| 1 |
+ |
2006-05-17 14:54 gezelter |
| 2 |
+ |
|
| 3 |
+ |
* configure, ac-tools/configure.in, make/Makefile.in, |
| 4 |
+ |
src/UseTheForce/doForces.F90, |
| 5 |
+ |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 6 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
| 7 |
+ |
src/UseTheForce/DarkSide/simParallel.F90, |
| 8 |
+ |
src/UseTheForce/DarkSide/simulation_interface.F90, |
| 9 |
+ |
src/utils/definitions.F90: Adding single precision capabilities to |
| 10 |
+ |
the fortran side |
| 11 |
+ |
|
| 12 |
+ |
2006-05-17 11:10 gezelter |
| 13 |
+ |
|
| 14 |
+ |
* configure, ac-tools/configure.in, src/config.h.in: adding |
| 15 |
+ |
--enable-single to configure script |
| 16 |
+ |
|
| 17 |
+ |
2006-05-17 10:37 gezelter |
| 18 |
+ |
|
| 19 |
+ |
* ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, |
| 20 |
+ |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
| 21 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 22 |
+ |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
| 23 |
+ |
src/UseTheForce/DarkSide/gb.F90, |
| 24 |
+ |
src/UseTheForce/DarkSide/lj_interface.F90, |
| 25 |
+ |
src/UseTheForce/DarkSide/shapes.F90, |
| 26 |
+ |
src/UseTheForce/DarkSide/sticky.F90, |
| 27 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90, |
| 28 |
+ |
src/UseTheForce/DarkSide/suttonchen_interface.F90, |
| 29 |
+ |
src/UseTheForce/DarkSide/switcheroo.F90, src/math/derfc.F90, |
| 30 |
+ |
src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran |
| 31 |
+ |
side prepped for single precision... |
| 32 |
+ |
|
| 33 |
+ |
2006-05-17 09:03 chrisfen |
| 34 |
+ |
|
| 35 |
+ |
* samples/water/ssd-ion/ssdCl.md, |
| 36 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90: electrostatic |
| 37 |
+ |
refinement |
| 38 |
+ |
|
| 39 |
+ |
2006-05-16 22:03 gezelter |
| 40 |
+ |
|
| 41 |
+ |
* configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes |
| 42 |
+ |
|
| 43 |
+ |
2006-05-16 15:38 gezelter |
| 44 |
+ |
|
| 45 |
+ |
* configure, ac-tools/OOPSE.m4, ac-tools/config.guess, |
| 46 |
+ |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, |
| 47 |
+ |
ac-tools/missing, ac-tools/mkinstalldirs, make/Makefile.in, |
| 48 |
+ |
src/config.h.in, src/applications/staticProps/Hxy.cpp, |
| 49 |
+ |
src/applications/staticProps/Hxy.hpp, |
| 50 |
+ |
src/applications/staticProps/StaticProps.cpp: Autoconf fixes for |
| 51 |
+ |
FFTW. Multiple FFTW version support. |
| 52 |
+ |
|
| 53 |
+ |
2006-05-15 21:06 gezelter |
| 54 |
+ |
|
| 55 |
+ |
* README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 56 |
+ |
make/Makefile.in, src/config.h.in, |
| 57 |
+ |
src/applications/hydrodynamics/AnalyticalModel.cpp, |
| 58 |
+ |
src/applications/hydrodynamics/AnalyticalModel.hpp, |
| 59 |
+ |
src/applications/staticProps/Hxy.cpp, |
| 60 |
+ |
src/applications/staticProps/Hxy.hpp, |
| 61 |
+ |
src/applications/staticProps/StaticProps.cpp, |
| 62 |
+ |
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
| 63 |
+ |
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
| 64 |
+ |
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
| 65 |
+ |
src/integrators/LDForceManager.cpp, |
| 66 |
+ |
src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, |
| 67 |
+ |
src/utils/HydroProps.hpp: [no log message] |
| 68 |
+ |
|
| 69 |
+ |
2006-05-12 16:34 xsun |
| 70 |
+ |
|
| 71 |
+ |
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, |
| 72 |
+ |
StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to |
| 73 |
+ |
calculate undulation spectrum |
| 74 |
+ |
|
| 75 |
+ |
2006-05-09 20:44 tim |
| 76 |
+ |
|
| 77 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 78 |
+ |
applications/dump2Xyz/Dump2XYZ.ggo, |
| 79 |
+ |
applications/dump2Xyz/Dump2XYZCmd.c, |
| 80 |
+ |
applications/dump2Xyz/Dump2XYZCmd.h, |
| 81 |
+ |
applications/hydrodynamics/ApproximationModel.cpp, |
| 82 |
+ |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a |
| 83 |
+ |
gay-berne switch to Dump2XYZ |
| 84 |
+ |
|
| 85 |
+ |
2006-05-05 12:58 gezelter |
| 86 |
+ |
|
| 87 |
+ |
* src/UseTheForce/DarkSide/qpole.F90: Adding qpole |
| 88 |
+ |
|
| 89 |
+ |
2006-05-05 09:34 tim |
| 90 |
+ |
|
| 91 |
+ |
* ac-tools/aclocal.m4: finding ifort arguments that won't die under |
| 92 |
+ |
two different versions of the intel fortran compiler |
| 93 |
+ |
|
| 94 |
+ |
2006-05-03 08:15 chrisfen |
| 95 |
+ |
|
| 96 |
+ |
* src/applications/randomBuilder/Makefile: missing makefile was |
| 97 |
+ |
hanging up 'make clean' |
| 98 |
+ |
|
| 99 |
+ |
2006-04-25 17:59 chuckv |
| 100 |
+ |
|
| 101 |
+ |
* src/applications/randomBuilder/: randomBuilder.cpp, |
| 102 |
+ |
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added |
| 103 |
+ |
random builder to cvs. |
| 104 |
+ |
|
| 105 |
+ |
2006-04-25 17:54 chuckv |
| 106 |
+ |
|
| 107 |
+ |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 108 |
+ |
Change in siminfo used in nanoparticleBuilder. |
| 109 |
+ |
|
| 110 |
+ |
2006-04-25 17:30 chuckv |
| 111 |
+ |
|
| 112 |
+ |
* make/Makefile.in: Added random builder |
| 113 |
+ |
|
| 114 |
+ |
2006-04-25 17:29 chuckv |
| 115 |
+ |
|
| 116 |
+ |
* src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, |
| 117 |
+ |
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a |
| 118 |
+ |
random builder to oopse. |
| 119 |
+ |
|
| 120 |
+ |
2006-04-25 08:35 gezelter |
| 121 |
+ |
|
| 122 |
+ |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
| 123 |
+ |
ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table |
| 124 |
+ |
to pick vdw radii for hydrodynamics if the LJ sigma can't be found. |
| 125 |
+ |
|
| 126 |
+ |
2006-04-24 21:09 gezelter |
| 127 |
+ |
|
| 128 |
+ |
* configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, |
| 129 |
+ |
src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, |
| 130 |
+ |
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
| 131 |
+ |
src/brains/SimInfo.hpp, src/brains/Thermo.cpp, |
| 132 |
+ |
src/brains/Thermo.hpp, src/integrators/LDForceManager.cpp, |
| 133 |
+ |
src/integrators/LDForceManager.hpp, |
| 134 |
+ |
src/integrators/LangevinDynamics.cpp, src/io/Globals.cpp, |
| 135 |
+ |
src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding |
| 136 |
+ |
spherical boundary conditions to LD integrator |
| 137 |
+ |
|
| 138 |
+ |
2006-04-24 21:06 gezelter |
| 139 |
+ |
|
| 140 |
+ |
* src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: |
| 141 |
+ |
Added EAM atom types to Hydro models |
| 142 |
+ |
|
| 143 |
+ |
2006-04-21 15:02 chrisfen |
| 144 |
+ |
|
| 145 |
+ |
* src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the |
| 146 |
+ |
EAM module |
| 147 |
+ |
|
| 148 |
+ |
2006-04-21 14:32 chrisfen |
| 149 |
+ |
|
| 150 |
+ |
* ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, |
| 151 |
+ |
samples/shape/C60.shape, samples/shape/C70.shape, |
| 152 |
+ |
samples/shape/Makefile, samples/shape/Shapes.frc, |
| 153 |
+ |
samples/shape/cholesterol.shape, samples/shape/ethylBenzene.shape, |
| 154 |
+ |
samples/shape/linear.in, samples/shape/linear.md, |
| 155 |
+ |
samples/shape/linear.shape, samples/shape/toluene.shape, |
| 156 |
+ |
samples/thermoIntegration/liquid/ssde.md, |
| 157 |
+ |
samples/thermoIntegration/solid/ssde.md, |
| 158 |
+ |
samples/water/spce/spce.md, samples/water/ssd/ssd.md, |
| 159 |
+ |
samples/water/ssd-ion/ssdCl.md, samples/water/ssde/ssde.md, |
| 160 |
+ |
samples/water/ssdrf/ssdrf.md, samples/water/tip3p_ice/tp3.md, |
| 161 |
+ |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90, |
| 162 |
+ |
src/UseTheForce/DarkSide/LJ.F90: Removed sqrt splines and shape |
| 163 |
+ |
stuff (doesn't work, so why was it in there?). Changed some of the |
| 164 |
+ |
water samples to use shifted_force. Probably should set the |
| 165 |
+ |
defaults to use the damped version now that we sped it up. |
| 166 |
+ |
|
| 167 |
+ |
2006-04-20 22:19 chrisfen |
| 168 |
+ |
|
| 169 |
+ |
* samples/water/spce/spce.md, |
| 170 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
| 171 |
+ |
|
| 172 |
+ |
2006-04-20 16:02 chrisfen |
| 173 |
+ |
|
| 174 |
+ |
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
| 175 |
+ |
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
| 176 |
+ |
|
| 177 |
+ |
2006-04-20 13:24 gezelter |
| 178 |
+ |
|
| 179 |
+ |
* samples/metals/EAM/Au_bulk_voter.md, |
| 180 |
+ |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 181 |
+ |
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
| 182 |
+ |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
| 183 |
+ |
src/UseTheForce/DarkSide/eam.F90, |
| 184 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 185 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90, |
| 186 |
+ |
src/UseTheForce/DarkSide/switcheroo.F90, |
| 187 |
+ |
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
| 188 |
+ |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
| 189 |
+ |
src/utils/interpolation.F90: Complete rewrite of spline code and |
| 190 |
+ |
everything that uses it. |
| 191 |
+ |
|
| 192 |
+ |
2006-04-17 16:49 gezelter |
| 193 |
+ |
|
| 194 |
+ |
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
| 195 |
+ |
samples/metals/EAM/Au_bulk_voter.md, |
| 196 |
+ |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
| 197 |
+ |
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
| 198 |
+ |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
| 199 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 200 |
+ |
src/UseTheForce/DarkSide/interpolation.F90, |
| 201 |
+ |
src/UseTheForce/DarkSide/sticky.F90, |
| 202 |
+ |
src/UseTheForce/DarkSide/suttonchen.F90, |
| 203 |
+ |
src/UseTheForce/DarkSide/switcheroo.F90, |
| 204 |
+ |
src/applications/hydrodynamics/Hydro.ggo, |
| 205 |
+ |
src/applications/hydrodynamics/HydroCmd.c, |
| 206 |
+ |
src/applications/hydrodynamics/HydroCmd.h, |
| 207 |
+ |
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
| 208 |
+ |
src/utils/interpolation.F90: Many performance improvements |
| 209 |
+ |
|
| 210 |
+ |
2006-04-15 21:51 chrisfen |
| 211 |
+ |
|
| 212 |
+ |
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
| 213 |
+ |
src/UseTheForce/fSwitchingFunction.h, |
| 214 |
+ |
src/UseTheForce/DarkSide/electrostatic.F90, |
| 215 |
+ |
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
| 216 |
+ |
switcheroo |
| 217 |
+ |
|
| 218 |
+ |
2006-04-15 16:58 chrisfen |
| 219 |
+ |
|
| 220 |
+ |
* src/utils/Makefile.in: Since status.F90 is used by |
| 221 |
+ |
interpolation.F90, the former needs to be listed above the later in |
| 222 |
+ |
the Makefile. |
| 223 |
+ |
|
| 224 |
+ |
2006-04-14 16:59 gezelter |
| 225 |
+ |
|
| 226 |
+ |
* src/utils/interpolation.F90: changed the interface a bit |
| 227 |
+ |
|
| 228 |
+ |
2006-04-14 16:49 gezelter |
| 229 |
+ |
|
| 230 |
+ |
* src/utils/interpolation.F90: added some logical flags |
| 231 |
+ |
|
| 232 |
+ |
2006-04-14 16:06 chrisfen |
| 233 |
+ |
|
| 234 |
+ |
* src/utils/interpolation.F90: Wiped the spline with derivatives |
| 235 |
+ |
and corrected a boundary comparision error by eliminating the |
| 236 |
+ |
check. This algorithm REQUIRES known first derivatives at the |
| 237 |
+ |
endpoints. |
| 238 |
+ |
|
| 239 |
+ |
2006-04-14 15:04 gezelter |
| 240 |
+ |
|
| 241 |
+ |
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
| 242 |
+ |
interpolation module |
| 243 |
+ |
|
| 244 |
+ |
2006-04-14 14:57 gezelter |
| 245 |
+ |
|
| 246 |
+ |
* src/utils/interpolation.F90: Heavily modified interpolation |
| 247 |
+ |
module, also moved to "utils" |
| 248 |
+ |
|
| 249 |
+ |
2006-04-12 16:15 chuckv |
| 250 |
+ |
|
| 251 |
+ |
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
| 252 |
+ |
module. |
| 253 |
+ |
|
| 254 |
+ |
2006-04-11 10:33 gezelter |
| 255 |
+ |
|
| 256 |
+ |
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
| 257 |
+ |
StaticPropsCmd.h: [no log message] |
| 258 |
+ |
|
| 259 |
+ |
2006-04-03 10:37 chuckv |
| 260 |
+ |
|
| 261 |
+ |
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
| 262 |
+ |
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
| 263 |
+ |
simParallel for error reporting. |
| 264 |
+ |
|
| 265 |
+ |
2006-03-31 13:09 tim |
| 266 |
+ |
|
| 267 |
+ |
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
| 268 |
+ |
|
| 269 |
+ |
2006-03-30 16:08 chuckv |
| 270 |
+ |
|
| 271 |
+ |
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
| 272 |
+ |
where SCList capacity was not reset to zero on destruction. |
| 273 |
+ |
|
| 274 |
+ |
2006-03-30 14:37 chuckv |
| 275 |
+ |
|
| 276 |
+ |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 277 |
+ |
More testing of nanoparticleBuilder. |
| 278 |
+ |
|
| 279 |
+ |
2006-03-29 17:24 chuckv |
| 280 |
+ |
|
| 281 |
+ |
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
| 282 |
+ |
file exists. |
| 283 |
+ |
|
| 284 |
+ |
2006-03-29 14:17 chuckv |
| 285 |
+ |
|
| 286 |
+ |
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
| 287 |
+ |
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
| 288 |
+ |
latticeOrt in shapedlatice and latticebuilder. |
| 289 |
+ |
|
| 290 |
+ |
2006-03-29 13:11 tim |
| 291 |
+ |
|
| 292 |
+ |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 293 |
+ |
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
| 294 |
+ |
in calculating correlation functions |
| 295 |
+ |
|
| 296 |
+ |
2006-03-29 13:09 tim |
| 297 |
+ |
|
| 298 |
+ |
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
| 299 |
+ |
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
| 300 |
+ |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
| 301 |
+ |
RoughShell Model is working; (20)Adding a new option into Hydro |
| 302 |
+ |
which allows user to generate the beads only |
| 303 |
+ |
|
| 304 |
+ |
2006-03-27 11:21 chuckv |
| 305 |
+ |
|
| 306 |
+ |
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
| 307 |
+ |
nanoparticle builder. |
| 308 |
+ |
|
| 309 |
+ |
2006-03-27 11:03 chuckv |
| 310 |
+ |
|
| 311 |
+ |
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
| 312 |
+ |
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
| 313 |
+ |
makefile |
| 314 |
+ |
|
| 315 |
+ |
2006-03-24 15:46 chuckv |
| 316 |
+ |
|
| 317 |
+ |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
| 318 |
+ |
Debugging changes to nanoparticle builder. |
| 319 |
+ |
|
| 320 |
+ |
2006-03-24 12:29 tim |
| 321 |
+ |
|
| 322 |
+ |
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 323 |
+ |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 324 |
+ |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
| 325 |
+ |
|
| 326 |
+ |
2006-03-24 11:49 tim |
| 327 |
+ |
|
| 328 |
+ |
* src/applications/dynamicProps/: DynamicProps.cpp, |
| 329 |
+ |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
| 330 |
+ |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
| 331 |
+ |
function. The command line option for DynamicProps is now changed. |
| 332 |
+ |
--rcorr is for position correlation and --rmsd is for mean square |
| 333 |
+ |
displacement. |
| 334 |
+ |
|
| 335 |
+ |
2006-03-23 10:03 tim |
| 336 |
+ |
|
| 337 |
+ |
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
| 338 |
+ |
AnalyticalModel.hpp, ApproximationModel.cpp, |
| 339 |
+ |
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
| 340 |
+ |
method |
| 341 |
+ |
|
| 342 |
+ |
2006-03-23 10:02 tim |
| 343 |
+ |
|
| 344 |
+ |
* src/io/Globals.hpp: remove a unknown method |
| 345 |
+ |
|
| 346 |
+ |
2006-03-23 10:00 tim |
| 347 |
+ |
|
| 348 |
+ |
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
| 349 |
+ |
|
| 350 |
+ |
2006-03-23 09:59 tim |
| 351 |
+ |
|
| 352 |
+ |
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
| 353 |
+ |
can not be opened for preprocessing |
| 354 |
+ |
|
| 355 |
+ |
2006-03-22 15:57 chuckv |
| 356 |
+ |
|
| 357 |
+ |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
| 358 |
+ |
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
| 359 |
+ |
shaped lattice. |
| 360 |
+ |
|
| 361 |
+ |
2006-03-21 10:33 tim |
| 362 |
+ |
|
| 363 |
+ |
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
| 364 |
+ |
in calculating hydrodynamics tensor when the radius of beads are |
| 365 |
+ |
not the same |
| 366 |
+ |
|
| 367 |
+ |
2006-03-20 19:26 tim |
| 368 |
+ |
|
| 369 |
+ |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 370 |
+ |
applications/hydrodynamics/BeadModel.cpp, |
| 371 |
+ |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 372 |
+ |
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
| 373 |
+ |
for ellipsoid |
| 374 |
+ |
|
| 375 |
+ |
2006-03-20 14:12 tim |
| 376 |
+ |
|
| 377 |
+ |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 378 |
+ |
applications/hydrodynamics/Ellipsoid.cpp, |
| 379 |
+ |
applications/hydrodynamics/Ellipsoid.hpp, |
| 380 |
+ |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 381 |
+ |
integrators/LDForceManager.cpp: Verify the correctness of |
| 382 |
+ |
Ellipsoid's hydrodynamics properties |
| 383 |
+ |
|
| 384 |
+ |
2006-03-17 18:51 tim |
| 385 |
+ |
|
| 386 |
+ |
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
| 387 |
+ |
version of Hydro is working now. |
| 388 |
+ |
|
| 389 |
+ |
2006-03-17 18:20 tim |
| 390 |
+ |
|
| 391 |
+ |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
| 392 |
+ |
applications/hydrodynamics/AnalyticalModel.hpp, |
| 393 |
+ |
applications/hydrodynamics/ApproximationModel.cpp, |
| 394 |
+ |
applications/hydrodynamics/ApproximationModel.hpp, |
| 395 |
+ |
applications/hydrodynamics/BeadModel.hpp, |
| 396 |
+ |
applications/hydrodynamics/CompositeShape.cpp, |
| 397 |
+ |
applications/hydrodynamics/CompositeShape.hpp, |
| 398 |
+ |
applications/hydrodynamics/Ellipsoid.cpp, |
| 399 |
+ |
applications/hydrodynamics/Ellipsoid.hpp, |
| 400 |
+ |
applications/hydrodynamics/Hydro.cpp, |
| 401 |
+ |
applications/hydrodynamics/Hydro.ggo, |
| 402 |
+ |
applications/hydrodynamics/HydroCmd.c, |
| 403 |
+ |
applications/hydrodynamics/HydroCmd.h, |
| 404 |
+ |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 405 |
+ |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 406 |
+ |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 407 |
+ |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 408 |
+ |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 409 |
+ |
applications/hydrodynamics/Makefile, |
| 410 |
+ |
applications/hydrodynamics/RoughShell.cpp, |
| 411 |
+ |
applications/hydrodynamics/RoughShell.hpp, |
| 412 |
+ |
applications/hydrodynamics/Shape.hpp, |
| 413 |
+ |
applications/hydrodynamics/ShapeBuilder.cpp, |
| 414 |
+ |
applications/hydrodynamics/ShapeBuilder.hpp, |
| 415 |
+ |
applications/hydrodynamics/Spheric.cpp, |
| 416 |
+ |
applications/hydrodynamics/Spheric.hpp, |
| 417 |
+ |
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 418 |
+ |
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 419 |
+ |
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
| 420 |
+ |
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
| 421 |
+ |
utils/HydroProps.hpp: refactor Hydrodynamics module. |
| 422 |
+ |
|
| 423 |
+ |
2006-03-17 11:10 chuckv |
| 424 |
+ |
|
| 425 |
+ |
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
| 426 |
+ |
Generic Shaped Lattice for oopse. Can overload to get spherical or |
| 427 |
+ |
nanorod. |
| 428 |
+ |
|
| 429 |
+ |
2006-03-16 17:50 tim |
| 430 |
+ |
|
| 431 |
+ |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 432 |
+ |
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
| 433 |
+ |
LagevinDynamics is working? |
| 434 |
+ |
|
| 435 |
+ |
2006-03-16 16:52 gezelter |
| 436 |
+ |
|
| 437 |
+ |
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
| 438 |
+ |
problem |
| 439 |
+ |
|
| 440 |
+ |
2006-03-15 17:08 tim |
| 441 |
+ |
|
| 442 |
+ |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
| 443 |
+ |
conversion for diffusion tensor is wrong |
| 444 |
+ |
|
| 445 |
+ |
2006-03-15 16:28 tim |
| 446 |
+ |
|
| 447 |
+ |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 448 |
+ |
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
| 449 |
+ |
|
| 450 |
+ |
2006-03-15 15:58 tim |
| 451 |
+ |
|
| 452 |
+ |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
| 453 |
+ |
the unit in HydrodynamicsModel |
| 454 |
+ |
|
| 455 |
+ |
2006-03-15 12:35 tim |
| 456 |
+ |
|
| 457 |
+ |
* src/primitives/RigidBody.cpp: using setFrc in |
| 458 |
+ |
RigidBody::calcForcesAndTorques will discard if there are force and |
| 459 |
+ |
torque applied in rigid body itself. use addFrc instead. |
| 460 |
+ |
|
| 461 |
+ |
2006-03-15 10:51 tim |
| 462 |
+ |
|
| 463 |
+ |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
| 464 |
+ |
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
| 465 |
+ |
|
| 466 |
+ |
2006-03-15 10:50 tim |
| 467 |
+ |
|
| 468 |
+ |
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
| 469 |
+ |
hydrodynamics module into build system |
| 470 |
+ |
|
| 471 |
+ |
2006-03-14 18:46 tim |
| 472 |
+ |
|
| 473 |
+ |
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
| 474 |
+ |
|
| 475 |
+ |
2006-03-13 17:42 tim |
| 476 |
+ |
|
| 477 |
+ |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 478 |
+ |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 479 |
+ |
applications/hydrodynamics/StuntDoubleShape.cpp, |
| 480 |
+ |
applications/hydrodynamics/StuntDoubleShape.hpp, |
| 481 |
+ |
brains/Register.cpp, integrators/LDForceManager.cpp, |
| 482 |
+ |
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
| 483 |
+ |
integrators/LangevinDynamics.hpp, integrators/Makefile, |
| 484 |
+ |
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
| 485 |
+ |
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
| 486 |
+ |
progress |
| 487 |
+ |
|
| 488 |
+ |
2006-03-07 11:43 gezelter |
| 489 |
+ |
|
| 490 |
+ |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
| 491 |
+ |
double/int bug. Surprised no one ever noticed before... |
| 492 |
+ |
|
| 493 |
+ |
2006-02-24 16:17 tim |
| 494 |
+ |
|
| 495 |
+ |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
| 496 |
+ |
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
| 497 |
+ |
product of Rij |
| 498 |
+ |
|
| 499 |
+ |
2006-02-23 18:16 tim |
| 500 |
+ |
|
| 501 |
+ |
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
| 502 |
+ |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
| 503 |
+ |
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
| 504 |
+ |
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
| 505 |
+ |
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
| 506 |
+ |
StuntDoubleShape.hpp: Bead Model is working |
| 507 |
+ |
|
| 508 |
+ |
2006-02-22 15:35 tim |
| 509 |
+ |
|
| 510 |
+ |
* src/: applications/hydrodynamics/Hydro.cpp, |
| 511 |
+ |
applications/hydrodynamics/Hydro.ggo, |
| 512 |
+ |
applications/hydrodynamics/HydroCmd.c, |
| 513 |
+ |
applications/hydrodynamics/HydroCmd.h, |
| 514 |
+ |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
| 515 |
+ |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
| 516 |
+ |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
| 517 |
+ |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
| 518 |
+ |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
| 519 |
+ |
applications/hydrodynamics/MoleculeShape.cpp, |
| 520 |
+ |
applications/hydrodynamics/MoleculeShape.hpp, |
| 521 |
+ |
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
| 522 |
+ |
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
| 523 |
+ |
Module |
| 524 |
+ |
|
| 525 |
+ |
2006-02-16 17:05 gezelter |
| 526 |
+ |
|
| 527 |
+ |
* src/brains/Snapshot.cpp: fixed a spelling error |
| 528 |
+ |
|
| 529 |
+ |
2006-02-16 16:40 gezelter |
| 530 |
+ |
|
| 531 |
+ |
* src/: UseTheForce/doForces.F90, |
| 532 |
+ |
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
| 533 |
+ |
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
| 534 |
+ |
larger than 1/2 the length of the shortest box dimension. added a |
| 535 |
+ |
few fortran utility routines |
| 536 |
+ |
|
| 537 |
+ |
2006-02-15 15:46 chuckv |
| 538 |
+ |
|
| 539 |
+ |
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
| 540 |
+ |
sphericalNanoparticle.hpp: Changed Names of class files. |
| 541 |
+ |
|
| 542 |
+ |
2006-02-10 10:45 kdaily |
| 543 |
+ |
|
| 544 |
+ |
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
| 545 |
+ |
message] |
| 546 |
+ |
|
| 547 |
+ |
2006-02-10 10:12 tim |
| 548 |
+ |
|
| 549 |
+ |
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
| 550 |
+ |
converting integer to double |
| 551 |
+ |
|
| 552 |
+ |
2006-02-08 13:21 chrisfen |
| 553 |
+ |
|
| 554 |
+ |
* forceFields/DUFF2.frc: added DPD molecule type parameters |
| 555 |
+ |
|
| 556 |
+ |
2006-02-07 11:39 tim |
| 557 |
+ |
|
| 558 |
+ |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
| 559 |
+ |
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
| 560 |
+ |
trajectory file during analysis |
| 561 |
+ |
|
| 562 |
+ |
2006-02-02 12:14 tim |
| 563 |
+ |
|
| 564 |
+ |
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
| 565 |
+ |
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
| 566 |
+ |
in AtomStamp where orientation is not set correctly. |
| 567 |
+ |
|
| 568 |
+ |
2006-02-02 11:49 gezelter |
| 569 |
+ |
|
| 570 |
+ |
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
| 571 |
+ |
contain directional atoms |
| 572 |
+ |
|
| 573 |
+ |
2006-02-02 10:49 xsun |
| 574 |
+ |
|
| 575 |
+ |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 576 |
+ |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
| 577 |
+ |
for GBlipid atom type |
| 578 |
+ |
|
| 579 |
+ |
2006-02-01 21:57 gezelter |
| 580 |
+ |
|
| 581 |
+ |
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
| 582 |
+ |
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
| 583 |
+ |
|
| 584 |
+ |
2006-02-01 16:06 chrisfen |
| 585 |
+ |
|
| 586 |
+ |
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
| 587 |
+ |
to build |
| 588 |
+ |
|
| 589 |
+ |
2006-02-01 15:54 chrisfen |
| 590 |
+ |
|
| 591 |
+ |
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
| 592 |
+ |
cutoff radius setting to a more logical procedure - still may |
| 593 |
+ |
change... |
| 594 |
+ |
|
| 595 |
+ |
2006-02-01 12:26 gezelter |
| 596 |
+ |
|
| 597 |
+ |
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
| 598 |
+ |
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
| 599 |
+ |
|
| 600 |
+ |
2006-01-30 17:25 tim |
| 601 |
+ |
|
| 602 |
+ |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
| 603 |
+ |
applications/dynamicProps/DynamicProps.cpp, |
| 604 |
+ |
applications/dynamicProps/DynamicProps.ggo, |
| 605 |
+ |
applications/dynamicProps/DynamicPropsCmd.c, |
| 606 |
+ |
applications/dynamicProps/DynamicPropsCmd.h, |
| 607 |
+ |
applications/dynamicProps/LegendreCorrFunc.cpp, |
| 608 |
+ |
applications/dynamicProps/LegendreCorrFunc.hpp, |
| 609 |
+ |
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
| 610 |
+ |
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
| 611 |
+ |
Adding :LegendrePolynomial |
| 612 |
+ |
|
| 613 |
+ |
2006-01-19 17:54 chuckv |
| 614 |
+ |
|
| 615 |
+ |
* src/applications/nanoparticleBuilder/: Makefile, |
| 616 |
+ |
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
| 617 |
+ |
nanoparticle builder |
| 618 |
+ |
|
| 619 |
+ |
2006-01-18 16:08 chuckv |
| 620 |
+ |
|
| 621 |
+ |
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
| 622 |
+ |
nanoparticle builder. |
| 623 |
+ |
|
| 624 |
+ |
2006-01-17 11:16 gezelter |
| 625 |
+ |
|
| 626 |
+ |
* AUTHORS, README: Cleaning up for 3.0.1 release |
| 627 |
+ |
|
| 628 |
+ |
2006-01-17 10:50 gezelter |
| 629 |
+ |
|
| 630 |
+ |
* ChangeLog: Prepping 3.0.1 release |
| 631 |
+ |
|
| 632 |
+ |
2006-01-17 10:32 gezelter |
| 633 |
+ |
|
| 634 |
+ |
* src/config.h.in: new version number |
| 635 |
+ |
|
| 636 |
+ |
2006-01-17 10:32 gezelter |
| 637 |
+ |
|
| 638 |
+ |
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
| 639 |
+ |
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
| 640 |
+ |
oopseManual.pdf: Updated Documentation |
| 641 |
+ |
|
| 642 |
+ |
2006-01-16 18:10 gezelter |
| 643 |
+ |
|
| 644 |
+ |
* ChangeLog, README: Getting ready for release! |
| 645 |
+ |
|
| 646 |
|
2006-01-16 10:26 gezelter |
| 647 |
|
|
| 648 |
|
* configure: Testing commit |
| 8316 |
|
|
| 8317 |
|
2004-09-29 12:56 gezelter |
| 8318 |
|
|
| 8319 |
< |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 8319 |
> |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
| 8320 |
> |
make stuff |
| 8321 |
|
|
| 8322 |
|
2004-09-29 12:46 tim |
| 8323 |
|
|
| 8583 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 8584 |
|
src/visitors/RigidBodyVisitor.cpp, |
| 8585 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 8586 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 8586 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 8587 |
> |
make/_files/style.css, samples/Makefile.in, |
| 8588 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 8589 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 8590 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 8759 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 8760 |
|
src/visitors/RigidBodyVisitor.cpp, |
| 8761 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 8762 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 8762 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 8763 |
> |
make/_files/style.css, samples/Makefile.in, |
| 8764 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 8765 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 8766 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
