> |
|
| 579 |
> |
2006-01-11 23:13 chrisfen |
| 580 |
> |
|
| 581 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 582 |
> |
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
| 583 |
> |
changes to electrostatics for shifted-potential and shifted-force |
| 584 |
> |
with mono and multipoles |
| 585 |
> |
|
| 586 |
> |
2006-01-11 18:04 gezelter |
| 587 |
> |
|
| 588 |
> |
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
| 589 |
> |
src/UseTheForce/DarkSide/atype_interface.h, |
| 590 |
> |
src/UseTheForce/DarkSide/eam_interface.h, |
| 591 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 592 |
> |
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
| 593 |
> |
src/UseTheForce/DarkSide/gb_interface.h, |
| 594 |
> |
src/UseTheForce/DarkSide/lj_interface.h, |
| 595 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
| 596 |
> |
src/UseTheForce/DarkSide/simParallel_interface.h, |
| 597 |
> |
src/UseTheForce/DarkSide/simulation_interface.h, |
| 598 |
> |
src/UseTheForce/DarkSide/sticky_interface.h, |
| 599 |
> |
src/UseTheForce/DarkSide/suttonchen_interface.h, |
| 600 |
> |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
| 601 |
> |
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
| 602 |
> |
src/utils/fError.c, configure, make/Makefile.in: autoconf |
| 603 |
> |
modernization and cruft removal |
| 604 |
> |
|
| 605 |
> |
2006-01-11 18:04 gezelter |
| 606 |
> |
|
| 607 |
> |
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
| 608 |
> |
modernization and cruft-removal |
| 609 |
> |
|
| 610 |
> |
2006-01-11 17:50 tim |
| 611 |
> |
|
| 612 |
> |
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
| 613 |
> |
some error messages |
| 614 |
> |
|
| 615 |
> |
2006-01-11 14:01 tim |
| 616 |
> |
|
| 617 |
> |
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
| 618 |
> |
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
| 619 |
> |
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
| 620 |
> |
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
| 621 |
> |
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
| 622 |
> |
an exception when error is found. |
| 623 |
> |
|
| 624 |
> |
2006-01-11 13:41 gezelter |
| 625 |
> |
|
| 626 |
> |
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
| 627 |
> |
error |
| 628 |
> |
|
| 629 |
> |
2006-01-10 17:55 chuckv |
| 630 |
> |
|
| 631 |
> |
* forceFields/SuttonChen.frc: Changed conversion factor. |
| 632 |
> |
|
| 633 |
> |
2006-01-10 16:14 chuckv |
| 634 |
> |
|
| 635 |
> |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 636 |
> |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
| 637 |
> |
working now. |
| 638 |
> |
|
| 639 |
> |
2006-01-09 17:22 chuckv |
| 640 |
> |
|
| 641 |
> |
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
| 642 |
> |
|
| 643 |
> |
2006-01-09 17:14 tim |
| 644 |
> |
|
| 645 |
> |
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
| 646 |
> |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
| 647 |
> |
StaticPropsCmd.h: fixing RhoZ |
| 648 |
> |
|
| 649 |
> |
2006-01-09 14:26 chuckv |
| 650 |
> |
|
| 651 |
> |
* forceFields/SuttonChen.frc, |
| 652 |
> |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 653 |
> |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
| 654 |
> |
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
| 655 |
> |
section parsers. |
| 656 |
> |
|
| 657 |
> |
2006-01-09 14:11 tim |
| 658 |
> |
|
| 659 |
> |
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
| 660 |
> |
utils/StringUtils.hpp: replace isType<int> with isInteger |
| 661 |
> |
|
| 662 |
> |
2006-01-06 16:15 tim |
| 663 |
> |
|
| 664 |
> |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
| 665 |
> |
forceFieldOptions from SC_FF |
| 666 |
> |
|
| 667 |
> |
2006-01-06 15:27 chuckv |
| 668 |
> |
|
| 669 |
> |
* forceFields/SuttonChen.frc: Add force file. |
| 670 |
> |
|
| 671 |
> |
2005-12-31 17:42 chuckv |
| 672 |
> |
|
| 673 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
| 674 |
> |
segfaults or produces 0 potential, but rather produces Inf for the |
| 675 |
> |
potential. Progress.... |
| 676 |
> |
|
| 677 |
> |
2005-12-30 18:15 chuckv |
| 678 |
> |
|
| 679 |
> |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 680 |
> |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
| 681 |
> |
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
| 682 |
> |
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
| 683 |
> |
Sutton-Chen bug fixes. |
| 684 |
> |
|
| 685 |
> |
2005-12-30 16:25 tim |
| 686 |
> |
|
| 687 |
> |
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
| 688 |
> |
potential return from fortran is already accumulated, it should not |
| 689 |
> |
be accumulated again; nGroupTypesCol is not initialized; |
| 690 |
> |
GroupMaxCutoffCol is not allocated; |
| 691 |
> |
|
| 692 |
> |
2005-12-30 10:32 tim |
| 693 |
> |
|
| 694 |
> |
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
| 695 |
> |
MPI version, we need to cast const char* to void* for |
| 696 |
> |
stringstream.str(); Previous Makefile use bjects of single version |
| 697 |
> |
to make the MPI library; |
| 698 |
> |
|
| 699 |
> |
2005-12-29 19:18 chuckv |
| 700 |
> |
|
| 701 |
> |
* make/Makefile.in, samples/metals/Makefile, |
| 702 |
> |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
| 703 |
> |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
| 704 |
> |
Almost there... |
| 705 |
> |
|
| 706 |
> |
2005-12-29 15:19 chuckv |
| 707 |
> |
|
| 708 |
> |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
| 709 |
> |
forcefield. |
| 710 |
> |
|
| 711 |
> |
2005-12-29 15:07 chuckv |
| 712 |
> |
|
| 713 |
> |
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
| 714 |
> |
metals.md: added files for sutton-chen |
| 715 |
> |
|
| 716 |
> |
2005-12-29 11:37 chuckv |
| 717 |
> |
|
| 718 |
> |
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
| 719 |
> |
metals.md: More cvs changing. |
| 720 |
> |
|
| 721 |
> |
2005-12-29 11:34 chuckv |
| 722 |
> |
|
| 723 |
> |
* samples/metals/Au_nanoparticle.in: More moving... |
| 724 |
> |
|
| 725 |
> |
2005-12-29 11:33 chuckv |
| 726 |
> |
|
| 727 |
> |
* samples/metals/EAM/nanoparticle/: |
| 728 |
> |
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
| 729 |
> |
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
| 730 |
> |
changes to directory structure. |
| 731 |
> |
|
| 732 |
> |
2005-12-29 11:21 chuckv |
| 733 |
> |
|
| 734 |
> |
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
| 735 |
> |
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
| 736 |
> |
|
| 737 |
> |
2005-12-29 11:17 chuckv |
| 738 |
> |
|
| 739 |
> |
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
| 740 |
> |
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
| 741 |
> |
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
| 742 |
> |
directory structure |
| 743 |
> |
|
| 744 |
> |
2005-12-29 11:03 chuckv |
| 745 |
> |
|
| 746 |
> |
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
| 747 |
> |
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
| 748 |
> |
call to set force options in SimCreator. |
| 749 |
> |
|
| 750 |
> |
2005-12-28 16:44 chuckv |
| 751 |
> |
|
| 752 |
> |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
| 753 |
> |
changes to forcefield options. |
| 754 |
> |
|
| 755 |
> |
2005-12-28 16:42 chuckv |
| 756 |
> |
|
| 757 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
| 758 |
> |
passed to fortran. |
| 759 |
> |
|
| 760 |
> |
2005-12-23 18:04 chuckv |
| 761 |
> |
|
| 762 |
> |
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
| 763 |
> |
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
| 764 |
> |
changes. |
| 765 |
> |
|
| 766 |
> |
2005-12-16 16:52 tim |
| 767 |
> |
|
| 768 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 769 |
> |
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
| 770 |
> |
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
| 771 |
> |
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
| 772 |
> |
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
| 773 |
> |
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
| 774 |
> |
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
| 775 |
> |
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
| 776 |
> |
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
| 777 |
> |
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
| 778 |
> |
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
| 779 |
> |
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
| 780 |
> |
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
| 781 |
> |
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
| 782 |
> |
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
| 783 |
> |
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
| 784 |
> |
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
| 785 |
> |
__FUNCTION__ to __func__ to match C99 standard, and then added an |
| 786 |
> |
autoconf test to check for __func__ usability. Changed some |
| 787 |
> |
default compile flags for the Sun architecture |
| 788 |
> |
|
| 789 |
> |
2005-12-16 14:01 gezelter |
| 790 |
> |
|
| 791 |
> |
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
| 792 |
> |
|
| 793 |
> |
2005-12-16 13:55 tim |
| 794 |
> |
|
| 795 |
> |
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
| 796 |
> |
change to build oopse under solaris |
| 797 |
> |
|
| 798 |
> |
2005-12-16 13:26 tim |
| 799 |
> |
|
| 800 |
> |
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
| 801 |
> |
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
| 802 |
> |
came with SUN compiler does not have a conforming std::use_facet, |
| 803 |
> |
define a macro to handle it. Adding exception handling to |
| 804 |
> |
SimCreator. |
| 805 |
> |
|
| 806 |
> |
2005-12-16 10:53 gezelter |
| 807 |
> |
|
| 808 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 809 |
> |
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
| 810 |
> |
which was living inside the GB particle. No alien-like ripping out |
| 811 |
> |
of the stomach was required. |
| 812 |
> |
|
| 813 |
> |
2005-12-15 21:57 tim |
| 814 |
> |
|
| 815 |
> |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
| 816 |
> |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
| 817 |
> |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
| 818 |
> |
replace grammar for numerical parsing |
| 819 |
> |
|
| 820 |
> |
2005-12-15 16:43 gezelter |
| 821 |
> |
|
| 822 |
> |
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
| 823 |
> |
|
| 824 |
> |
2005-12-15 09:48 gezelter |
| 825 |
> |
|
| 826 |
> |
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
| 827 |
> |
dependencies and replacing them with real autoconf checks |
| 828 |
> |
|
| 829 |
> |
2005-12-15 09:47 gezelter |
| 830 |
> |
|
| 831 |
> |
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
| 832 |
> |
ac-tools/configure.in, src/config.h.in: Adding checks for various |
| 833 |
> |
features used by ANTLR |
| 834 |
> |
|
| 835 |
> |
2005-12-14 13:02 tim |
| 836 |
> |
|
| 837 |
> |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
| 838 |
> |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
| 839 |
> |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
| 840 |
> |
nasty negative integer parsing problem by refining the grammar |
| 841 |
> |
|
| 842 |
> |
2005-12-12 14:32 gezelter |
| 843 |
> |
|
| 844 |
> |
* src/: UseTheForce/doForces_interface.F90, |
| 845 |
> |
UseTheForce/doForces_interface.h, |
| 846 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 847 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 848 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 849 |
> |
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
| 850 |
> |
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
| 851 |
> |
some minor changes to allow compilation with the portland group |
| 852 |
> |
compilers |
| 853 |
> |
|
| 854 |
> |
2005-12-10 11:54 tim |
| 855 |
> |
|
| 856 |
> |
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
| 857 |
> |
problem for icc7 |
| 858 |
> |
|
| 859 |
> |
2005-12-09 16:18 gezelter |
| 860 |
> |
|
| 861 |
> |
* src/utils/CaseConversion.hpp: added missing include |
| 862 |
> |
|
| 863 |
> |
2005-12-09 12:11 gezelter |
| 864 |
> |
|
| 865 |
> |
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
| 866 |
> |
compiler |
| 867 |
> |
|
| 868 |
> |
2005-12-08 17:05 gezelter |
| 869 |
> |
|
| 870 |
> |
* src/io/ForceFieldOptions.cpp: added copyright |
| 871 |
> |
|
| 872 |
> |
2005-12-08 17:04 gezelter |
| 873 |
> |
|
| 874 |
> |
* src/UseTheForce/doForces.F90: added info printout |
| 875 |
> |
|
| 876 |
> |
2005-12-08 17:04 gezelter |
| 877 |
> |
|
| 878 |
> |
* configure, ac-tools/configure.in: added pathscale |
| 879 |
> |
|
| 880 |
> |
2005-12-08 10:38 chuckv |
| 881 |
> |
|
| 882 |
> |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
| 883 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
| 884 |
> |
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
| 885 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 886 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 887 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 888 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 889 |
> |
io/DirectionalAtomTypesSectionParser.hpp, |
| 890 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 891 |
> |
io/GayBerneAtomTypesSectionParser.cpp, |
| 892 |
> |
io/GayBerneAtomTypesSectionParser.hpp, |
| 893 |
> |
io/MultipoleAtomTypesSectionParser.cpp, |
| 894 |
> |
io/MultipoleAtomTypesSectionParser.hpp, |
| 895 |
> |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
| 896 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
| 897 |
> |
io/ShapeAtomTypesSectionParser.hpp, |
| 898 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 899 |
> |
io/StickyAtomTypesSectionParser.hpp, |
| 900 |
> |
io/StickyPowerAtomTypesSectionParser.cpp, |
| 901 |
> |
io/StickyPowerAtomTypesSectionParser.hpp, |
| 902 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
| 903 |
> |
Wow thats alot o' files. Now passing forceFieldOptions to all of |
| 904 |
> |
the parsers. |
| 905 |
> |
|
| 906 |
> |
2005-12-07 18:10 chuckv |
| 907 |
> |
|
| 908 |
> |
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
| 909 |
> |
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
| 910 |
> |
Started adding support for ForceOptions to section parsers. |
| 911 |
> |
|
| 912 |
> |
2005-12-07 18:01 gezelter |
| 913 |
> |
|
| 914 |
> |
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
| 915 |
> |
|
| 916 |
> |
2005-12-07 18:00 chuckv |
| 917 |
> |
|
| 918 |
> |
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
| 919 |
> |
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
| 920 |
> |
section parser |
| 921 |
> |
|
| 922 |
> |
2005-12-07 14:58 chuckv |
| 923 |
> |
|
| 924 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
| 925 |
> |
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
| 926 |
> |
suttonchen_interface.h: Removed geometric distance mixing from |
| 927 |
> |
individual modules and now use force options to detemine what the |
| 928 |
> |
deal is. |
| 929 |
> |
|
| 930 |
> |
2005-12-07 14:46 chuckv |
| 931 |
> |
|
| 932 |
> |
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
| 933 |
> |
Further fixes for compiler issues. |
| 934 |
> |
|
| 935 |
> |
2005-12-07 14:44 chuckv |
| 936 |
> |
|
| 937 |
> |
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
| 938 |
> |
|
| 939 |
> |
2005-12-07 14:38 chuckv |
| 940 |
> |
|
| 941 |
> |
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
| 942 |
> |
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
| 943 |
> |
support for fortran force options. |
| 944 |
> |
|
| 945 |
> |
2005-12-06 16:01 tim |
| 946 |
> |
|
| 947 |
> |
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
| 948 |
> |
|
| 949 |
> |
2005-12-06 14:26 chuckv |
| 950 |
> |
|
| 951 |
> |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
| 952 |
> |
|
| 953 |
> |
2005-12-06 12:53 chuckv |
| 954 |
> |
|
| 955 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 956 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
| 957 |
> |
crystal |
| 958 |
> |
|
| 959 |
> |
2005-12-06 12:52 chuckv |
| 960 |
> |
|
| 961 |
> |
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
| 962 |
> |
dumpwriter. |
| 963 |
> |
|
| 964 |
> |
2005-12-06 11:49 tim |
| 965 |
> |
|
| 966 |
> |
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
| 967 |
> |
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
| 968 |
> |
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
| 969 |
> |
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
| 970 |
> |
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
| 971 |
> |
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
| 972 |
> |
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
| 973 |
> |
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
| 974 |
> |
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
| 975 |
> |
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
| 976 |
> |
minimizer/water.md, shape/linear.md, |
| 977 |
> |
thermoIntegration/liquid/ssde.md, |
| 978 |
> |
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
| 979 |
> |
thermoIntegration/solid/water.md, water/dimer/cl.md, |
| 980 |
> |
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
| 981 |
> |
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
| 982 |
> |
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
| 983 |
> |
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
| 984 |
> |
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
| 985 |
> |
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
| 986 |
> |
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
| 987 |
> |
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
| 988 |
> |
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
| 989 |
> |
keywords from samples |
| 990 |
> |
|
| 991 |
> |
2005-12-05 18:37 tim |
| 992 |
> |
|
| 993 |
> |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
| 994 |
> |
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
| 995 |
> |
|
| 996 |
> |
2005-12-05 17:23 gezelter |
| 997 |
> |
|
| 998 |
> |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
| 999 |
> |
UseTheForce/Makefile, brains/Register.cpp, |
| 1000 |
> |
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
| 1001 |
> |
handler for CLAY force field |
| 1002 |
> |
|
| 1003 |
> |
2005-12-05 16:45 chuckv |
| 1004 |
> |
|
| 1005 |
> |
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
| 1006 |
> |
in openbabel. |
| 1007 |
> |
|
| 1008 |
> |
2005-12-05 14:10 tim |
| 1009 |
> |
|
| 1010 |
> |
* src/types/MoleculeStamp.cpp: reformat error message |
| 1011 |
> |
|
| 1012 |
> |
2005-12-05 14:07 gezelter |
| 1013 |
> |
|
| 1014 |
> |
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
| 1015 |
> |
|
| 1016 |
> |
2005-12-05 13:23 tim |
| 1017 |
> |
|
| 1018 |
> |
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 1019 |
> |
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
| 1020 |
> |
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
| 1021 |
> |
adding more checking for topology |
| 1022 |
> |
|
| 1023 |
> |
2005-12-02 17:37 gezelter |
| 1024 |
> |
|
| 1025 |
> |
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
| 1026 |
> |
removal |
| 1027 |
> |
|
| 1028 |
> |
2005-12-02 17:37 gezelter |
| 1029 |
> |
|
| 1030 |
> |
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
| 1031 |
> |
|
| 1032 |
> |
2005-12-02 17:37 gezelter |
| 1033 |
> |
|
| 1034 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 1035 |
> |
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
| 1036 |
> |
traditional.md: removing deprecated nAtoms and nComponents lines |
| 1037 |
> |
|
| 1038 |
> |
2005-12-02 15:34 tim |
| 1039 |
> |
|
| 1040 |
> |
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
| 1041 |
> |
|
| 1042 |
> |
2005-12-02 15:18 tim |
| 1043 |
> |
|
| 1044 |
> |
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
| 1045 |
> |
FragmentStamp |
| 1046 |
> |
|
| 1047 |
> |
2005-12-02 15:11 gezelter |
| 1048 |
> |
|
| 1049 |
> |
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
| 1050 |
> |
longer thrown with consts (fixes compilation bug on the Mac). |
| 1051 |
> |
|
| 1052 |
> |
2005-12-02 15:10 gezelter |
| 1053 |
> |
|
| 1054 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
| 1055 |
> |
printing out of timestep |
| 1056 |
> |
|
| 1057 |
> |
2005-12-02 15:10 gezelter |
| 1058 |
> |
|
| 1059 |
> |
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
| 1060 |
> |
junk |
| 1061 |
> |
|
| 1062 |
> |
2005-12-02 15:10 gezelter |
| 1063 |
> |
|
| 1064 |
> |
* make/Makefile.in: Change build process for libOOPSE.a so that the |
| 1065 |
> |
libraries aren't unpacked. libOOPSE.a is now made directly from |
| 1066 |
> |
the object files |
| 1067 |
> |
|
| 1068 |
> |
2005-12-02 15:09 gezelter |
| 1069 |
> |
|
| 1070 |
> |
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
| 1071 |
> |
needed for new build of libOOPSE.a |
| 1072 |
> |
|
| 1073 |
> |
2005-12-02 13:43 tim |
| 1074 |
> |
|
| 1075 |
> |
* src/types/DataHolder.hpp: adding DataHolder |
| 1076 |
> |
|
| 1077 |
> |
2005-12-02 12:01 gezelter |
| 1078 |
> |
|
| 1079 |
> |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
| 1080 |
> |
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
| 1081 |
> |
case for the cutoff policies |
| 1082 |
> |
|
| 1083 |
> |
2005-12-02 10:38 tim |
| 1084 |
> |
|
| 1085 |
> |
* make/Makefile.in: update Makefile |
| 1086 |
> |
|
| 1087 |
> |
2005-12-02 10:38 tim |
| 1088 |
> |
|
| 1089 |
> |
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
| 1090 |
> |
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
| 1091 |
> |
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
| 1092 |
> |
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
| 1093 |
> |
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
| 1094 |
> |
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
| 1095 |
> |
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
| 1096 |
> |
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
| 1097 |
> |
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
| 1098 |
> |
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
| 1099 |
> |
antlr/CommonASTWithHiddenTokens.cpp, |
| 1100 |
> |
antlr/CommonASTWithHiddenTokens.hpp, |
| 1101 |
> |
antlr/CommonHiddenStreamToken.cpp, |
| 1102 |
> |
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
| 1103 |
> |
antlr/CommonToken.hpp, antlr/IOException.hpp, |
| 1104 |
> |
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
| 1105 |
> |
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
| 1106 |
> |
antlr/Makefile, antlr/MismatchedCharException.cpp, |
| 1107 |
> |
antlr/MismatchedCharException.hpp, |
| 1108 |
> |
antlr/MismatchedTokenException.cpp, |
| 1109 |
> |
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
| 1110 |
> |
antlr/NoViableAltException.hpp, |
| 1111 |
> |
antlr/NoViableAltForCharException.cpp, |
| 1112 |
> |
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
| 1113 |
> |
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
| 1114 |
> |
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
| 1115 |
> |
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
| 1116 |
> |
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
| 1117 |
> |
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
| 1118 |
> |
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
| 1119 |
> |
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
| 1120 |
> |
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
| 1121 |
> |
antlr/TokenStreamHiddenTokenFilter.cpp, |
| 1122 |
> |
antlr/TokenStreamHiddenTokenFilter.hpp, |
| 1123 |
> |
antlr/TokenStreamIOException.hpp, |
| 1124 |
> |
antlr/TokenStreamRecognitionException.hpp, |
| 1125 |
> |
antlr/TokenStreamRetryException.hpp, |
| 1126 |
> |
antlr/TokenStreamRewriteEngine.cpp, |
| 1127 |
> |
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
| 1128 |
> |
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
| 1129 |
> |
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
| 1130 |
> |
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
| 1131 |
> |
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
| 1132 |
> |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
| 1133 |
> |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 1134 |
> |
constraints/ZconstraintForceManager.cpp, |
| 1135 |
> |
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
| 1136 |
> |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
| 1137 |
> |
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
| 1138 |
> |
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
| 1139 |
> |
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
| 1140 |
> |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
| 1141 |
> |
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
| 1142 |
> |
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
| 1143 |
> |
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
| 1144 |
> |
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
| 1145 |
> |
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
| 1146 |
> |
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
| 1147 |
> |
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
| 1148 |
> |
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
| 1149 |
> |
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
| 1150 |
> |
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
| 1151 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 1152 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 1153 |
> |
selection/Makefile, selection/NameFinder.cpp, |
| 1154 |
> |
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
| 1155 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 1156 |
> |
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
| 1157 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
| 1158 |
> |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
| 1159 |
> |
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
| 1160 |
> |
types/Component.cpp, types/Component.hpp, |
| 1161 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 1162 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
| 1163 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 1164 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 1165 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 1166 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
| 1167 |
> |
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
| 1168 |
> |
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
| 1169 |
> |
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
| 1170 |
> |
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
| 1171 |
> |
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
| 1172 |
> |
with antlr parser |
| 1173 |
> |
|
| 1174 |
> |
2005-11-30 16:00 chuckv |
| 1175 |
> |
|
| 1176 |
> |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
| 1177 |
> |
calculate rho(Z) to calculate density profiles for water slabs. |
| 1178 |
> |
|
| 1179 |
> |
2005-11-29 17:54 chuckv |
| 1180 |
> |
|
| 1181 |
> |
* configure, ac-tools/configure.in: added checks for some functions |
| 1182 |
> |
to configure script |
| 1183 |
> |
|
| 1184 |
> |
2005-11-22 20:05 chuckv |
| 1185 |
> |
|
| 1186 |
> |
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
| 1187 |
> |
obbond.cpp: Changed file names that conflict w/ oopse file name |
| 1188 |
> |
object files. |
| 1189 |
> |
|
| 1190 |
> |
2005-11-21 17:59 gezelter |
| 1191 |
> |
|
| 1192 |
> |
* src/utils/residentMem.c: compilation bug |
| 1193 |
> |
|
| 1194 |
> |
2005-11-21 17:59 gezelter |
| 1195 |
> |
|
| 1196 |
> |
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
| 1197 |
> |
|
| 1198 |
> |
2005-11-21 17:59 gezelter |
| 1199 |
> |
|
| 1200 |
> |
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
| 1201 |
> |
|
| 1202 |
> |
2005-11-21 17:59 gezelter |
| 1203 |
> |
|
| 1204 |
> |
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
| 1205 |
> |
issue |
| 1206 |
> |
|
| 1207 |
> |
2005-11-21 17:58 gezelter |
| 1208 |
> |
|
| 1209 |
> |
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
| 1210 |
> |
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
| 1211 |
> |
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
| 1212 |
> |
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
| 1213 |
> |
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
| 1214 |
> |
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
| 1215 |
> |
|
| 1216 |
> |
2005-11-21 11:22 tim |
| 1217 |
> |
|
| 1218 |
> |
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
| 1219 |
> |
|
| 1220 |
> |
2005-11-21 09:59 tim |
| 1221 |
> |
|
| 1222 |
> |
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
| 1223 |
> |
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
| 1224 |
> |
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
| 1225 |
> |
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
| 1226 |
> |
|
| 1227 |
> |
2005-11-18 15:17 tim |
| 1228 |
> |
|
| 1229 |
> |
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
| 1230 |
> |
adding support for soft linking |
| 1231 |
> |
|
| 1232 |
> |
2005-11-18 15:17 tim |
| 1233 |
> |
|
| 1234 |
> |
* make/Makefile.in: Adding support for soft linking |
| 1235 |
> |
|
| 1236 |
> |
2005-11-18 12:50 gezelter |
| 1237 |
> |
|
| 1238 |
> |
* make/Makefile.in: Adding linking stuff |
| 1239 |
> |
|
| 1240 |
> |
2005-11-18 11:38 tim |
| 1241 |
> |
|
| 1242 |
> |
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
| 1243 |
> |
src/applications/atom2mdin/atom2mdin.cpp, |
| 1244 |
> |
src/applications/mdinConverter/Makefile, |
| 1245 |
> |
src/applications/mdinConverter/mdinConverter.cpp, |
| 1246 |
> |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
| 1247 |
> |
rename mdinConverter to atom2mdin |
| 1248 |
> |
|
| 1249 |
> |
2005-11-17 15:44 gezelter |
| 1250 |
> |
|
| 1251 |
> |
* src/openbabel/obconversion.cpp: fixed a bug |
| 1252 |
> |
|
| 1253 |
> |
2005-11-17 15:39 gezelter |
| 1254 |
> |
|
| 1255 |
> |
* configure: Adding some config checks for OpenBabel codes we are |
| 1256 |
> |
using |
| 1257 |
> |
|
| 1258 |
> |
2005-11-17 15:39 gezelter |
| 1259 |
> |
|
| 1260 |
> |
* ac-tools/configure.in: Adding some checks for OpenBabel code |
| 1261 |
> |
|
| 1262 |
> |
2005-11-17 15:39 gezelter |
| 1263 |
> |
|
| 1264 |
> |
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
| 1265 |
> |
|
| 1266 |
> |
2005-11-17 15:38 gezelter |
| 1267 |
> |
|
| 1268 |
> |
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
| 1269 |
> |
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
| 1270 |
> |
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
| 1271 |
> |
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
| 1272 |
> |
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
| 1273 |
> |
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
| 1274 |
> |
Unifying config.h stuff and making sure the OpenBabel codes can |
| 1275 |
> |
find our default (and environment variable) Force Field |
| 1276 |
> |
directories. |
| 1277 |
> |
|
| 1278 |
> |
2005-11-17 13:35 tim |
| 1279 |
> |
|
| 1280 |
> |
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
| 1281 |
> |
|
| 1282 |
> |
2005-11-16 18:10 tim |
| 1283 |
> |
|
| 1284 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 1285 |
> |
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
| 1286 |
> |
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
| 1287 |
> |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 1288 |
> |
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
| 1289 |
> |
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
| 1290 |
> |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 1291 |
> |
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
| 1292 |
> |
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
| 1293 |
> |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
| 1294 |
> |
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
| 1295 |
> |
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
| 1296 |
> |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
| 1297 |
> |
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
| 1298 |
> |
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
| 1299 |
> |
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
| 1300 |
> |
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
| 1301 |
> |
get compiled |
| 1302 |
> |
|
| 1303 |
> |
2005-11-16 16:37 chuckv |
| 1304 |
> |
|
| 1305 |
> |
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
| 1306 |
> |
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
| 1307 |
> |
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
| 1308 |
> |
optional parameters.... |
| 1309 |
> |
|
| 1310 |
> |
2005-11-16 16:24 tim |
| 1311 |
> |
|
| 1312 |
> |
* src/applications/mdinConverter/: Makefile, mdinConverter.cpp: |
| 1313 |
> |
adding mdinConverter |
| 1314 |
> |
|
| 1315 |
> |
2005-11-16 16:22 tim |
| 1316 |
> |
|
| 1317 |
> |
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
| 1318 |
> |
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
| 1319 |
> |
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
| 1320 |
> |
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
| 1321 |
> |
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
| 1322 |
> |
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
| 1323 |
> |
adding more readers/writers |
| 1324 |
> |
|
| 1325 |
> |
2005-11-16 16:20 tim |
| 1326 |
> |
|
| 1327 |
> |
* make/Makefile.in: adding openbabel |
| 1328 |
> |
|
| 1329 |
> |
2005-11-16 16:20 tim |
| 1330 |
> |
|
| 1331 |
> |
* src/brains/: Register.cpp, Register.hpp: register openbabel |
| 1332 |
> |
readers/writers |
| 1333 |
> |
|
| 1334 |
> |
2005-11-16 14:57 chrisfen |
| 1335 |
> |
|
| 1336 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
| 1337 |
> |
potential self term |
| 1338 |
> |
|
| 1339 |
> |
2005-11-16 14:57 chrisfen |
| 1340 |
> |
|
| 1341 |
> |
* samples/water/spce/spce.md: just some parameters |
| 1342 |
> |
|
| 1343 |
> |
2005-11-16 14:42 tim |
| 1344 |
> |
|
| 1345 |
> |
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
| 1346 |
> |
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
| 1347 |
> |
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
| 1348 |
> |
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
| 1349 |
> |
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
| 1350 |
> |
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
| 1351 |
> |
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
| 1352 |
> |
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
| 1353 |
> |
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
| 1354 |
> |
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
| 1355 |
> |
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
| 1356 |
> |
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
| 1357 |
> |
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
| 1358 |
> |
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
| 1359 |
> |
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
| 1360 |
> |
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
| 1361 |
> |
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
| 1362 |
> |
zipstreamimpl.hpp: adding openbabel |
| 1363 |
> |
|
| 1364 |
> |
2005-11-15 14:42 chrisfen |
| 1365 |
> |
|
| 1366 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
| 1367 |
> |
commented code |
| 1368 |
> |
|
| 1369 |
> |
2005-11-15 14:04 chrisfen |
| 1370 |
> |
|
| 1371 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
| 1372 |
> |
charge-charge interactions a bit... |
| 1373 |
> |
|
| 1374 |
> |
2005-11-15 14:03 chrisfen |
| 1375 |
> |
|
| 1376 |
> |
* samples/water/spce/: spce.md, water.md: just playing |
| 1377 |
> |
|
| 1378 |
> |
2005-11-15 11:38 chrisfen |
| 1379 |
> |
|
| 1380 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
| 1381 |
> |
shifted_potential case |
| 1382 |
> |
|
| 1383 |
> |
2005-11-15 11:37 chrisfen |
| 1384 |
> |
|
| 1385 |
> |
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
| 1386 |
> |
just playing around - we need to refresh all the samples sometime |
| 1387 |
> |
soon... |
| 1388 |
> |
|
| 1389 |
> |
2005-11-15 11:18 chuckv |
| 1390 |
> |
|
| 1391 |
> |
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
| 1392 |
> |
preforce calc public in suttonchen. |
| 1393 |
> |
|
| 1394 |
> |
2005-11-15 11:05 chuckv |
| 1395 |
> |
|
| 1396 |
> |
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
| 1397 |
> |
SimInfo |
| 1398 |
> |
|
| 1399 |
> |
2005-11-15 11:01 chuckv |
| 1400 |
> |
|
| 1401 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
| 1402 |
> |
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
| 1403 |
> |
|
| 1404 |
> |
2005-11-15 10:34 chuckv |
| 1405 |
> |
|
| 1406 |
> |
* forceFields/Makefile: Added sutton-chen to makefile. |
| 1407 |
> |
|
| 1408 |
> |
2005-11-14 17:20 chuckv |
| 1409 |
> |
|
| 1410 |
> |
* src/UseTheForce/DarkSide/: suttonchen.F90, |
| 1411 |
> |
suttonchen_interface.h: Build Fixes for sutton-chen. |
| 1412 |
> |
|
| 1413 |
> |
2005-11-14 17:03 chuckv |
| 1414 |
> |
|
| 1415 |
> |
* src/io/Makefile: Missed makefile for sutton-chen. |
| 1416 |
> |
|
| 1417 |
> |
2005-11-14 17:03 chuckv |
| 1418 |
> |
|
| 1419 |
> |
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
| 1420 |
> |
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
| 1421 |
> |
|
| 1422 |
> |
2005-11-14 16:29 chuckv |
| 1423 |
> |
|
| 1424 |
> |
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
| 1425 |
> |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
| 1426 |
> |
UseTheForce/DarkSide/suttonchen.F90, |
| 1427 |
> |
UseTheForce/DarkSide/suttonchen_interface.F90, |
| 1428 |
> |
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
| 1429 |
> |
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
| 1430 |
> |
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
| 1431 |
> |
fix do_forces to use Sutton-Chen. |
| 1432 |
> |
|
| 1433 |
> |
2005-11-11 12:21 chrisfen |
| 1434 |
> |
|
| 1435 |
> |
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
| 1436 |
> |
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
| 1437 |
> |
some files |
| 1438 |
> |
|
| 1439 |
> |
2005-11-11 10:22 chrisfen |
| 1440 |
> |
|
| 1441 |
> |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
| 1442 |
> |
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
| 1443 |
> |
switching function option |
| 1444 |
> |
|
| 1445 |
> |
2005-11-11 10:21 chrisfen |
| 1446 |
> |
|
| 1447 |
> |
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
| 1448 |
> |
5th order polynomial switching function |
| 1449 |
> |
|
| 1450 |
> |
2005-11-11 10:21 chrisfen |
| 1451 |
> |
|
| 1452 |
> |
* samples/water/ssd/ssd.md: playing with switching functions again |
| 1453 |
> |
|
| 1454 |
> |
2005-11-11 10:21 chrisfen |
| 1455 |
> |
|
| 1456 |
> |
* samples/argon/500.md: playing with switching functions |
| 1457 |
> |
|
| 1458 |
> |
2005-11-08 19:11 chuckv |
| 1459 |
> |
|
| 1460 |
> |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
| 1461 |
> |
files for Sutton-Chen and Quantum Sutton-Chen |
| 1462 |
> |
|
| 1463 |
> |
2005-11-08 08:32 chrisfen |
| 1464 |
> |
|
| 1465 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
| 1466 |
> |
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
| 1467 |
> |
ability to output forces and torques |
| 1468 |
> |
|
| 1469 |
> |
2005-11-08 08:32 chrisfen |
| 1470 |
> |
|
| 1471 |
> |
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
| 1472 |
> |
output of forces and torques |
| 1473 |
> |
|
| 1474 |
> |
2005-11-08 08:31 chrisfen |
| 1475 |
> |
|
| 1476 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
| 1477 |
> |
Working on shifted_force... |
| 1478 |
> |
|
| 1479 |
> |
2005-11-08 08:31 chrisfen |
| 1480 |
> |
|
| 1481 |
> |
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
| 1482 |
> |
|
| 1483 |
> |
2005-11-03 18:22 chrisfen |
| 1484 |
> |
|
| 1485 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
| 1486 |
> |
commented section |
| 1487 |
> |
|
| 1488 |
> |
2005-11-03 18:12 chrisfen |
| 1489 |
> |
|
| 1490 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 1491 |
> |
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
| 1492 |
> |
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
| 1493 |
> |
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
| 1494 |
> |
|
| 1495 |
> |
2005-11-03 18:11 chrisfen |
| 1496 |
> |
|
| 1497 |
> |
* samples/water/spce/spce.md: mmm... damped shifted force... |
| 1498 |
> |
|
| 1499 |
> |
2005-11-03 18:06 chuckv |
| 1500 |
> |
|
| 1501 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
| 1502 |
> |
|
| 1503 |
> |
2005-11-02 18:50 chuckv |
| 1504 |
> |
|
| 1505 |
> |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
| 1506 |
> |
|
| 1507 |
> |
2005-11-02 16:01 chrisfen |
| 1508 |
> |
|
| 1509 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 1510 |
> |
removed some test code |
| 1511 |
> |
|
| 1512 |
> |
2005-11-02 15:45 chrisfen |
| 1513 |
> |
|
| 1514 |
> |
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
| 1515 |
> |
screening method header |
| 1516 |
> |
|
| 1517 |
> |
2005-11-02 15:36 chrisfen |
| 1518 |
> |
|
| 1519 |
> |
* src/brains/SimInfo.cpp: again, changing how we deal with |
| 1520 |
> |
summation and screening methods |
| 1521 |
> |
|
| 1522 |
> |
2005-11-02 15:36 chrisfen |
| 1523 |
> |
|
| 1524 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
| 1525 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 1526 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 1527 |
> |
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
| 1528 |
> |
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
| 1529 |
> |
and screening methods |
| 1530 |
> |
|
| 1531 |
> |
2005-11-02 15:35 chrisfen |
| 1532 |
> |
|
| 1533 |
> |
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
| 1534 |
> |
|
| 1535 |
> |
2005-11-01 18:32 chuckv |
| 1536 |
> |
|
| 1537 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 1538 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
| 1539 |
> |
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
| 1540 |
> |
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
| 1541 |
> |
sutton-chen |
| 1542 |
> |
|
| 1543 |
> |
2005-11-01 14:24 chrisfen |
| 1544 |
> |
|
| 1545 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 1546 |
> |
removed some testing code... |
| 1547 |
> |
|
| 1548 |
> |
2005-11-01 14:14 chrisfen |
| 1549 |
> |
|
| 1550 |
> |
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
| 1551 |
> |
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
| 1552 |
> |
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
| 1553 |
> |
initialization |
| 1554 |
> |
|
| 1555 |
> |
2005-11-01 14:13 chrisfen |
| 1556 |
> |
|
| 1557 |
> |
* src/applications/oopse/oopse.cpp: nothing |
| 1558 |
> |
|
| 1559 |
> |
2005-11-01 14:09 chrisfen |
| 1560 |
> |
|
| 1561 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 1562 |
> |
DarkSide/simulation.F90: still fixing up wolf... |
| 1563 |
> |
|
| 1564 |
> |
2005-11-01 13:29 chuckv |
| 1565 |
> |
|
| 1566 |
> |
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
| 1567 |
> |
process of adding sutton-chen forcefield. |
| 1568 |
> |
|
| 1569 |
> |
2005-10-26 18:32 chrisfen |
| 1570 |
> |
|
| 1571 |
> |
* src/brains/SimInfo.cpp: changed the default switching radius to |
| 1572 |
> |
85% of rcut |
| 1573 |
> |
|
| 1574 |
> |
2005-10-26 18:31 chrisfen |
| 1575 |
> |
|
| 1576 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
| 1577 |
> |
to be working now - for charges and dipoles alike |
| 1578 |
> |
|
| 1579 |
> |
2005-10-26 18:31 chrisfen |
| 1580 |
> |
|
| 1581 |
> |
* src/UseTheForce/doForces.F90: reaction field looks to be working |
| 1582 |
> |
now |
| 1583 |
> |
|
| 1584 |
> |
2005-10-26 18:30 chrisfen |
| 1585 |
> |
|
| 1586 |
> |
* samples/water/ssdrf/water.md: added a test molecule |
| 1587 |
> |
|
| 1588 |
> |
2005-10-26 18:30 chrisfen |
| 1589 |
> |
|
| 1590 |
> |
* forceFields/DUFF2.frc: added a test atom type |
| 1591 |
> |
|
| 1592 |
> |
2005-10-24 09:06 chrisfen |
| 1593 |
> |
|
| 1594 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
| 1595 |
> |
reaction field - don't know if it works... |
| 1596 |
> |
|
| 1597 |
> |
2005-10-23 16:08 chrisfen |
| 1598 |
> |
|
| 1599 |
> |
* src/: UseTheForce/doForces.F90, |
| 1600 |
> |
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
| 1601 |
> |
streamlined reaction field for dipoles (now a good bit faster) and |
| 1602 |
> |
added reaction field for charges - still need to do charge-dipole |
| 1603 |
> |
RF |
| 1604 |
> |
|
| 1605 |
> |
2005-10-23 16:07 chrisfen |
| 1606 |
> |
|
| 1607 |
> |
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
| 1608 |
> |
field |
| 1609 |
> |
|
| 1610 |
> |
2005-10-23 16:06 chrisfen |
| 1611 |
> |
|
| 1612 |
> |
* samples/water/spce/spce.md: reaction field now works for charges |
| 1613 |
> |
|
| 1614 |
> |
2005-10-20 15:27 tim |
| 1615 |
> |
|
| 1616 |
> |
* src/primitives/Torsion.cpp: Fix the other branch of force |
| 1617 |
> |
calculation in Torision.cpp |
| 1618 |
> |
|
| 1619 |
> |
2005-10-19 14:24 chrisfen |
| 1620 |
> |
|
| 1621 |
> |
* src/: UseTheForce/doForces.F90, |
| 1622 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 1623 |
> |
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
| 1624 |
> |
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
| 1625 |
> |
toUpper problems - these changes should fix those... |
| 1626 |
> |
|
| 1627 |
> |
2005-10-19 14:23 chrisfen |
| 1628 |
> |
|
| 1629 |
> |
* samples/water/ssdrf/ssdrf.md: nothing |
| 1630 |
> |
|
| 1631 |
> |
2005-10-19 12:03 gezelter |
| 1632 |
> |
|
| 1633 |
> |
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
| 1634 |
> |
GayBerne |
| 1635 |
> |
|
| 1636 |
> |
2005-10-19 11:49 tim |
| 1637 |
> |
|
| 1638 |
> |
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
| 1639 |
> |
brains/ForceManager.cpp: fix an index mismathcing between c and |
| 1640 |
> |
fortran |
| 1641 |
> |
|
| 1642 |
> |
2005-10-18 18:03 gezelter |
| 1643 |
> |
|
| 1644 |
> |
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
| 1645 |
> |
samples for the cutoff methods that Yang Zheng has been working on |
| 1646 |
> |
|
| 1647 |
> |
2005-10-18 16:13 gezelter |
| 1648 |
> |
|
| 1649 |
> |
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
| 1650 |
> |
and a rotation matrix bug |
| 1651 |
> |
|
| 1652 |
> |
2005-10-18 16:13 gezelter |
| 1653 |
> |
|
| 1654 |
> |
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
| 1655 |
> |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
| 1656 |
> |
added a few GB test cases |
| 1657 |
> |
|
| 1658 |
> |
2005-10-18 16:13 gezelter |
| 1659 |
> |
|
| 1660 |
> |
* forceFields/DUFF2.frc: Fixing GB parameters |
| 1661 |
> |
|
| 1662 |
> |
2005-10-18 13:36 kdaily |
| 1663 |
> |
|
| 1664 |
> |
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
| 1665 |
> |
type |
| 1666 |
> |
|
| 1667 |
> |
2005-10-18 10:01 chrisfen |
| 1668 |
> |
|
| 1669 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
| 1670 |
> |
UseTheForce/DarkSide/Makefile, |
| 1671 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 1672 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 1673 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 1674 |
> |
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
| 1675 |
> |
reaction field with electrostatics.F90 |
| 1676 |
> |
|
| 1677 |
> |
2005-10-17 18:13 tim |
| 1678 |
> |
|
| 1679 |
> |
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
| 1680 |
> |
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
| 1681 |
> |
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
| 1682 |
> |
io/StatWriter.hpp: Customized StatWriter is working |
| 1683 |
> |
|
| 1684 |
> |
2005-10-17 17:42 kdaily |
| 1685 |
> |
|
| 1686 |
> |
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
| 1687 |
> |
paper |
| 1688 |
> |
|
| 1689 |
> |
2005-10-17 16:47 gezelter |
| 1690 |
> |
|
| 1691 |
> |
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
| 1692 |
> |
|
| 1693 |
> |
2005-10-17 14:24 tim |
| 1694 |
> |
|
| 1695 |
> |
* src/io/ParamConstraint.hpp: Another bug fix |
| 1696 |
> |
|
| 1697 |
> |
2005-10-17 14:22 tim |
| 1698 |
> |
|
| 1699 |
> |
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
| 1700 |
> |
issues in Globals |
| 1701 |
> |
|
| 1702 |
> |
2005-10-17 14:12 gezelter |
| 1703 |
> |
|
| 1704 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
| 1705 |
> |
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
| 1706 |
> |
UseTheForce/DarkSide/gb_interface.F90, |
| 1707 |
> |
UseTheForce/DarkSide/gb_interface.h, |
| 1708 |
> |
io/GayBerneAtomTypesSectionParser.cpp, |
| 1709 |
> |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
| 1710 |
> |
changing GB architecture |
| 1711 |
> |
|
| 1712 |
> |
2005-10-17 14:12 gezelter |
| 1713 |
> |
|
| 1714 |
> |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
| 1715 |
> |
gbRotRoundZ.in: Adding samples for gb tests |
| 1716 |
> |
|
| 1717 |
> |
2005-10-16 22:06 tim |
| 1718 |
> |
|
| 1719 |
> |
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
| 1720 |
> |
a string to event's err_msg, there are still tons of memory |
| 1721 |
> |
leaking problem in Globals |
| 1722 |
> |
|
| 1723 |
> |
2005-10-16 19:51 tim |
| 1724 |
> |
|
| 1725 |
> |
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
| 1726 |
> |
error message in Globals |
| 1727 |
> |
|
| 1728 |
> |
2005-10-14 16:43 tim |
| 1729 |
> |
|
| 1730 |
> |
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
| 1731 |
> |
parameters are working now |
| 1732 |
> |
|
| 1733 |
> |
2005-10-14 11:43 gezelter |
| 1734 |
> |
|
| 1735 |
> |
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
| 1736 |
> |
|
| 1737 |
> |
2005-10-14 11:05 gezelter |
| 1738 |
> |
|
| 1739 |
> |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
| 1740 |
> |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
| 1741 |
> |
Adding some Gay Berne tests |
| 1742 |
> |
|
| 1743 |
> |
2005-10-14 11:05 gezelter |
| 1744 |
> |
|
| 1745 |
> |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
| 1746 |
> |
cutoff tests |
| 1747 |
> |
|
| 1748 |
> |
2005-10-14 10:44 kdaily |
| 1749 |
> |
|
| 1750 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
| 1751 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
| 1752 |
> |
src/UseTheForce/DarkSide/gb_interface.F90, |
| 1753 |
> |
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
| 1754 |
> |
LJ |
| 1755 |
> |
|
| 1756 |
> |
2005-10-14 09:48 tim |
| 1757 |
> |
|
| 1758 |
> |
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
| 1759 |
> |
|
| 1760 |
> |
2005-10-14 09:18 chrisfen |
| 1761 |
> |
|
| 1762 |
> |
* samples/thermoIntegration/liquid/ssde.md, |
| 1763 |
> |
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
| 1764 |
> |
src/restraints/Restraints.cpp: added default restraint spring |
| 1765 |
> |
constants into Globals |
| 1766 |
> |
|
| 1767 |
> |
2005-10-13 17:26 tim |
| 1768 |
> |
|
| 1769 |
> |
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
| 1770 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
| 1771 |
> |
constraints/ZconstraintForceManager.cpp, |
| 1772 |
> |
integrators/Integrator.cpp, integrators/NPT.cpp, |
| 1773 |
> |
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
| 1774 |
> |
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
| 1775 |
> |
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
| 1776 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
| 1777 |
> |
visitors/ZconsVisitor.cpp: rewrite Globals |
| 1778 |
> |
|
| 1779 |
> |
2005-10-12 16:57 chuckv |
| 1780 |
> |
|
| 1781 |
> |
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
| 1782 |
> |
potential array to fortran. |
| 1783 |
> |
|
| 1784 |
> |
2005-10-12 16:00 gezelter |
| 1785 |
> |
|
| 1786 |
> |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
| 1787 |
> |
remember what we did |
| 1788 |
> |
|
| 1789 |
> |
2005-10-12 16:00 gezelter |
| 1790 |
> |
|
| 1791 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
| 1792 |
> |
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
| 1793 |
> |
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
| 1794 |
> |
DarkSide/sticky.F90: simplifying long range potential array |
| 1795 |
> |
|
| 1796 |
> |
2005-10-12 16:00 gezelter |
| 1797 |
> |
|
| 1798 |
> |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
| 1799 |
> |
cutoff methods |
| 1800 |
> |
|
| 1801 |
> |
2005-10-12 16:00 gezelter |
| 1802 |
> |
|
| 1803 |
> |
* forceFields/DUFF2.frc: Messing with 2-point water models |
| 1804 |
> |
|
| 1805 |
> |
2005-10-12 15:22 chuckv |
| 1806 |
> |
|
| 1807 |
> |
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
| 1808 |
> |
interface now expects an array for pot. |
| 1809 |
> |
|
| 1810 |
> |
2005-10-12 15:18 chuckv |
| 1811 |
> |
|
| 1812 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
| 1813 |
> |
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
| 1814 |
> |
calculation of potential. |
| 1815 |
> |
|
| 1816 |
> |
2005-10-12 14:55 chuckv |
| 1817 |
> |
|
| 1818 |
> |
* src/UseTheForce/doForces.F90: More changes to MPI potential |
| 1819 |
> |
calculations. |
| 1820 |
> |
|
| 1821 |
> |
2005-10-12 13:59 chuckv |
| 1822 |
> |
|
| 1823 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
| 1824 |
> |
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
| 1825 |
> |
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
| 1826 |
> |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
| 1827 |
> |
Breaky: Add Support for seperating potential contributions. |
| 1828 |
> |
|
| 1829 |
> |
2005-10-11 17:00 chuckv |
| 1830 |
> |
|
| 1831 |
> |
* src/UseTheForce/doForces.F90: Free some variables that weren't |
| 1832 |
> |
freed before. |
| 1833 |
> |
|
| 1834 |
> |
2005-10-11 16:59 chuckv |
| 1835 |
> |
|
| 1836 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 1837 |
> |
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
| 1838 |
> |
builder --twinned. |
| 1839 |
> |
|
| 1840 |
> |
2005-10-11 16:57 chuckv |
| 1841 |
> |
|
| 1842 |
> |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
| 1843 |
> |
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
| 1844 |
> |
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
| 1845 |
> |
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
| 1846 |
> |
cvs. |
| 1847 |
> |
|
| 1848 |
> |
2005-10-10 16:34 chuckv |
| 1849 |
> |
|
| 1850 |
> |
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
| 1851 |
> |
in MPI. |
| 1852 |
> |
|
| 1853 |
> |
2005-10-10 16:20 chuckv |
| 1854 |
> |
|
| 1855 |
> |
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
| 1856 |
> |
indexing of groupToGtype. We now have two seperate maps |
| 1857 |
> |
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
| 1858 |
> |
that is set to groupToGtypeRow in the single processor version. |
| 1859 |
> |
|
| 1860 |
> |
2005-10-06 13:44 chrisfen |
| 1861 |
> |
|
| 1862 |
> |
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
| 1863 |
> |
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
| 1864 |
> |
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
| 1865 |
> |
|
| 1866 |
> |
2005-10-05 16:12 tim |
| 1867 |
> |
|
| 1868 |
> |
* src/primitives/RigidBody.cpp: There is still something wrong with |
| 1869 |
> |
inertia tensor projection |
| 1870 |
> |
|
| 1871 |
> |
2005-10-05 14:35 tim |
| 1872 |
> |
|
| 1873 |
> |
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
| 1874 |
> |
There is still something wrong with current implementation. |
| 1875 |
> |
|
| 1876 |
> |
2005-10-05 14:34 tim |
| 1877 |
> |
|
| 1878 |
> |
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
| 1879 |
> |
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
| 1880 |
> |
between group and center of mass array |
| 1881 |
> |
|
| 1882 |
> |
2005-10-05 14:12 tim |
| 1883 |
> |
|
| 1884 |
> |
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
| 1885 |
> |
When cutoffGroup is turned off, there is a mismatch between group |
| 1886 |
> |
and center of mass array |
| 1887 |
> |
|
| 1888 |
> |
2005-10-04 14:34 chrisfen |
| 1889 |
> |
|
| 1890 |
> |
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
| 1891 |
> |
mass ratio bug that results in simulation failure with massless |
| 1892 |
> |
particles |
| 1893 |
> |
|
| 1894 |
> |
2005-10-04 14:33 chrisfen |
| 1895 |
> |
|
| 1896 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
| 1897 |
> |
wolf |
| 1898 |
> |
|
| 1899 |
> |
2005-10-04 14:32 chrisfen |
| 1900 |
> |
|
| 1901 |
> |
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
| 1902 |
> |
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
| 1903 |
> |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
| 1904 |
> |
random changes when testing |
| 1905 |
> |
|
| 1906 |
> |
2005-10-03 10:54 tim |
| 1907 |
> |
|
| 1908 |
> |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
| 1909 |
> |
projecting the inertia tensor of directional atom in rigibody into |
| 1910 |
> |
rigidbody's body frame (previous commit is wrong) |
| 1911 |
> |
|
| 1912 |
> |
2005-10-03 09:31 tim |
| 1913 |
> |
|
| 1914 |
> |
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
| 1915 |
> |
tensor of directional atom in rigibody into rigidbody's body frame |
| 1916 |
> |
|
| 1917 |
> |
2005-09-28 13:47 chrisfen |
| 1918 |
> |
|
| 1919 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
| 1920 |
> |
|
| 1921 |
> |
2005-09-28 13:46 chrisfen |
| 1922 |
> |
|
| 1923 |
> |
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
| 1924 |
> |
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
| 1925 |
> |
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
| 1926 |
> |
tip4p/tp4.md: fixed some samples |
| 1927 |
> |
|
| 1928 |
> |
2005-09-28 13:46 chrisfen |
| 1929 |
> |
|
| 1930 |
> |
* ChangeLog: updated |
| 1931 |
> |
|
| 1932 |
> |
2005-09-28 11:55 tim |
| 1933 |
> |
|
| 1934 |
> |
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
| 1935 |
> |
divergence in rotation matrix to quaternion transformation |
| 1936 |
> |
|
| 1937 |
> |
2005-09-28 11:32 gezelter |
| 1938 |
> |
|
| 1939 |
> |
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
| 1940 |
> |
order error |
| 1941 |
> |
|
| 1942 |
> |
2005-09-28 11:32 gezelter |
| 1943 |
> |
|
| 1944 |
> |
* src/io/DumpReader.cpp: tracking down quaternion bug |
| 1945 |
> |
|
| 1946 |
> |
2005-09-28 11:32 gezelter |
| 1947 |
> |
|
| 1948 |
> |
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
| 1949 |
> |
model |
| 1950 |
> |
|
| 1951 |
> |
2005-09-27 15:02 tim |
| 1952 |
> |
|
| 1953 |
> |
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
| 1954 |
> |
to quaternion |
| 1955 |
> |
|
| 1956 |
> |
2005-09-26 13:38 chuckv |
| 1957 |
> |
|
| 1958 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
| 1959 |
> |
7 so derfc is external. Other compilers should treat erfc as |
| 1960 |
> |
intrinsic. |
| 1961 |
> |
|
| 1962 |
> |
2005-09-26 12:07 chuckv |
| 1963 |
> |
|
| 1964 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
| 1965 |
> |
and declared it to be external to fix issure with ifc7. Hopefully |
| 1966 |
> |
this will not cause a problem with other compilers where derfc is |
| 1967 |
> |
an intrinsic function. |
| 1968 |
> |
|
| 1969 |
> |
2005-09-26 11:42 chuckv |
| 1970 |
> |
|
| 1971 |
> |
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
| 1972 |
> |
in simulation module. We needed a seperate receive buffer. |
| 1973 |
> |
|
| 1974 |
> |
2005-09-26 10:58 chuckv |
| 1975 |
> |
|
| 1976 |
> |
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
| 1977 |
> |
support for skinThickness keyword to Globals. |
| 1978 |
> |
|
| 1979 |
> |
2005-09-26 10:56 tim |
| 1980 |
> |
|
| 1981 |
> |
* src/io/DumpReader.cpp: fix a typo in DumpReader |
| 1982 |
> |
|
| 1983 |
> |
2005-09-26 09:27 chrisfen |
| 1984 |
> |
|
| 1985 |
> |
* samples/: minimizer/tip4p_two.md, |
| 1986 |
> |
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
| 1987 |
> |
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
| 1988 |
> |
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
| 1989 |
> |
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
| 1990 |
> |
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
| 1991 |
> |
water/tip4p/tp4.md: fixing up some samples |
| 1992 |
> |
|
| 1993 |
> |
2005-09-24 12:39 chrisfen |
| 1994 |
> |
|
| 1995 |
> |
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
| 1996 |
> |
roughly the same speed as the old version when using dipoles |
| 1997 |
> |
|
| 1998 |
> |
energies are now exactly the same between the old version of OOPSE |
| 1999 |
> |
and this version |
| 2000 |
> |
|
| 2001 |
> |
2005-09-24 12:38 chrisfen |
| 2002 |
> |
|
| 2003 |
> |
* samples/water/ssdrf/ssdrf.md: turned rf on |
| 2004 |
> |
|
| 2005 |
> |
2005-09-23 15:31 chuckv |
| 2006 |
> |
|
| 2007 |
> |
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
| 2008 |
> |
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
| 2009 |
> |
from skin. This will get fixed to where we can manually set skin |
| 2010 |
> |
thickness. |
| 2011 |
> |
|
| 2012 |
> |
2005-09-22 13:50 gezelter |
| 2013 |
> |
|
| 2014 |
> |
* src/math/derfc.F90: added error function |
| 2015 |
> |
|
| 2016 |
> |
2005-09-21 19:08 chuckv |
| 2017 |
> |
|
| 2018 |
> |
* src/integrators/Velocitizer.cpp: Removed print statement for |
| 2019 |
> |
angular momentum and inertia tensor from velocitizer. |
| 2020 |
> |
|
| 2021 |
> |
2005-09-21 19:04 chuckv |
| 2022 |
> |
|
| 2023 |
> |
* src/integrators/Velocitizer.cpp: Removed print statements for |
| 2024 |
> |
remove angular momentum. |
| 2025 |
> |
|
| 2026 |
> |
2005-09-21 18:45 chuckv |
| 2027 |
> |
|
| 2028 |
> |
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
| 2029 |
> |
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
| 2030 |
> |
map. |
| 2031 |
> |
|
| 2032 |
> |
2005-09-21 15:59 tim |
| 2033 |
> |
|
| 2034 |
> |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
| 2035 |
> |
DumpReader using pure c++ io |
| 2036 |
> |
|
| 2037 |
> |
2005-09-21 12:20 chrisfen |
| 2038 |
> |
|
| 2039 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
| 2040 |
> |
defaultCutoff bug (HEMES!) |
| 2041 |
> |
|
| 2042 |
> |
2005-09-20 17:13 gezelter |
| 2043 |
> |
|
| 2044 |
> |
* make/Makefile.in: libz additions |
| 2045 |
> |
|
| 2046 |
> |
2005-09-20 17:03 gezelter |
| 2047 |
> |
|
| 2048 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 2049 |
> |
src/config.h.in: added check for zlib in configure |
| 2050 |
> |
|
| 2051 |
> |
2005-09-20 16:22 tim |
| 2052 |
> |
|
| 2053 |
> |
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
| 2054 |
> |
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
| 2055 |
> |
|
| 2056 |
> |
2005-09-20 11:22 tim |
| 2057 |
> |
|
| 2058 |
> |
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
| 2059 |
> |
testcase for zipstream |
| 2060 |
> |
|
| 2061 |
> |
2005-09-20 10:41 tim |
| 2062 |
> |
|
| 2063 |
> |
* src/io/zipstream.hpp: adding zipstream.hpp |
| 2064 |
> |
|
| 2065 |
> |
2005-09-20 10:34 chrisfen |
| 2066 |
> |
|
| 2067 |
> |
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
| 2068 |
> |
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
| 2069 |
> |
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
| 2070 |
> |
zcons/zconsMoving.md: fixed up some sample md files |
| 2071 |
> |
|
| 2072 |
> |
2005-09-19 18:21 chrisfen |
| 2073 |
> |
|
| 2074 |
> |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
| 2075 |
> |
src/UseTheForce/doForces.F90, |
| 2076 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 2077 |
> |
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
| 2078 |
> |
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
| 2079 |
> |
appears as though it really is working... |
| 2080 |
> |
|
| 2081 |
> |
2005-09-18 15:45 chrisfen |
| 2082 |
> |
|
| 2083 |
> |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
| 2084 |
> |
src/UseTheForce/doForces.F90, |
| 2085 |
> |
src/UseTheForce/doForces_interface.F90, |
| 2086 |
> |
src/UseTheForce/doForces_interface.h, |
| 2087 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 2088 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
| 2089 |
> |
src/brains/SimInfo.cpp: reaction field seems to work now, still |
| 2090 |
> |
need to do some testing... |
| 2091 |
> |
|
| 2092 |
> |
2005-09-16 18:04 chuckv |
| 2093 |
> |
|
| 2094 |
> |
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
| 2095 |
> |
dump files. |
| 2096 |
> |
|
| 2097 |
> |
2005-09-16 16:07 chrisfen |
| 2098 |
> |
|
| 2099 |
> |
* src/: UseTheForce/doForces_interface.F90, |
| 2100 |
> |
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
| 2101 |
> |
bug that ifc missed... |
| 2102 |
> |
|
| 2103 |
> |
2005-09-16 15:36 chrisfen |
| 2104 |
> |
|
| 2105 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
| 2106 |
> |
fixing some summation method issues |
| 2107 |
> |
|
| 2108 |
> |
2005-09-16 14:35 chrisfen |
| 2109 |
> |
|
| 2110 |
> |
* src/brains/SimInfo.cpp: fixed a capitalization error |
| 2111 |
> |
|
| 2112 |
> |
2005-09-16 14:34 chrisfen |
| 2113 |
> |
|
| 2114 |
> |
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
| 2115 |
> |
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
| 2116 |
> |
around |
| 2117 |
> |
|
| 2118 |
> |
2005-09-16 14:00 chrisfen |
| 2119 |
> |
|
| 2120 |
> |
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
| 2121 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
| 2122 |
> |
are known issues - particularly with reaction field... |
| 2123 |
> |
|
| 2124 |
> |
2005-09-16 11:07 chrisfen |
| 2125 |
> |
|
| 2126 |
> |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
| 2127 |
> |
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
| 2128 |
> |
(cutting out the old way to do reaction field) |
| 2129 |
> |
|
| 2130 |
> |
2005-09-15 17:05 gezelter |
| 2131 |
> |
|
| 2132 |
> |
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
| 2133 |
> |
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
| 2134 |
> |
DarkSide/electrostatic_interface.F90, |
| 2135 |
> |
DarkSide/electrostatic_interface.h: Working on adding WOLF |
| 2136 |
> |
|
| 2137 |
> |
2005-09-15 14:17 tim |
| 2138 |
> |
|
| 2139 |
> |
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
| 2140 |
> |
is called without calling getNFrames |
| 2141 |
> |
|
| 2142 |
> |
2005-09-15 08:47 chrisfen |
| 2143 |
> |
|
| 2144 |
> |
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
| 2145 |
> |
|
| 2146 |
> |
2005-09-14 21:48 chuckv |
| 2147 |
> |
|
| 2148 |
> |
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
| 2149 |
> |
not initialized after creation. When maxval(gtypeMaxCutoff) was |
| 2150 |
> |
called, the largest random garbage value was returned from the |
| 2151 |
> |
array. |
| 2152 |
> |
|
| 2153 |
> |
2005-09-14 19:14 chrisfen |
| 2154 |
> |
|
| 2155 |
> |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
| 2156 |
> |
io/Globals.hpp: changes to include the coulombicCorrection selector |
| 2157 |
> |
|
| 2158 |
> |
2005-09-14 19:13 chrisfen |
| 2159 |
> |
|
| 2160 |
> |
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
| 2161 |
> |
reactionField.F90: added in the undamped wolf, in the process of |
| 2162 |
> |
doing the damped wolf |
| 2163 |
> |
|
| 2164 |
> |
2005-09-14 19:13 chrisfen |
| 2165 |
> |
|
| 2166 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
| 2167 |
> |
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
| 2168 |
> |
the coulombicCorrection selector |
| 2169 |
> |
|
| 2170 |
> |
2005-09-14 19:11 chrisfen |
| 2171 |
> |
|
| 2172 |
> |
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
| 2173 |
> |
|
| 2174 |
> |
2005-09-14 19:11 chrisfen |
| 2175 |
> |
|
| 2176 |
> |
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
| 2177 |
> |
|
| 2178 |
> |
2005-09-14 19:10 chrisfen |
| 2179 |
> |
|
| 2180 |
> |
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
| 2181 |
> |
|
| 2182 |
> |
2005-09-14 15:31 chuckv |
| 2183 |
> |
|
| 2184 |
> |
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
| 2185 |
> |
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
| 2186 |
> |
|
| 2187 |
> |
2005-09-14 15:28 gezelter |
| 2188 |
> |
|
| 2189 |
> |
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
| 2190 |
> |
do_prepair |
| 2191 |
> |
|
| 2192 |
> |
2005-09-14 14:02 gezelter |
| 2193 |
> |
|
| 2194 |
> |
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
| 2195 |
> |
createMixingMap routine. It should now set doShift correctly |
| 2196 |
> |
|
| 2197 |
> |
2005-09-07 17:44 chuckv |
| 2198 |
> |
|
| 2199 |
> |
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
| 2200 |
> |
|
| 2201 |
> |
2005-09-07 17:23 chuckv |
| 2202 |
> |
|
| 2203 |
> |
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
| 2204 |
> |
logical variables |
| 2205 |
> |
|
| 2206 |
> |
2005-09-07 17:08 gezelter |
| 2207 |
> |
|
| 2208 |
> |
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
| 2209 |
> |
algorithm |
| 2210 |
> |
|
| 2211 |
> |
2005-09-07 15:46 gezelter |
| 2212 |
> |
|
| 2213 |
> |
* src/: UseTheForce/doForces.F90, |
| 2214 |
> |
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
| 2215 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
| 2216 |
> |
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
| 2217 |
> |
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
| 2218 |
> |
cutoff Policy |
| 2219 |
> |
|
| 2220 |
> |
2005-09-07 14:18 gezelter |
| 2221 |
> |
|
| 2222 |
> |
* src/UseTheForce/doForces.F90: Some bug hunting |
| 2223 |
> |
|
| 2224 |
> |
2005-09-07 14:18 gezelter |
| 2225 |
> |
|
| 2226 |
> |
* samples/argon/argonNVT.md: Just a longer test |
| 2227 |
> |
|
| 2228 |
> |
2005-09-06 12:32 chuckv |
| 2229 |
> |
|
| 2230 |
> |
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
| 2231 |
> |
etc.. |
| 2232 |
> |
|
| 2233 |
> |
2005-09-01 17:56 gezelter |
| 2234 |
> |
|
| 2235 |
> |
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
| 2236 |
> |
zero |
| 2237 |
> |
|
| 2238 |
> |
2005-09-01 15:17 gezelter |
| 2239 |
> |
|
| 2240 |
> |
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
| 2241 |
> |
createGtypeCutoffMap |
| 2242 |
> |
|
| 2243 |
> |
2005-08-30 13:23 chrisfen |
| 2244 |
> |
|
| 2245 |
> |
* src/: UseTheForce/doForces.F90, |
| 2246 |
> |
UseTheForce/doForces_interface.F90, |
| 2247 |
> |
UseTheForce/doForces_interface.h, |
| 2248 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 2249 |
> |
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
| 2250 |
> |
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
| 2251 |
> |
changes for implementing the wolf potential |
| 2252 |
> |
|
| 2253 |
> |
2005-08-26 17:39 chrisfen |
| 2254 |
> |
|
| 2255 |
> |
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
| 2256 |
> |
|
| 2257 |
> |
2005-08-26 16:30 chrisfen |
| 2258 |
> |
|
| 2259 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
| 2260 |
> |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
| 2261 |
> |
some probably nonfunctional get*cut routines |
| 2262 |
> |
|
| 2263 |
> |
2005-08-26 15:34 chuckv |
| 2264 |
> |
|
| 2265 |
> |
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
| 2266 |
> |
|
| 2267 |
> |
2005-08-26 11:36 gezelter |
| 2268 |
> |
|
| 2269 |
> |
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
| 2270 |
> |
interactionHash and gtypeCutoff routines |
| 2271 |
> |
|
| 2272 |
> |
2005-08-17 10:26 gezelter |
| 2273 |
> |
|
| 2274 |
> |
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
| 2275 |
> |
DarkSide/simulation.F90: added fCutoffPolicy.h |
| 2276 |
> |
|
| 2277 |
> |
2005-08-11 16:04 gezelter |
| 2278 |
> |
|
| 2279 |
> |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
| 2280 |
> |
progress |
| 2281 |
> |
|
| 2282 |
> |
2005-08-10 14:17 gezelter |
| 2283 |
> |
|
| 2284 |
> |
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
| 2285 |
> |
they belong |
| 2286 |
> |
|
| 2287 |
> |
2005-08-09 17:33 gezelter |
| 2288 |
> |
|
| 2289 |
> |
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
| 2290 |
> |
Jones module |
| 2291 |
> |
|
| 2292 |
> |
2005-08-09 17:33 gezelter |
| 2293 |
> |
|
| 2294 |
> |
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
| 2295 |
> |
|
| 2296 |
> |
2005-08-09 14:40 chuckv |
| 2297 |
> |
|
| 2298 |
> |
* src/UseTheForce/doForces.F90: In process of re-write for group |
| 2299 |
> |
based cutoff.... |
| 2300 |
> |
|
| 2301 |
> |
2005-07-29 14:38 gezelter |
| 2302 |
> |
|
| 2303 |
> |
* src/UseTheForce/doForces.F90: fixes in progress |
| 2304 |
> |
|
| 2305 |
> |
2005-07-29 12:34 tim |
| 2306 |
> |
|
| 2307 |
> |
* src/UseTheForce/doForces.F90: fix a bug which does not update |
| 2308 |
> |
me_i and me_j correctly |
| 2309 |
> |
|
| 2310 |
> |
2005-07-28 17:12 chuckv |
| 2311 |
> |
|
| 2312 |
> |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
| 2313 |
> |
cutoffs... Segfaults nicely now... |
| 2314 |
> |
|
| 2315 |
> |
2005-07-20 12:04 gezelter |
| 2316 |
> |
|
| 2317 |
> |
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
| 2318 |
> |
error messages from pathscale compiler |
| 2319 |
> |
|
| 2320 |
> |
2005-07-13 11:48 tim |
| 2321 |
> |
|
| 2322 |
> |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
| 2323 |
> |
<functional> |
| 2324 |
> |
|
| 2325 |
> |
2005-07-13 10:54 tim |
| 2326 |
> |
|
| 2327 |
> |
* src/: UseTheForce/fSwitchingFunction.h, |
| 2328 |
> |
UseTheForce/mpiComponentPlan.h, |
| 2329 |
> |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
| 2330 |
> |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
| 2331 |
> |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
| 2332 |
> |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
| 2333 |
> |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
| 2334 |
> |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
| 2335 |
> |
files |
| 2336 |
> |
|
| 2337 |
> |
2005-07-03 15:53 chuckv |
| 2338 |
> |
|
| 2339 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
| 2340 |
> |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
| 2341 |
> |
subroutine to set cuttoff for Interaction map and function in |
| 2342 |
> |
simulation.F90 to determine if a particular atype is present in a |
| 2343 |
> |
simulation. |
| 2344 |
> |
|
| 2345 |
> |
2005-06-28 08:58 gezelter |
| 2346 |
> |
|
| 2347 |
> |
* src/UseTheForce/doForces.F90: [no log message] |
| 2348 |
> |
|
| 2349 |
> |
2005-06-27 17:21 chuckv |
| 2350 |
> |
|
| 2351 |
> |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
| 2352 |
> |
force code. Does not build at this point... |
| 2353 |
> |
|
| 2354 |
> |
2005-06-27 16:01 gezelter |
| 2355 |
> |
|
| 2356 |
> |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
| 2357 |
> |
UseTheForce/DarkSide/fInteractionMap.h, |
| 2358 |
> |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
| 2359 |
> |
Breaky breaky! |
| 2360 |
> |
|
| 2361 |
> |
2005-06-20 11:03 gezelter |
| 2362 |
> |
|
| 2363 |
> |
* samples/water/ssd/ssd.md, |
| 2364 |
> |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
| 2365 |
> |
simulation |
| 2366 |
> |
|
| 2367 |
> |
2005-06-13 13:25 tim |
| 2368 |
> |
|
| 2369 |
> |
* src/: applications/staticProps/DensityPlot.cpp, |
| 2370 |
> |
applications/staticProps/DensityPlot.hpp, |
| 2371 |
> |
applications/staticProps/SCDOrderParameter.cpp, |
| 2372 |
> |
applications/staticProps/StaticProps.cpp, |
| 2373 |
> |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
| 2374 |
> |
|
| 2375 |
> |
2005-05-31 17:31 chuckv |
| 2376 |
> |
|
| 2377 |
> |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
| 2378 |
> |
remove angular momentum. |
| 2379 |
> |
|
| 2380 |
> |
2005-05-31 12:34 chuckv |
| 2381 |
> |
|
| 2382 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
| 2383 |
> |
typo in nanorodBuilder. |
| 2384 |
> |
|
| 2385 |
> |
2005-05-30 09:01 chuckv |
| 2386 |
> |
|
| 2387 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 2388 |
> |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
| 2389 |
> |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
| 2390 |
> |
integrators/Velocitizer.hpp: Added method to remove system angular |
| 2391 |
> |
momentum to velocitizer and added method to calculate system |
| 2392 |
> |
angular momentum to siminfo. |
| 2393 |
> |
|
| 2394 |
> |
2005-05-29 16:16 chrisfen |
| 2395 |
> |
|
| 2396 |
> |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
| 2397 |
> |
balance from the Darkside (files) |
| 2398 |
> |
|
| 2399 |
> |
2005-05-29 16:15 chrisfen |
| 2400 |
> |
|
| 2401 |
> |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
| 2402 |
> |
|
| 2403 |
> |
2005-05-29 16:15 chrisfen |
| 2404 |
> |
|
| 2405 |
> |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
| 2406 |
> |
|
| 2407 |
> |
2005-05-29 16:15 chrisfen |
| 2408 |
> |
|
| 2409 |
> |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
| 2410 |
> |
dimer for testing purposes |
| 2411 |
> |
|
| 2412 |
> |
2005-05-29 16:14 chrisfen |
| 2413 |
> |
|
| 2414 |
> |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
| 2415 |
> |
was apparently wiped earlier this month... |
| 2416 |
> |
|
| 2417 |
> |
2005-05-29 16:13 chrisfen |
| 2418 |
> |
|
| 2419 |
> |
* ChangeLog: ran make cvslog |
| 2420 |
> |
|
| 2421 |
> |
2005-05-28 19:16 tim |
| 2422 |
> |
|
| 2423 |
> |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
| 2424 |
> |
AtomNameVisitor |
| 2425 |
> |
|
| 2426 |
> |
2005-05-28 19:09 tim |
| 2427 |
> |
|
| 2428 |
> |
* src/integrators/Integrator.cpp: dding resetIntegrator |
| 2429 |
> |
|
| 2430 |
> |
2005-05-28 19:06 tim |
| 2431 |
> |
|
| 2432 |
> |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
| 2433 |
> |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
| 2434 |
> |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
| 2435 |
> |
resetIntegrator |
| 2436 |
> |
|
| 2437 |
> |
2005-05-27 16:11 tim |
| 2438 |
> |
|
| 2439 |
> |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
| 2440 |
> |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
| 2441 |
> |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
| 2442 |
> |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
| 2443 |
> |
StaticProps |
| 2444 |
> |
|
| 2445 |
> |
2005-05-26 23:41 tim |
| 2446 |
> |
|
| 2447 |
> |
* src/: applications/staticProps/Makefile, |
| 2448 |
> |
applications/staticProps/P2OrderParameter.cpp, |
| 2449 |
> |
applications/staticProps/P2OrderParameter.hpp, |
| 2450 |
> |
applications/staticProps/StaticProps.cpp, |
| 2451 |
> |
applications/staticProps/StaticProps.ggo, |
| 2452 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 2453 |
> |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
| 2454 |
> |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
| 2455 |
> |
|
| 2456 |
> |
2005-05-26 17:45 tim |
| 2457 |
> |
|
| 2458 |
> |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 2459 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 2460 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 2461 |
> |
applications/staticProps/Makefile, |
| 2462 |
> |
applications/staticProps/P2OrderParameter.cpp, |
| 2463 |
> |
applications/staticProps/P2OrderParameter.hpp, |
| 2464 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 2465 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 2466 |
> |
applications/staticProps/StaticAnalyser.hpp, |
| 2467 |
> |
applications/staticProps/StaticProps.cpp, |
| 2468 |
> |
applications/staticProps/StaticProps.ggo, |
| 2469 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 2470 |
> |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
| 2471 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
| 2472 |
> |
AtomNameVisitor to convert atom name to its base name; |
| 2473 |
> |
wrappingvisitor now wrap back to the center of the mass; adding |
| 2474 |
> |
P2OrderParameter into StaticProps |
| 2475 |
> |
|
| 2476 |
> |
2005-05-22 16:36 chuckv |
| 2477 |
> |
|
| 2478 |
> |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
| 2479 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 2480 |
> |
applications/nanoRodBuilder/GeometryFactory.cpp, |
| 2481 |
> |
applications/nanoRodBuilder/GeometryFactory.hpp, |
| 2482 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 2483 |
> |
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
| 2484 |
> |
tensor. |
| 2485 |
> |
|
| 2486 |
> |
2005-05-22 16:05 tim |
| 2487 |
> |
|
| 2488 |
> |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 2489 |
> |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
| 2490 |
> |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
| 2491 |
> |
printPressureTensor |
| 2492 |
> |
|
| 2493 |
> |
2005-05-20 14:27 tim |
| 2494 |
> |
|
| 2495 |
> |
* src/integrators/NPrT.cpp: NPrT in progress |
| 2496 |
> |
|
| 2497 |
> |
2005-05-20 11:01 tim |
| 2498 |
> |
|
| 2499 |
> |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
| 2500 |
> |
utils/OOPSEConstant.hpp: NPrT in progress |
| 2501 |
> |
|
| 2502 |
> |
2005-05-19 16:31 tim |
| 2503 |
> |
|
| 2504 |
> |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
| 2505 |
> |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
| 2506 |
> |
io/Globals.hpp: NPAT is working |
| 2507 |
> |
|
| 2508 |
> |
2005-05-19 10:49 tim |
| 2509 |
> |
|
| 2510 |
> |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
| 2511 |
> |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
| 2512 |
> |
|
| 2513 |
> |
2005-05-18 23:28 tim |
| 2514 |
> |
|
| 2515 |
> |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
| 2516 |
> |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
| 2517 |
> |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
| 2518 |
> |
|
| 2519 |
> |
2005-05-18 14:06 chrisfen |
| 2520 |
> |
|
| 2521 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
| 2522 |
> |
some tap changes |
| 2523 |
> |
|
| 2524 |
> |
2005-05-18 13:31 chrisfen |
| 2525 |
> |
|
| 2526 |
> |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 2527 |
> |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
| 2528 |
> |
in the first solvation shell for tap |
| 2529 |
> |
|
| 2530 |
> |
2005-05-18 07:35 chrisfen |
| 2531 |
> |
|
| 2532 |
> |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
| 2533 |
> |
for testing purposes |
| 2534 |
> |
|
| 2535 |
> |
2005-05-17 17:35 chrisfen |
| 2536 |
> |
|
| 2537 |
> |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
| 2538 |
> |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
| 2539 |
> |
src/UseTheForce/doForces.F90, |
| 2540 |
> |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 2541 |
> |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 2542 |
> |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
| 2543 |
> |
correcting changes to the previous merge that were not caught |
| 2544 |
> |
|
| 2545 |
> |
2005-05-16 23:20 chuckv |
| 2546 |
> |
|
| 2547 |
> |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
| 2548 |
> |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
| 2549 |
> |
build. |
| 2550 |
> |
|
| 2551 |
> |
2005-05-16 22:46 kdaily |
| 2552 |
> |
|
| 2553 |
> |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
| 2554 |
> |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
| 2555 |
> |
|
| 2556 |
> |
2005-05-16 21:08 kdaily |
| 2557 |
> |
|
| 2558 |
> |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
| 2559 |
> |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
| 2560 |
> |
src/types/DirectionalAtomType.cpp, |
| 2561 |
> |
src/types/DirectionalAtomType.hpp: added gb |
| 2562 |
> |
|
| 2563 |
> |
2005-05-13 15:36 chrisfen |
| 2564 |
> |
|
| 2565 |
> |
* forceFields/DUFF2.frc: Better tap |
| 2566 |
> |
|
| 2567 |
> |
2005-05-12 14:43 chrisfen |
| 2568 |
> |
|
| 2569 |
> |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
| 2570 |
> |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
| 2571 |
> |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
| 2572 |
> |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
| 2573 |
> |
Need to parametrize. |
| 2574 |
> |
|
| 2575 |
> |
2005-05-11 18:15 chuckv |
| 2576 |
> |
|
| 2577 |
> |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
| 2578 |
> |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
| 2579 |
> |
build issues under ifc7. |
| 2580 |
> |
|
| 2581 |
> |
2005-05-09 17:07 chuckv |
| 2582 |
> |
|
| 2583 |
> |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
| 2584 |
> |
builder changes. |
| 2585 |
> |
|
| 2586 |
> |
2005-05-05 10:06 chrisfen |
| 2587 |
> |
|
| 2588 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
| 2589 |
> |
to TAP |
| 2590 |
> |
|
| 2591 |
> |
2005-05-05 09:47 chrisfen |
| 2592 |
> |
|
| 2593 |
> |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
| 2594 |
> |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
| 2595 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
| 2596 |
> |
src/UseTheForce/DarkSide/atype.F90, |
| 2597 |
> |
src/UseTheForce/DarkSide/atype_interface.F90, |
| 2598 |
> |
src/UseTheForce/DarkSide/simulation.F90, |
| 2599 |
> |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
| 2600 |
> |
src/brains/fSimulation.h, src/io/Makefile, |
| 2601 |
> |
src/io/StickyAtomTypesSectionParser.cpp, |
| 2602 |
> |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
| 2603 |
> |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
| 2604 |
> |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
| 2605 |
> |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
| 2606 |
> |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
| 2607 |
> |
not parametrized, but OOPSE will now let me run it... |
| 2608 |
> |
|
| 2609 |
> |
2005-05-03 17:55 chuckv |
| 2610 |
> |
|
| 2611 |
> |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
| 2612 |
> |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
| 2613 |
> |
Adding support for generic geometry to nanorodbuilder. |
| 2614 |
> |
|
| 2615 |
> |
2005-05-03 12:55 chuckv |
| 2616 |
> |
|
| 2617 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 2618 |
> |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
| 2619 |
> |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
| 2620 |
> |
|
| 2621 |
> |
2005-04-29 14:16 gezelter |
| 2622 |
> |
|
| 2623 |
> |
* make/Makefile.in: [no log message] |
| 2624 |
> |
|
| 2625 |
> |
2005-04-29 11:26 chrisfen |
| 2626 |
> |
|
| 2627 |
> |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
| 2628 |
> |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
| 2629 |
> |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
| 2630 |
> |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
| 2631 |
> |
samples/water/tip4p/water.md: Added TIP4P-Ew |
| 2632 |
> |
|
| 2633 |
> |
2005-04-27 19:24 chuckv |
| 2634 |
> |
|
| 2635 |
> |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
| 2636 |
> |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
| 2637 |
> |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
| 2638 |
> |
nanoRodBuilder.... |
| 2639 |
> |
|
| 2640 |
> |
2005-04-27 15:13 chrisfen |
| 2641 |
> |
|
| 2642 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
| 2643 |
> |
src/UseTheForce/DarkSide/atype.F90, |
| 2644 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
| 2645 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 2646 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
| 2647 |
> |
write statements and am closer to a working shapes |
| 2648 |
> |
|
| 2649 |
> |
2005-04-22 16:57 chuckv |
| 2650 |
> |
|
| 2651 |
> |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
| 2652 |
> |
|
| 2653 |
> |
2005-04-22 16:52 tim |
| 2654 |
> |
|
| 2655 |
> |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
| 2656 |
> |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
| 2657 |
> |
problem of c++ |
| 2658 |
> |
|
| 2659 |
> |
2005-04-21 09:12 chrisfen |
| 2660 |
> |
|
| 2661 |
> |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
| 2662 |
> |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
| 2663 |
> |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
| 2664 |
> |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
| 2665 |
> |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
| 2666 |
> |
src/UseTheForce/DarkSide/shapes.F90, |
| 2667 |
> |
src/UseTheForce/DarkSide/shapes_interface.F90, |
| 2668 |
> |
src/UseTheForce/DarkSide/shapes_interface.h, |
| 2669 |
> |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
| 2670 |
> |
src/io/Makefile, src/io/SectionParser.cpp, |
| 2671 |
> |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
| 2672 |
> |
src/io/ShapeAtomTypesSectionParser.cpp, |
| 2673 |
> |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
| 2674 |
> |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
| 2675 |
> |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
| 2676 |
> |
bounds overwrite (I think...). At least the parser loads the |
| 2677 |
> |
forcefield fine... |
| 2678 |
> |
|
| 2679 |
> |
2005-04-18 10:44 chrisfen |
| 2680 |
> |
|
| 2681 |
> |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
| 2682 |
> |
Mac (capitalization confusion of filenames) |
| 2683 |
> |
|
| 2684 |
> |
2005-04-17 22:50 chrisfen |
| 2685 |
> |
|
| 2686 |
> |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
| 2687 |
> |
UseTheForce/Shapes_FF.cpp, |
| 2688 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 2689 |
> |
io/ShapeAtomTypesSectionParser.cpp, |
| 2690 |
> |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
| 2691 |
> |
|
| 2692 |
> |
2005-04-15 17:43 gezelter |
| 2693 |
> |
|
| 2694 |
> |
* README: gmake in case people forget |
| 2695 |
> |
|
| 2696 |
> |
2005-04-15 17:40 gezelter |
| 2697 |
> |
|
| 2698 |
> |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
| 2699 |
> |
banner. Vanity. |
| 2700 |
> |
|
| 2701 |
> |
2005-04-15 17:22 gezelter |
| 2702 |
> |
|
| 2703 |
> |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
| 2704 |
> |
in banner (and version numbers in config.h) |
| 2705 |
> |
|
| 2706 |
> |
2005-04-15 17:22 gezelter |
| 2707 |
> |
|
| 2708 |
> |
* ChangeLog, LICENSE, README: Documentation changes |
| 2709 |
> |
|
| 2710 |
> |
2005-04-15 17:03 gezelter |
| 2711 |
> |
|
| 2712 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 2713 |
> |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
| 2714 |
> |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 2715 |
> |
UseTheForce/ForceFieldCreator.hpp, |
| 2716 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 2717 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
| 2718 |
> |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
| 2719 |
> |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
| 2720 |
> |
UseTheForce/notifyCutoffs.F90, |
| 2721 |
> |
UseTheForce/notifyCutoffs_interface.F90, |
| 2722 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
| 2723 |
> |
UseTheForce/DarkSide/atype.F90, |
| 2724 |
> |
UseTheForce/DarkSide/atype_interface.F90, |
| 2725 |
> |
UseTheForce/DarkSide/eam.F90, |
| 2726 |
> |
UseTheForce/DarkSide/eam_interface.F90, |
| 2727 |
> |
UseTheForce/DarkSide/eam_interface.h, |
| 2728 |
> |
UseTheForce/DarkSide/electrostatic.F90, |
| 2729 |
> |
UseTheForce/DarkSide/electrostatic_interface.F90, |
| 2730 |
> |
UseTheForce/DarkSide/electrostatic_interface.h, |
| 2731 |
> |
UseTheForce/DarkSide/force_globals.F90, |
| 2732 |
> |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
| 2733 |
> |
UseTheForce/DarkSide/lj_interface.F90, |
| 2734 |
> |
UseTheForce/DarkSide/lj_interface.h, |
| 2735 |
> |
UseTheForce/DarkSide/neighborLists.F90, |
| 2736 |
> |
UseTheForce/DarkSide/reactionField.F90, |
| 2737 |
> |
UseTheForce/DarkSide/shapes.F90, |
| 2738 |
> |
UseTheForce/DarkSide/shapes_interface.F90, |
| 2739 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
| 2740 |
> |
UseTheForce/DarkSide/simParallel.F90, |
| 2741 |
> |
UseTheForce/DarkSide/simParallel_interface.F90, |
| 2742 |
> |
UseTheForce/DarkSide/simParallel_interface.h, |
| 2743 |
> |
UseTheForce/DarkSide/simulation.F90, |
| 2744 |
> |
UseTheForce/DarkSide/simulation_interface.F90, |
| 2745 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
| 2746 |
> |
UseTheForce/DarkSide/sticky.F90, |
| 2747 |
> |
UseTheForce/DarkSide/sticky_interface.F90, |
| 2748 |
> |
UseTheForce/DarkSide/sticky_interface.h, |
| 2749 |
> |
UseTheForce/DarkSide/switcheroo.F90, |
| 2750 |
> |
applications/dump2Xyz/Dump2XYZ.cpp, |
| 2751 |
> |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 2752 |
> |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 2753 |
> |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
| 2754 |
> |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
| 2755 |
> |
applications/dynamicProps/DipoleCorrFunc.cpp, |
| 2756 |
> |
applications/dynamicProps/DipoleCorrFunc.hpp, |
| 2757 |
> |
applications/dynamicProps/DynamicProps.cpp, |
| 2758 |
> |
applications/dynamicProps/DynamicPropsCmd.c, |
| 2759 |
> |
applications/dynamicProps/DynamicPropsCmd.h, |
| 2760 |
> |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
| 2761 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
| 2762 |
> |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
| 2763 |
> |
applications/dynamicProps/RCorrFunc.cpp, |
| 2764 |
> |
applications/dynamicProps/RCorrFunc.hpp, |
| 2765 |
> |
applications/dynamicProps/TimeCorrFunc.cpp, |
| 2766 |
> |
applications/dynamicProps/TimeCorrFunc.hpp, |
| 2767 |
> |
applications/dynamicProps/VCorrFunc.cpp, |
| 2768 |
> |
applications/dynamicProps/VCorrFunc.hpp, |
| 2769 |
> |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 2770 |
> |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 2771 |
> |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 2772 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 2773 |
> |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
| 2774 |
> |
applications/oopse/oopse.cpp, |
| 2775 |
> |
applications/simpleBuilder/simpleBuilder.cpp, |
| 2776 |
> |
applications/simpleBuilder/simpleBuilderCmd.c, |
| 2777 |
> |
applications/simpleBuilder/simpleBuilderCmd.h, |
| 2778 |
> |
applications/staticProps/GofAngle2.cpp, |
| 2779 |
> |
applications/staticProps/GofAngle2.hpp, |
| 2780 |
> |
applications/staticProps/GofR.cpp, |
| 2781 |
> |
applications/staticProps/GofR.hpp, |
| 2782 |
> |
applications/staticProps/GofRAngle.cpp, |
| 2783 |
> |
applications/staticProps/GofRAngle.hpp, |
| 2784 |
> |
applications/staticProps/GofXyz.cpp, |
| 2785 |
> |
applications/staticProps/GofXyz.hpp, |
| 2786 |
> |
applications/staticProps/RadialDistrFunc.cpp, |
| 2787 |
> |
applications/staticProps/RadialDistrFunc.hpp, |
| 2788 |
> |
applications/staticProps/StaticProps.cpp, |
| 2789 |
> |
applications/staticProps/StaticPropsCmd.c, |
| 2790 |
> |
applications/staticProps/StaticPropsCmd.h, |
| 2791 |
> |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
| 2792 |
> |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
| 2793 |
> |
brains/Exclude.hpp, brains/ForceManager.cpp, |
| 2794 |
> |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
| 2795 |
> |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
| 2796 |
> |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
| 2797 |
> |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
| 2798 |
> |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
| 2799 |
> |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
| 2800 |
> |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 2801 |
> |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
| 2802 |
> |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
| 2803 |
> |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
| 2804 |
> |
constraints/ZconstraintForceManager.cpp, |
| 2805 |
> |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
| 2806 |
> |
integrators/DLM.hpp, integrators/Integrator.cpp, |
| 2807 |
> |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
| 2808 |
> |
integrators/IntegratorFactory.cpp, |
| 2809 |
> |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
| 2810 |
> |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
| 2811 |
> |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
| 2812 |
> |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
| 2813 |
> |
integrators/NVT.cpp, integrators/NVT.hpp, |
| 2814 |
> |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
| 2815 |
> |
integrators/Velocitizer.hpp, |
| 2816 |
> |
integrators/VelocityVerletIntegrator.cpp, |
| 2817 |
> |
integrators/VelocityVerletIntegrator.hpp, |
| 2818 |
> |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
| 2819 |
> |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
| 2820 |
> |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
| 2821 |
> |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
| 2822 |
> |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 2823 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 2824 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 2825 |
> |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
| 2826 |
> |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
| 2827 |
> |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
| 2828 |
> |
io/Globals.cpp, io/Globals.hpp, |
| 2829 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 2830 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
| 2831 |
> |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
| 2832 |
> |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
| 2833 |
> |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
| 2834 |
> |
io/SectionParser.cpp, io/SectionParser.hpp, |
| 2835 |
> |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
| 2836 |
> |
io/StatWriter.cpp, io/StatWriter.hpp, |
| 2837 |
> |
io/StickyAtomTypesSectionParser.cpp, |
| 2838 |
> |
io/StickyAtomTypesSectionParser.hpp, |
| 2839 |
> |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
| 2840 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 2841 |
> |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
| 2842 |
> |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
| 2843 |
> |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
| 2844 |
> |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
| 2845 |
> |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
| 2846 |
> |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 2847 |
> |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
| 2848 |
> |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
| 2849 |
> |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
| 2850 |
> |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
| 2851 |
> |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
| 2852 |
> |
math/Quaternion.hpp, math/RandNumGen.hpp, |
| 2853 |
> |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
| 2854 |
> |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
| 2855 |
> |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
| 2856 |
> |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
| 2857 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
| 2858 |
> |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
| 2859 |
> |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
| 2860 |
> |
minimizers/MinimizerFactory.hpp, |
| 2861 |
> |
minimizers/MinimizerParameterSet.cpp, |
| 2862 |
> |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
| 2863 |
> |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
| 2864 |
> |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
| 2865 |
> |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
| 2866 |
> |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
| 2867 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 2868 |
> |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
| 2869 |
> |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
| 2870 |
> |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
| 2871 |
> |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
| 2872 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 2873 |
> |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
| 2874 |
> |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
| 2875 |
> |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
| 2876 |
> |
profiling/timing.F90, restraints/Restraints.cpp, |
| 2877 |
> |
restraints/Restraints.hpp, |
| 2878 |
> |
restraints/ThermoIntegrationForceManager.cpp, |
| 2879 |
> |
restraints/ThermoIntegrationForceManager.hpp, |
| 2880 |
> |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
| 2881 |
> |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
| 2882 |
> |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
| 2883 |
> |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
| 2884 |
> |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
| 2885 |
> |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
| 2886 |
> |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
| 2887 |
> |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
| 2888 |
> |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
| 2889 |
> |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
| 2890 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
| 2891 |
> |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
| 2892 |
> |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
| 2893 |
> |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
| 2894 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 2895 |
> |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
| 2896 |
> |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
| 2897 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 2898 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 2899 |
> |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
| 2900 |
> |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
| 2901 |
> |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
| 2902 |
> |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
| 2903 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 2904 |
> |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
| 2905 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 2906 |
> |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
| 2907 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
| 2908 |
> |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
| 2909 |
> |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
| 2910 |
> |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 2911 |
> |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
| 2912 |
> |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
| 2913 |
> |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
| 2914 |
> |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
| 2915 |
> |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
| 2916 |
> |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
| 2917 |
> |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
| 2918 |
> |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
| 2919 |
> |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
| 2920 |
> |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
| 2921 |
> |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
| 2922 |
> |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
| 2923 |
> |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
| 2924 |
> |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
| 2925 |
> |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
| 2926 |
> |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
| 2927 |
> |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
| 2928 |
> |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
| 2929 |
> |
been drafted to perform our indentation services |
| 2930 |
> |
|
| 2931 |
> |
2005-04-15 17:03 gezelter |
| 2932 |
> |
|
| 2933 |
> |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
| 2934 |
> |
messages have been added to make users ignore CGAL. |
| 2935 |
> |
|
| 2936 |
> |
2005-04-15 13:41 tim |
| 2937 |
> |
|
| 2938 |
> |
* make/Makefile.in: fix make install |
| 2939 |
> |
|
| 2940 |
> |
2005-04-15 13:41 tim |
| 2941 |
> |
|
| 2942 |
> |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
| 2943 |
> |
add Makefile of samples |
| 2944 |
> |
|
| 2945 |
> |
2005-04-15 13:33 tim |
| 2946 |
> |
|
| 2947 |
> |
* samples/: lipid/Makefile, water/dimer/Makefile, |
| 2948 |
> |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
| 2949 |
> |
installed correctly |
| 2950 |
> |
|
| 2951 |
> |
2005-04-14 16:41 gezelter |
| 2952 |
> |
|
| 2953 |
> |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 2954 |
> |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
| 2955 |
> |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
| 2956 |
> |
to use with filepp |
| 2957 |
> |
|
| 2958 |
> |
2005-04-14 16:20 gezelter |
| 2959 |
> |
|
| 2960 |
> |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
| 2961 |
> |
MoLocator |
| 2962 |
> |
|
| 2963 |
> |
2005-04-14 14:12 gezelter |
| 2964 |
> |
|
| 2965 |
> |
* LICENSE: [no log message] |
| 2966 |
> |
|
| 2967 |
> |
2005-04-14 11:10 chuckv |
| 2968 |
> |
|
| 2969 |
> |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
| 2970 |
> |
nanorodbuilder now exit's when libCGAL is not present. |
| 2971 |
> |
|
| 2972 |
> |
2005-04-14 10:20 tim |
| 2973 |
> |
|
| 2974 |
> |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
| 2975 |
> |
|
| 2976 |
> |
2005-04-13 18:36 chuckv |
| 2977 |
> |
|
| 2978 |
> |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
| 2979 |
> |
interface name for SGI Compiler |
| 2980 |
> |
|
| 2981 |
> |
2005-04-13 18:29 chrisfen |
| 2982 |
> |
|
| 2983 |
> |
* samples/water/ssde/ssde.md: oops... bad sample |
| 2984 |
> |
|
| 2985 |
> |
2005-04-13 18:00 chuckv |
| 2986 |
> |
|
| 2987 |
> |
* src/config.h.in: Change typo in CGAL. |
| 2988 |
> |
|
| 2989 |
> |
2005-04-13 17:43 tim |
| 2990 |
> |
|
| 2991 |
> |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
| 2992 |
> |
selection/SelectionCompiler.hpp: fix some warning messages |
| 2993 |
> |
|
| 2994 |
> |
2005-04-13 17:30 gezelter |
| 2995 |
> |
|
| 2996 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 2997 |
> |
make/Makefile.in, src/config.h.in, |
| 2998 |
> |
src/applications/nanoRodBuilder/Makefile, |
| 2999 |
> |
src/applications/nanoRodBuilder/Makefile.in, |
| 3000 |
> |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
| 3001 |
> |
checks |
| 3002 |
> |
|
| 3003 |
> |
2005-04-13 15:36 chuckv |
| 3004 |
> |
|
| 3005 |
> |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
| 3006 |
> |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
| 3007 |
> |
DarkSide/electrostatic_interface.F90, |
| 3008 |
> |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
| 3009 |
> |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
| 3010 |
> |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
| 3011 |
> |
destroy methods for Fortran modules. |
| 3012 |
> |
|
| 3013 |
> |
2005-04-13 15:17 chuckv |
| 3014 |
> |
|
| 3015 |
> |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
| 3016 |
> |
shapes_interface.h: Added destroy method to clean up memory |
| 3017 |
> |
|
| 3018 |
> |
2005-04-13 13:41 tim |
| 3019 |
> |
|
| 3020 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3021 |
> |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3022 |
> |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
| 3023 |
> |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
| 3024 |
> |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
| 3025 |
> |
fixed |
| 3026 |
> |
|
| 3027 |
> |
2005-04-12 17:44 chuckv |
| 3028 |
> |
|
| 3029 |
> |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
| 3030 |
> |
for nanoRodBuilder. |
| 3031 |
> |
|
| 3032 |
> |
2005-04-12 17:42 tim |
| 3033 |
> |
|
| 3034 |
> |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
| 3035 |
> |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
| 3036 |
> |
and simpleBuilder(forget to delete lattice) |
| 3037 |
> |
|
| 3038 |
> |
2005-04-12 17:33 tim |
| 3039 |
> |
|
| 3040 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3041 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
| 3042 |
> |
refactory lattice |
| 3043 |
> |
|
| 3044 |
> |
2005-04-12 17:07 tim |
| 3045 |
> |
|
| 3046 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
| 3047 |
> |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
| 3048 |
> |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
| 3049 |
> |
LatticeFactory and LatticeCreator |
| 3050 |
> |
|
| 3051 |
> |
2005-04-12 16:58 tim |
| 3052 |
> |
|
| 3053 |
> |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 3054 |
> |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
| 3055 |
> |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 3056 |
> |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
| 3057 |
> |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
| 3058 |
> |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
| 3059 |
> |
|
| 3060 |
> |
2005-04-12 16:28 gezelter |
| 3061 |
> |
|
| 3062 |
> |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
| 3063 |
> |
vector_class.F90: cleaned up vector_class memory leak fix by |
| 3064 |
> |
deallocating in reverse order of how we allocated. Also migrated |
| 3065 |
> |
MoLocator into utils directory |
| 3066 |
> |
|
| 3067 |
> |
2005-04-12 16:27 gezelter |
| 3068 |
> |
|
| 3069 |
> |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
| 3070 |
> |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 3071 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
| 3072 |
> |
directory |
| 3073 |
> |
|
| 3074 |
> |
2005-04-12 16:27 gezelter |
| 3075 |
> |
|
| 3076 |
> |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
| 3077 |
> |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
| 3078 |
> |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
| 3079 |
> |
nanoRodBuilder/LatticeCreator.hpp, |
| 3080 |
> |
nanoRodBuilder/LatticeFactory.cpp, |
| 3081 |
> |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
| 3082 |
> |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
| 3083 |
> |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
| 3084 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 3085 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 3086 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 3087 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
| 3088 |
> |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
| 3089 |
> |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
| 3090 |
> |
these files are now redundant |
| 3091 |
> |
|
| 3092 |
> |
2005-04-12 16:27 gezelter |
| 3093 |
> |
|
| 3094 |
> |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
| 3095 |
> |
atype_interface.h: cleaned up memory leak fix |
| 3096 |
> |
|
| 3097 |
> |
2005-04-12 16:26 gezelter |
| 3098 |
> |
|
| 3099 |
> |
* make/Makefile.in: added lattice subdirectory |
| 3100 |
> |
|
| 3101 |
> |
2005-04-12 15:57 chrisfen |
| 3102 |
> |
|
| 3103 |
> |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
| 3104 |
> |
a space by accident |
| 3105 |
> |
|
| 3106 |
> |
2005-04-12 15:56 chrisfen |
| 3107 |
> |
|
| 3108 |
> |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
| 3109 |
> |
quadrupole sample |
| 3110 |
> |
|
| 3111 |
> |
2005-04-12 15:56 chrisfen |
| 3112 |
> |
|
| 3113 |
> |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
| 3114 |
> |
samples |
| 3115 |
> |
|
| 3116 |
> |
2005-04-12 13:30 tim |
| 3117 |
> |
|
| 3118 |
> |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
| 3119 |
> |
type in fortran side |
| 3120 |
> |
|
| 3121 |
> |
2005-04-12 12:45 chuckv |
| 3122 |
> |
|
| 3123 |
> |
* src/utils/vector_class.F90: Further changes to vector_class |
| 3124 |
> |
destroy function. |
| 3125 |
> |
|
| 3126 |
> |
2005-04-12 12:39 chuckv |
| 3127 |
> |
|
| 3128 |
> |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
| 3129 |
> |
vector_class. |
| 3130 |
> |
|
| 3131 |
> |
2005-04-12 12:12 chuckv |
| 3132 |
> |
|
| 3133 |
> |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
| 3134 |
> |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
| 3135 |
> |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
| 3136 |
> |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
| 3137 |
> |
|
| 3138 |
> |
2005-04-12 09:24 chrisfen |
| 3139 |
> |
|
| 3140 |
> |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
| 3141 |
> |
output |
| 3142 |
> |
|
| 3143 |
> |
2005-04-11 19:29 chuckv |
| 3144 |
> |
|
| 3145 |
> |
* src/: UseTheForce/DarkSide/atype.F90, |
| 3146 |
> |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
| 3147 |
> |
|
| 3148 |
> |
2005-04-11 19:28 chuckv |
| 3149 |
> |
|
| 3150 |
> |
* src/utils/vector_class.F90: Added code to delete vector. |
| 3151 |
|
|
| 3152 |
|
2005-04-11 16:58 tim |
| 3153 |
|
|
