| 1 |
+ |
2005-04-14 16:20 gezelter |
| 2 |
+ |
|
| 3 |
+ |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
| 4 |
+ |
MoLocator |
| 5 |
+ |
|
| 6 |
+ |
2005-04-14 14:12 gezelter |
| 7 |
+ |
|
| 8 |
+ |
* LICENSE: [no log message] |
| 9 |
+ |
|
| 10 |
+ |
2005-04-14 11:10 chuckv |
| 11 |
+ |
|
| 12 |
+ |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
| 13 |
+ |
nanorodbuilder now exit's when libCGAL is not present. |
| 14 |
+ |
|
| 15 |
+ |
2005-04-14 10:20 tim |
| 16 |
+ |
|
| 17 |
+ |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
| 18 |
+ |
|
| 19 |
+ |
2005-04-13 18:36 chuckv |
| 20 |
+ |
|
| 21 |
+ |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
| 22 |
+ |
interface name for SGI Compiler |
| 23 |
+ |
|
| 24 |
+ |
2005-04-13 18:29 chrisfen |
| 25 |
+ |
|
| 26 |
+ |
* samples/water/ssde/ssde.md: oops... bad sample |
| 27 |
+ |
|
| 28 |
+ |
2005-04-13 18:00 chuckv |
| 29 |
+ |
|
| 30 |
+ |
* src/config.h.in: Change typo in CGAL. |
| 31 |
+ |
|
| 32 |
+ |
2005-04-13 17:43 tim |
| 33 |
+ |
|
| 34 |
+ |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
| 35 |
+ |
selection/SelectionCompiler.hpp: fix some warning messages |
| 36 |
+ |
|
| 37 |
+ |
2005-04-13 17:30 gezelter |
| 38 |
+ |
|
| 39 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 40 |
+ |
make/Makefile.in, src/config.h.in, |
| 41 |
+ |
src/applications/nanoRodBuilder/Makefile, |
| 42 |
+ |
src/applications/nanoRodBuilder/Makefile.in, |
| 43 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
| 44 |
+ |
checks |
| 45 |
+ |
|
| 46 |
+ |
2005-04-13 15:36 chuckv |
| 47 |
+ |
|
| 48 |
+ |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
| 49 |
+ |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
| 50 |
+ |
DarkSide/electrostatic_interface.F90, |
| 51 |
+ |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
| 52 |
+ |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
| 53 |
+ |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
| 54 |
+ |
destroy methods for Fortran modules. |
| 55 |
+ |
|
| 56 |
+ |
2005-04-13 15:17 chuckv |
| 57 |
+ |
|
| 58 |
+ |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
| 59 |
+ |
shapes_interface.h: Added destroy method to clean up memory |
| 60 |
+ |
|
| 61 |
+ |
2005-04-13 13:41 tim |
| 62 |
+ |
|
| 63 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 64 |
+ |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 65 |
+ |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
| 66 |
+ |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
| 67 |
+ |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
| 68 |
+ |
fixed |
| 69 |
+ |
|
| 70 |
+ |
2005-04-12 17:44 chuckv |
| 71 |
+ |
|
| 72 |
+ |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
| 73 |
+ |
for nanoRodBuilder. |
| 74 |
+ |
|
| 75 |
+ |
2005-04-12 17:42 tim |
| 76 |
+ |
|
| 77 |
+ |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
| 78 |
+ |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
| 79 |
+ |
and simpleBuilder(forget to delete lattice) |
| 80 |
+ |
|
| 81 |
+ |
2005-04-12 17:33 tim |
| 82 |
+ |
|
| 83 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 84 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
| 85 |
+ |
refactory lattice |
| 86 |
+ |
|
| 87 |
+ |
2005-04-12 17:07 tim |
| 88 |
+ |
|
| 89 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
| 90 |
+ |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
| 91 |
+ |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
| 92 |
+ |
LatticeFactory and LatticeCreator |
| 93 |
+ |
|
| 94 |
+ |
2005-04-12 16:58 tim |
| 95 |
+ |
|
| 96 |
+ |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 97 |
+ |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
| 98 |
+ |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
| 99 |
+ |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
| 100 |
+ |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
| 101 |
+ |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
| 102 |
+ |
|
| 103 |
+ |
2005-04-12 16:28 gezelter |
| 104 |
+ |
|
| 105 |
+ |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
| 106 |
+ |
vector_class.F90: cleaned up vector_class memory leak fix by |
| 107 |
+ |
deallocating in reverse order of how we allocated. Also migrated |
| 108 |
+ |
MoLocator into utils directory |
| 109 |
+ |
|
| 110 |
+ |
2005-04-12 16:27 gezelter |
| 111 |
+ |
|
| 112 |
+ |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
| 113 |
+ |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 114 |
+ |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
| 115 |
+ |
directory |
| 116 |
+ |
|
| 117 |
+ |
2005-04-12 16:27 gezelter |
| 118 |
+ |
|
| 119 |
+ |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
| 120 |
+ |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
| 121 |
+ |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
| 122 |
+ |
nanoRodBuilder/LatticeCreator.hpp, |
| 123 |
+ |
nanoRodBuilder/LatticeFactory.cpp, |
| 124 |
+ |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
| 125 |
+ |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
| 126 |
+ |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
| 127 |
+ |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 128 |
+ |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 129 |
+ |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 130 |
+ |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
| 131 |
+ |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
| 132 |
+ |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
| 133 |
+ |
these files are now redundant |
| 134 |
+ |
|
| 135 |
+ |
2005-04-12 16:27 gezelter |
| 136 |
+ |
|
| 137 |
+ |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
| 138 |
+ |
atype_interface.h: cleaned up memory leak fix |
| 139 |
+ |
|
| 140 |
+ |
2005-04-12 16:26 gezelter |
| 141 |
+ |
|
| 142 |
+ |
* make/Makefile.in: added lattice subdirectory |
| 143 |
+ |
|
| 144 |
+ |
2005-04-12 15:57 chrisfen |
| 145 |
+ |
|
| 146 |
+ |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
| 147 |
+ |
a space by accident |
| 148 |
+ |
|
| 149 |
+ |
2005-04-12 15:56 chrisfen |
| 150 |
+ |
|
| 151 |
+ |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
| 152 |
+ |
quadrupole sample |
| 153 |
+ |
|
| 154 |
+ |
2005-04-12 15:56 chrisfen |
| 155 |
+ |
|
| 156 |
+ |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
| 157 |
+ |
samples |
| 158 |
+ |
|
| 159 |
+ |
2005-04-12 13:30 tim |
| 160 |
+ |
|
| 161 |
+ |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
| 162 |
+ |
type in fortran side |
| 163 |
+ |
|
| 164 |
+ |
2005-04-12 12:45 chuckv |
| 165 |
+ |
|
| 166 |
+ |
* src/utils/vector_class.F90: Further changes to vector_class |
| 167 |
+ |
destroy function. |
| 168 |
+ |
|
| 169 |
+ |
2005-04-12 12:39 chuckv |
| 170 |
+ |
|
| 171 |
+ |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
| 172 |
+ |
vector_class. |
| 173 |
+ |
|
| 174 |
+ |
2005-04-12 12:12 chuckv |
| 175 |
+ |
|
| 176 |
+ |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
| 177 |
+ |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
| 178 |
+ |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
| 179 |
+ |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
| 180 |
+ |
|
| 181 |
+ |
2005-04-12 09:24 chrisfen |
| 182 |
+ |
|
| 183 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
| 184 |
+ |
output |
| 185 |
+ |
|
| 186 |
+ |
2005-04-11 19:29 chuckv |
| 187 |
+ |
|
| 188 |
+ |
* src/: UseTheForce/DarkSide/atype.F90, |
| 189 |
+ |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
| 190 |
+ |
|
| 191 |
+ |
2005-04-11 19:28 chuckv |
| 192 |
+ |
|
| 193 |
+ |
* src/utils/vector_class.F90: Added code to delete vector. |
| 194 |
+ |
|
| 195 |
+ |
2005-04-11 17:03 chuckv |
| 196 |
+ |
|
| 197 |
+ |
* samples/metals/nanorod/: Au_nanoparticle.md, |
| 198 |
+ |
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
| 199 |
+ |
aren't these here? |
| 200 |
+ |
|
| 201 |
+ |
2005-04-11 16:58 tim |
| 202 |
+ |
|
| 203 |
+ |
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
| 204 |
+ |
basic_ifstrstream |
| 205 |
+ |
|
| 206 |
+ |
2005-04-11 16:37 chuckv |
| 207 |
+ |
|
| 208 |
+ |
* make/Makefile.in, |
| 209 |
+ |
src/applications/nanoRodBuilder/BaseLattice.cpp, |
| 210 |
+ |
src/applications/nanoRodBuilder/BaseLattice.hpp, |
| 211 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
| 212 |
+ |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
| 213 |
+ |
src/applications/nanoRodBuilder/Lattice.cpp, |
| 214 |
+ |
src/applications/nanoRodBuilder/Lattice.hpp, |
| 215 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
| 216 |
+ |
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
| 217 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
| 218 |
+ |
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
| 219 |
+ |
src/applications/nanoRodBuilder/Makefile, |
| 220 |
+ |
src/applications/nanoRodBuilder/MoLocator.cpp, |
| 221 |
+ |
src/applications/nanoRodBuilder/MoLocator.hpp, |
| 222 |
+ |
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
| 223 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
| 224 |
+ |
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
| 225 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
| 226 |
+ |
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
| 227 |
+ |
nanoRodBuilder application (may not work yet). ((Doesn't work |
| 228 |
+ |
yet.)) (((May never work....))) |
| 229 |
+ |
|
| 230 |
+ |
2005-04-11 15:54 tim |
| 231 |
+ |
|
| 232 |
+ |
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
| 233 |
+ |
prepareVisitor in Dump2XYZ |
| 234 |
+ |
|
| 235 |
+ |
2005-04-11 15:19 chrisfen |
| 236 |
+ |
|
| 237 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
| 238 |
+ |
quadrupoles. look! it's divide by 3 like stone says! |
| 239 |
+ |
|
| 240 |
+ |
2005-04-11 15:18 chrisfen |
| 241 |
+ |
|
| 242 |
+ |
* forceFields/DUFF2.frc: fixing of the quadrupoles |
| 243 |
+ |
|
| 244 |
+ |
2005-04-11 15:16 tim |
| 245 |
+ |
|
| 246 |
+ |
* src/selection/Token.hpp: change the parameter name in |
| 247 |
+ |
constructors |
| 248 |
+ |
|
| 249 |
+ |
2005-04-11 14:49 gezelter |
| 250 |
+ |
|
| 251 |
+ |
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
| 252 |
+ |
|
| 253 |
+ |
2005-04-11 14:06 gezelter |
| 254 |
+ |
|
| 255 |
+ |
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
| 256 |
+ |
versions < 3.80 |
| 257 |
+ |
|
| 258 |
+ |
2005-04-11 11:13 gezelter |
| 259 |
+ |
|
| 260 |
+ |
* make/Makefile.in, src/UseTheForce/Makefile, |
| 261 |
+ |
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
| 262 |
+ |
some stuff to clean out module files during "make clean" |
| 263 |
+ |
|
| 264 |
+ |
2005-04-08 17:13 chrisfen |
| 265 |
+ |
|
| 266 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
| 267 |
+ |
interactions should be working with a remaining question of |
| 268 |
+ |
interaction magnitude |
| 269 |
+ |
|
| 270 |
+ |
2005-04-08 17:12 chrisfen |
| 271 |
+ |
|
| 272 |
+ |
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
| 273 |
+ |
samples |
| 274 |
+ |
|
| 275 |
+ |
2005-04-08 13:48 chrisfen |
| 276 |
+ |
|
| 277 |
+ |
* samples/water/ssd/ssd.md: oops... messed up a sample |
| 278 |
+ |
|
| 279 |
+ |
2005-04-08 09:43 chrisfen |
| 280 |
+ |
|
| 281 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
| 282 |
+ |
charge-dipole interactions |
| 283 |
+ |
|
| 284 |
+ |
2005-04-08 09:42 chrisfen |
| 285 |
+ |
|
| 286 |
+ |
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
| 287 |
+ |
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
| 288 |
+ |
|
| 289 |
+ |
2005-04-08 09:41 chrisfen |
| 290 |
+ |
|
| 291 |
+ |
* forceFields/DUFF2.frc: added Cl- and Na+ |
| 292 |
+ |
|
| 293 |
+ |
2005-04-06 18:59 tim |
| 294 |
+ |
|
| 295 |
+ |
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
| 296 |
+ |
|
| 297 |
+ |
2005-04-05 18:09 tim |
| 298 |
+ |
|
| 299 |
+ |
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
| 300 |
+ |
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
| 301 |
+ |
in atom type name;clean the code a little bit |
| 302 |
+ |
|
| 303 |
+ |
2005-03-29 16:00 tim |
| 304 |
+ |
|
| 305 |
+ |
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
| 306 |
+ |
in converting rotation matrix to quaternion |
| 307 |
+ |
|
| 308 |
+ |
2005-03-28 17:41 tim |
| 309 |
+ |
|
| 310 |
+ |
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
| 311 |
+ |
|
| 312 |
+ |
2005-03-28 17:30 tim |
| 313 |
+ |
|
| 314 |
+ |
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
| 315 |
+ |
the wrapping |
| 316 |
+ |
|
| 317 |
+ |
2005-03-28 10:54 tim |
| 318 |
+ |
|
| 319 |
+ |
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
| 320 |
+ |
dimension of histogram |
| 321 |
+ |
|
| 322 |
+ |
2005-03-22 11:38 tim |
| 323 |
+ |
|
| 324 |
+ |
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
| 325 |
+ |
src/applications/dynamicProps/Makefile, |
| 326 |
+ |
src/applications/oopse/Makefile, |
| 327 |
+ |
src/applications/simpleBuilder/Makefile, |
| 328 |
+ |
src/applications/staticProps/Makefile: avoid building parallel |
| 329 |
+ |
executable for dump2XYZ, simpleBuilder, staticProps and |
| 330 |
+ |
dynamicProps |
| 331 |
+ |
|
| 332 |
+ |
2005-03-21 17:34 chrisfen |
| 333 |
+ |
|
| 334 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
| 335 |
+ |
forcefield files |
| 336 |
+ |
|
| 337 |
+ |
2005-03-21 15:51 chrisfen |
| 338 |
+ |
|
| 339 |
+ |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
| 340 |
+ |
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
| 341 |
+ |
data for reaction_field |
| 342 |
+ |
|
| 343 |
+ |
2005-03-21 15:50 chrisfen |
| 344 |
+ |
|
| 345 |
+ |
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
| 346 |
+ |
WILL CHANGE THIS BACK, RIGHT? |
| 347 |
+ |
|
| 348 |
+ |
2005-03-21 14:23 gezelter |
| 349 |
+ |
|
| 350 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
| 351 |
+ |
correct value |
| 352 |
+ |
|
| 353 |
+ |
2005-03-21 14:22 gezelter |
| 354 |
+ |
|
| 355 |
+ |
* make/Makefile.in: fixed an install-related bug. |
| 356 |
+ |
$(InstallCommand) had been set to $(InstallData) |
| 357 |
+ |
|
| 358 |
+ |
2005-03-15 09:21 gezelter |
| 359 |
+ |
|
| 360 |
+ |
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
| 361 |
+ |
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
| 362 |
+ |
|
| 363 |
+ |
2005-03-15 09:20 gezelter |
| 364 |
+ |
|
| 365 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
| 366 |
+ |
|
| 367 |
+ |
2005-03-13 02:39 gezelter |
| 368 |
+ |
|
| 369 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
| 370 |
+ |
charge-quadrupole interactions |
| 371 |
+ |
|
| 372 |
+ |
2005-03-12 14:12 chrisfen |
| 373 |
+ |
|
| 374 |
+ |
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
| 375 |
+ |
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
| 376 |
+ |
|
| 377 |
+ |
2005-03-12 14:05 chrisfen |
| 378 |
+ |
|
| 379 |
+ |
* samples/thermoIntegration/liquid/ssde.in, |
| 380 |
+ |
samples/thermoIntegration/liquid/ssde.md, |
| 381 |
+ |
samples/thermoIntegration/liquid/water.md, |
| 382 |
+ |
samples/thermoIntegration/solid/idealCrystal.in, |
| 383 |
+ |
samples/thermoIntegration/solid/ssde.in, |
| 384 |
+ |
samples/thermoIntegration/solid/ssde.md, |
| 385 |
+ |
samples/thermoIntegration/solid/ssde.zang0, |
| 386 |
+ |
samples/thermoIntegration/solid/water.md, |
| 387 |
+ |
samples/water/tip3p_ice/tp3.md, |
| 388 |
+ |
src/UseTheForce/DarkSide/sticky.F90, |
| 389 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: added some |
| 390 |
+ |
samples |
| 391 |
+ |
|
| 392 |
+ |
2005-03-11 12:50 tim |
| 393 |
+ |
|
| 394 |
+ |
* src/: brains/SimCreator.cpp, |
| 395 |
+ |
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
| 396 |
+ |
MultipoleAtomTypesSectionParser |
| 397 |
+ |
|
| 398 |
+ |
2005-03-11 10:55 tim |
| 399 |
+ |
|
| 400 |
+ |
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
| 401 |
+ |
excluded |
| 402 |
+ |
|
| 403 |
+ |
2005-03-11 10:53 gezelter |
| 404 |
+ |
|
| 405 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
| 406 |
+ |
quadrupoles |
| 407 |
+ |
|
| 408 |
+ |
2005-03-11 10:52 gezelter |
| 409 |
+ |
|
| 410 |
+ |
* forceFields/DUFF2.frc: quadrupoles for SSD models |
| 411 |
+ |
|
| 412 |
+ |
2005-03-11 10:00 tim |
| 413 |
+ |
|
| 414 |
+ |
* ChangeLog, doc/SelectionExpression.html, |
| 415 |
+ |
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
| 416 |
+ |
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
| 417 |
+ |
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
| 418 |
+ |
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
| 419 |
+ |
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
| 420 |
+ |
SelectionExpression.html |
| 421 |
+ |
|
| 422 |
+ |
2005-03-10 19:43 chrisfen |
| 423 |
+ |
|
| 424 |
+ |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
| 425 |
+ |
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
| 426 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
| 427 |
+ |
MPI restraints |
| 428 |
+ |
|
| 429 |
+ |
2005-03-10 18:56 tim |
| 430 |
+ |
|
| 431 |
+ |
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
| 432 |
+ |
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
| 433 |
+ |
and cutoff group |
| 434 |
+ |
|
| 435 |
+ |
2005-03-10 17:06 gezelter |
| 436 |
+ |
|
| 437 |
+ |
* src/types/MorseBondType.hpp: fixed a doxygen problem |
| 438 |
+ |
|
| 439 |
+ |
2005-03-10 16:51 gezelter |
| 440 |
+ |
|
| 441 |
+ |
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
| 442 |
+ |
the split dipole test cases |
| 443 |
+ |
|
| 444 |
+ |
2005-03-10 16:51 gezelter |
| 445 |
+ |
|
| 446 |
+ |
* doc/SelectionExpression.html: updated some documentation |
| 447 |
+ |
|
| 448 |
+ |
2005-03-10 15:40 gezelter |
| 449 |
+ |
|
| 450 |
+ |
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
| 451 |
+ |
Makefile: LinkedList removal project starts now |
| 452 |
+ |
|
| 453 |
+ |
2005-03-10 15:28 tim |
| 454 |
+ |
|
| 455 |
+ |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 456 |
+ |
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
| 457 |
+ |
using map to replace link list |
| 458 |
+ |
|
| 459 |
+ |
2005-03-10 14:11 tim |
| 460 |
+ |
|
| 461 |
+ |
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
| 462 |
+ |
case of split dipole |
| 463 |
+ |
|
| 464 |
+ |
2005-03-10 14:10 chrisfen |
| 465 |
+ |
|
| 466 |
+ |
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
| 467 |
+ |
src/io/RestWriter.cpp, |
| 468 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
| 469 |
+ |
builds... |
| 470 |
+ |
|
| 471 |
+ |
2005-03-10 13:44 tim |
| 472 |
+ |
|
| 473 |
+ |
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
| 474 |
+ |
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
| 475 |
+ |
adding test case for split dipole |
| 476 |
+ |
|
| 477 |
+ |
2005-03-10 12:54 gezelter |
| 478 |
+ |
|
| 479 |
+ |
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
| 480 |
+ |
support for split dipoles |
| 481 |
+ |
|
| 482 |
+ |
2005-03-10 11:27 chrisfen |
| 483 |
+ |
|
| 484 |
+ |
* samples/water/tip3p_ice/tp3.md, |
| 485 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
| 486 |
+ |
restraints |
| 487 |
+ |
|
| 488 |
+ |
2005-03-10 11:15 chrisfen |
| 489 |
+ |
|
| 490 |
+ |
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
| 491 |
+ |
src/UseTheForce/ForceFields.hpp, |
| 492 |
+ |
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
| 493 |
+ |
|
| 494 |
+ |
2005-03-10 11:14 tim |
| 495 |
+ |
|
| 496 |
+ |
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
| 497 |
+ |
src/io/MultipoleAtomTypesSectionParser.cpp, |
| 498 |
+ |
src/selection/SelectionEvaluator.cpp: minor change |
| 499 |
+ |
|
| 500 |
|
2005-03-10 10:10 chrisfen |
| 501 |
|
|
| 502 |
|
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
| 773 |
|
adding basic_teebuf which can operate on multiple stream |
| 774 |
|
simutaneously. |
| 775 |
|
|
| 776 |
+ |
2005-02-22 14:26 chrisfen |
| 777 |
+ |
|
| 778 |
+ |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
| 779 |
+ |
sample |
| 780 |
+ |
|
| 781 |
|
2005-02-22 13:56 tim |
| 782 |
|
|
| 783 |
|
* src/: UseTheForce/DarkSide/reactionField.F90, |
| 1983 |
|
|
| 1984 |
|
2005-01-11 10:52 tim |
| 1985 |
|
|
| 1986 |
< |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
| 1986 |
> |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
| 1987 |
|
on branch new_design. |
| 1988 |
|
|
| 1989 |
|
2005-01-11 10:52 tim |
| 1990 |
|
|
| 1991 |
< |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
| 1991 |
> |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
| 1992 |
> |
on branch new_design. |
| 1993 |
|
|
| 1994 |
|
2005-01-11 10:52 tim |
| 1995 |
|
|
| 1996 |
< |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
| 1492 |
< |
on branch new_design. |
| 1996 |
> |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
| 1997 |
|
|
| 1998 |
|
2005-01-11 10:47 tim |
| 1999 |
|
|
| 2061 |
|
|
| 2062 |
|
2005-01-07 16:50 tim |
| 2063 |
|
|
| 2064 |
+ |
* src/constraints/ZconstraintForceManager.cpp: file |
| 2065 |
+ |
ZconstraintForceManager.cpp was initially added on branch |
| 2066 |
+ |
new_design. |
| 2067 |
+ |
|
| 2068 |
+ |
2005-01-07 16:50 tim |
| 2069 |
+ |
|
| 2070 |
+ |
* src/constraints/ZconstraintForceManager.hpp: file |
| 2071 |
+ |
ZconstraintForceManager.hpp was initially added on branch |
| 2072 |
+ |
new_design. |
| 2073 |
+ |
|
| 2074 |
+ |
2005-01-07 16:50 tim |
| 2075 |
+ |
|
| 2076 |
|
* src/: applications/simpleBuilder/BaseLattice.hpp, |
| 2077 |
|
applications/simpleBuilder/Lattice.hpp, |
| 2078 |
|
applications/simpleBuilder/LatticeCreator.hpp, |
| 2090 |
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
| 2091 |
|
initially added on branch new_design. |
| 2092 |
|
|
| 1577 |
– |
2005-01-07 16:50 tim |
| 1578 |
– |
|
| 1579 |
– |
* src/constraints/ZconstraintForceManager.cpp: file |
| 1580 |
– |
ZconstraintForceManager.cpp was initially added on branch |
| 1581 |
– |
new_design. |
| 1582 |
– |
|
| 1583 |
– |
2005-01-07 16:50 tim |
| 1584 |
– |
|
| 1585 |
– |
* src/constraints/ZconstraintForceManager.hpp: file |
| 1586 |
– |
ZconstraintForceManager.hpp was initially added on branch |
| 1587 |
– |
new_design. |
| 1588 |
– |
|
| 2093 |
|
2005-01-06 17:31 tim |
| 2094 |
|
|
| 2095 |
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
| 2126 |
|
|
| 2127 |
|
2005-01-05 12:35 tim |
| 2128 |
|
|
| 2129 |
+ |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
| 2130 |
+ |
added on branch new_design. |
| 2131 |
+ |
|
| 2132 |
+ |
2005-01-05 12:35 tim |
| 2133 |
+ |
|
| 2134 |
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 2135 |
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
| 2136 |
|
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
| 2139 |
|
|
| 2140 |
|
2005-01-05 12:35 tim |
| 2141 |
|
|
| 2142 |
< |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
| 2143 |
< |
added on branch new_design. |
| 2142 |
> |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
| 2143 |
> |
was initially added on branch new_design. |
| 2144 |
|
|
| 2145 |
|
2005-01-05 12:35 tim |
| 2146 |
|
|
| 2147 |
< |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
| 2147 |
> |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
| 2148 |
|
was initially added on branch new_design. |
| 2149 |
|
|
| 2150 |
|
2005-01-05 12:35 tim |
| 2151 |
|
|
| 2152 |
< |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
| 2152 |
> |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
| 2153 |
|
was initially added on branch new_design. |
| 2154 |
|
|
| 2155 |
|
2005-01-05 12:35 tim |
| 2157 |
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
| 2158 |
|
added on branch new_design. |
| 2159 |
|
|
| 1651 |
– |
2005-01-05 12:35 tim |
| 1652 |
– |
|
| 1653 |
– |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
| 1654 |
– |
was initially added on branch new_design. |
| 1655 |
– |
|
| 2160 |
|
2005-01-04 17:18 tim |
| 2161 |
|
|
| 1658 |
– |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
| 1659 |
– |
initially added on branch new_design. |
| 1660 |
– |
|
| 1661 |
– |
2005-01-04 17:18 tim |
| 1662 |
– |
|
| 2162 |
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
| 2163 |
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
| 2164 |
|
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
| 2170 |
|
|
| 2171 |
|
2005-01-04 17:18 tim |
| 2172 |
|
|
| 2173 |
< |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 2174 |
< |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
| 1676 |
< |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
| 1677 |
< |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
| 2173 |
> |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
| 2174 |
> |
initially added on branch new_design. |
| 2175 |
|
|
| 2176 |
|
2005-01-04 17:18 tim |
| 2177 |
|
|
| 1681 |
– |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
| 1682 |
– |
was initially added on branch new_design. |
| 1683 |
– |
|
| 1684 |
– |
2005-01-04 17:18 tim |
| 1685 |
– |
|
| 2178 |
|
* src/minimizers/MinimizerParameterSet.cpp: file |
| 2179 |
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
| 2180 |
|
|
| 2185 |
|
|
| 2186 |
|
2005-01-04 17:18 tim |
| 2187 |
|
|
| 2188 |
+ |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
| 2189 |
+ |
was initially added on branch new_design. |
| 2190 |
+ |
|
| 2191 |
+ |
2005-01-04 17:18 tim |
| 2192 |
+ |
|
| 2193 |
+ |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
| 2194 |
+ |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
| 2195 |
+ |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
| 2196 |
+ |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
| 2197 |
+ |
|
| 2198 |
+ |
2005-01-04 17:18 tim |
| 2199 |
+ |
|
| 2200 |
|
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
| 2201 |
|
branch new_design. |
| 2202 |
|
|
| 2515 |
|
|
| 2516 |
|
2004-12-02 19:26 tim |
| 2517 |
|
|
| 2518 |
+ |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
| 2519 |
+ |
new_design. |
| 2520 |
+ |
|
| 2521 |
+ |
2004-12-02 19:26 tim |
| 2522 |
+ |
|
| 2523 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 2524 |
|
UseTheForce/ForceFieldCreator.cpp, |
| 2525 |
|
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
| 2528 |
|
io/SectionParserManager.hpp, utils/Makefile, |
| 2529 |
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
| 2530 |
|
bug in countTokens in StringTokenizer |
| 2022 |
– |
|
| 2023 |
– |
2004-12-02 19:26 tim |
| 2024 |
– |
|
| 2025 |
– |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
| 2026 |
– |
new_design. |
| 2531 |
|
|
| 2532 |
|
2004-12-02 19:06 tim |
| 2533 |
|
|
| 2536 |
|
2004-12-02 18:15 tim |
| 2537 |
|
|
| 2538 |
|
* forceFields/newDUFF.frc: new ForceField format |
| 2035 |
– |
|
| 2036 |
– |
2004-12-02 17:15 tim |
| 2037 |
– |
|
| 2038 |
– |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
| 2039 |
– |
was initially added on branch new_design. |
| 2040 |
– |
|
| 2041 |
– |
2004-12-02 17:15 tim |
| 2539 |
|
|
| 2043 |
– |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
| 2044 |
– |
was initially added on branch new_design. |
| 2045 |
– |
|
| 2540 |
|
2004-12-02 17:15 tim |
| 2541 |
|
|
| 2048 |
– |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
| 2049 |
– |
was initially added on branch new_design. |
| 2050 |
– |
|
| 2051 |
– |
2004-12-02 17:15 tim |
| 2052 |
– |
|
| 2542 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 2543 |
|
UseTheForce/ForceFieldCreator.cpp, |
| 2544 |
|
UseTheForce/ForceFieldCreator.hpp, |
| 2561 |
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
| 2562 |
|
was initially added on branch new_design. |
| 2563 |
|
|
| 2564 |
+ |
2004-12-02 17:15 tim |
| 2565 |
+ |
|
| 2566 |
+ |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
| 2567 |
+ |
was initially added on branch new_design. |
| 2568 |
+ |
|
| 2569 |
+ |
2004-12-02 17:15 tim |
| 2570 |
+ |
|
| 2571 |
+ |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
| 2572 |
+ |
was initially added on branch new_design. |
| 2573 |
+ |
|
| 2574 |
+ |
2004-12-02 17:15 tim |
| 2575 |
+ |
|
| 2576 |
+ |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
| 2577 |
+ |
was initially added on branch new_design. |
| 2578 |
+ |
|
| 2579 |
|
2004-12-02 11:53 tim |
| 2580 |
|
|
| 2581 |
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
| 2734 |
|
|
| 2735 |
|
2004-12-01 19:09 tim |
| 2736 |
|
|
| 2737 |
< |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
| 2738 |
< |
was initially added on branch new_design. |
| 2737 |
> |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
| 2738 |
> |
branch new_design. |
| 2739 |
|
|
| 2740 |
|
2004-12-01 19:09 tim |
| 2741 |
|
|
| 2742 |
+ |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
| 2743 |
+ |
branch new_design. |
| 2744 |
+ |
|
| 2745 |
+ |
2004-12-01 19:09 tim |
| 2746 |
+ |
|
| 2747 |
|
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
| 2748 |
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
| 2749 |
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
| 2753 |
|
integrators/VelocityVerletIntegrator.cpp, |
| 2754 |
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
| 2755 |
|
get built |
| 2247 |
– |
|
| 2248 |
– |
2004-12-01 19:09 tim |
| 2249 |
– |
|
| 2250 |
– |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
| 2251 |
– |
branch new_design. |
| 2756 |
|
|
| 2757 |
|
2004-12-01 19:09 tim |
| 2758 |
|
|
| 2759 |
< |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
| 2760 |
< |
branch new_design. |
| 2759 |
> |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
| 2760 |
> |
was initially added on branch new_design. |
| 2761 |
|
|
| 2762 |
|
2004-12-01 17:45 tim |
| 2763 |
|
|
| 2857 |
|
|
| 2858 |
|
2004-11-30 14:58 tim |
| 2859 |
|
|
| 2356 |
– |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
| 2357 |
– |
added on branch new_design. |
| 2358 |
– |
|
| 2359 |
– |
2004-11-30 14:58 tim |
| 2360 |
– |
|
| 2860 |
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
| 2861 |
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
| 2862 |
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
| 2866 |
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
| 2867 |
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
| 2868 |
|
|
| 2869 |
+ |
2004-11-30 14:58 tim |
| 2870 |
+ |
|
| 2871 |
+ |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
| 2872 |
+ |
added on branch new_design. |
| 2873 |
+ |
|
| 2874 |
|
2004-11-30 12:54 tim |
| 2875 |
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| 2876 |
|
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
| 2879 |
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|
| 2880 |
|
2004-11-30 00:03 tim |
| 2881 |
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|
| 2882 |
< |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
| 2883 |
< |
LocalndexManager.hpp to LocalIndexManager.hpp |
| 2882 |
> |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
| 2883 |
> |
initially added on branch new_design. |
| 2884 |
|
|
| 2885 |
|
2004-11-30 00:03 tim |
| 2886 |
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|
| 2887 |
< |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
| 2888 |
< |
initially added on branch new_design. |
| 2887 |
> |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
| 2888 |
> |
LocalndexManager.hpp to LocalIndexManager.hpp |
| 2889 |
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|
| 2890 |
|
2004-11-29 23:43 tim |
| 2891 |
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|
| 3010 |
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
| 3011 |
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
| 3012 |
|
files |
| 3013 |
+ |
|
| 3014 |
+ |
2004-11-25 15:18 tim |
| 3015 |
+ |
|
| 3016 |
+ |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
| 3017 |
+ |
initially added on branch new_design. |
| 3018 |
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|
| 3019 |
|
2004-11-25 15:18 tim |
| 3020 |
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| 3030 |
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
| 3031 |
|
initially added on branch new_design. |
| 3032 |
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|
| 2524 |
– |
2004-11-25 15:18 tim |
| 2525 |
– |
|
| 2526 |
– |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
| 2527 |
– |
initially added on branch new_design. |
| 2528 |
– |
|
| 3033 |
|
2004-11-24 17:12 tim |
| 3034 |
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|
| 3035 |
|
* src/: io/AtomTypesSectionParser.cpp, |
| 3142 |
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|
| 3143 |
|
2004-11-23 12:53 tim |
| 3144 |
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|
| 2641 |
– |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
| 2642 |
– |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
| 2643 |
– |
branch new_design. |
| 2644 |
– |
|
| 2645 |
– |
2004-11-23 12:53 tim |
| 2646 |
– |
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| 3145 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3146 |
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 3147 |
|
applications/simpleBuilder/simpleBuilder.cpp, |
| 3159 |
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
| 3160 |
|
branch new_design. |
| 3161 |
|
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| 3162 |
< |
2004-11-23 01:03 tim |
| 3162 |
> |
2004-11-23 12:53 tim |
| 3163 |
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|
| 3164 |
< |
* src/io/EAMAtomTypesSectionParser.cpp: file |
| 3165 |
< |
EAMAtomTypesSectionParser.cpp was initially added on branch |
| 3166 |
< |
new_design. |
| 3164 |
> |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
| 3165 |
> |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
| 3166 |
> |
branch new_design. |
| 3167 |
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| 3168 |
|
2004-11-23 01:03 tim |
| 3169 |
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| 3174 |
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| 3175 |
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2004-11-23 01:03 tim |
| 3176 |
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| 3177 |
+ |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
| 3178 |
+ |
was initially added on branch new_design. |
| 3179 |
+ |
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| 3180 |
+ |
2004-11-23 01:03 tim |
| 3181 |
+ |
|
| 3182 |
|
* src/io/EAMAtomTypesSectionParser.hpp: file |
| 3183 |
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
| 3184 |
|
new_design. |
| 3185 |
|
|
| 3186 |
|
2004-11-23 01:03 tim |
| 3187 |
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|
| 3188 |
< |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
| 3189 |
< |
was initially added on branch new_design. |
| 3188 |
> |
* src/io/EAMAtomTypesSectionParser.cpp: file |
| 3189 |
> |
EAMAtomTypesSectionParser.cpp was initially added on branch |
| 3190 |
> |
new_design. |
| 3191 |
|
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| 3192 |
|
2004-11-22 23:35 tim |
| 3193 |
|
|
| 3194 |
< |
* src/io/TorsionTypesSectionParser.cpp: file |
| 3195 |
< |
TorsionTypesSectionParser.cpp was initially added on branch |
| 3194 |
> |
* src/io/TorsionTypesSectionParser.hpp: file |
| 3195 |
> |
TorsionTypesSectionParser.hpp was initially added on branch |
| 3196 |
|
new_design. |
| 3197 |
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| 3198 |
|
2004-11-22 23:35 tim |
| 3203 |
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|
| 3204 |
|
2004-11-22 23:35 tim |
| 3205 |
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|
| 2702 |
– |
* src/io/BondTypesSectionParser.cpp: file |
| 2703 |
– |
BondTypesSectionParser.cpp was initially added on branch |
| 2704 |
– |
new_design. |
| 2705 |
– |
|
| 2706 |
– |
2004-11-22 23:35 tim |
| 2707 |
– |
|
| 3206 |
|
* src/io/BondTypesSectionParser.hpp: file |
| 3207 |
|
BondTypesSectionParser.hpp was initially added on branch |
| 3208 |
|
new_design. |
| 3209 |
|
|
| 3210 |
|
2004-11-22 23:35 tim |
| 3211 |
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|
| 3212 |
< |
* src/io/TorsionTypesSectionParser.hpp: file |
| 3213 |
< |
TorsionTypesSectionParser.hpp was initially added on branch |
| 3212 |
> |
* src/io/BondTypesSectionParser.cpp: file |
| 3213 |
> |
BondTypesSectionParser.cpp was initially added on branch |
| 3214 |
|
new_design. |
| 3215 |
|
|
| 3216 |
|
2004-11-22 23:35 tim |
| 3217 |
|
|
| 3218 |
< |
* src/io/BendTypesSectionParser.cpp: file |
| 3219 |
< |
BendTypesSectionParser.cpp was initially added on branch |
| 3218 |
> |
* src/io/TorsionTypesSectionParser.cpp: file |
| 3219 |
> |
TorsionTypesSectionParser.cpp was initially added on branch |
| 3220 |
|
new_design. |
| 3221 |
|
|
| 3222 |
|
2004-11-22 23:35 tim |
| 3227 |
|
BondTypesSectionParser, BendTypesSectionParser and |
| 3228 |
|
TorsionTypeSectionParser |
| 3229 |
|
|
| 3230 |
+ |
2004-11-22 23:35 tim |
| 3231 |
+ |
|
| 3232 |
+ |
* src/io/BendTypesSectionParser.cpp: file |
| 3233 |
+ |
BendTypesSectionParser.cpp was initially added on branch |
| 3234 |
+ |
new_design. |
| 3235 |
+ |
|
| 3236 |
|
2004-11-22 18:04 tim |
| 3237 |
|
|
| 3238 |
|
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
| 3240 |
|
|
| 3241 |
|
2004-11-22 18:02 tim |
| 3242 |
|
|
| 3243 |
< |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
| 3244 |
< |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
| 2741 |
< |
new_design. |
| 3243 |
> |
* src/io/: DirectionalAtomTypesParser.hpp, |
| 3244 |
> |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
| 3245 |
|
|
| 3246 |
|
2004-11-22 18:02 tim |
| 3247 |
|
|
| 3248 |
< |
* src/io/: DirectionalAtomTypesParser.hpp, |
| 3249 |
< |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
| 3248 |
> |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
| 3249 |
> |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
| 3250 |
> |
new_design. |
| 3251 |
|
|
| 3252 |
|
2004-11-22 15:55 tim |
| 3253 |
|
|
| 3254 |
< |
* src/io/DirectionalAtomTypesParser.hpp: file |
| 3255 |
< |
DirectionalAtomTypesParser.hpp was initially added on branch |
| 3254 |
> |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
| 3255 |
> |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
| 3256 |
|
new_design. |
| 3257 |
|
|
| 3258 |
|
2004-11-22 15:55 tim |
| 3259 |
|
|
| 3260 |
< |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
| 3261 |
< |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
| 3260 |
> |
* src/io/AtomTypesSectionParser.hpp: file |
| 3261 |
> |
AtomTypesSectionParser.hpp was initially added on branch |
| 3262 |
|
new_design. |
| 3263 |
|
|
| 3264 |
|
2004-11-22 15:55 tim |
| 3265 |
|
|
| 3266 |
< |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
| 3267 |
< |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
| 3266 |
> |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
| 3267 |
> |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
| 3268 |
|
new_design. |
| 3269 |
|
|
| 3270 |
|
2004-11-22 15:55 tim |
| 3271 |
|
|
| 3272 |
< |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
| 3273 |
< |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
| 3272 |
> |
* src/io/StickyAtomTypesSectionParser.cpp: file |
| 3273 |
> |
StickyAtomTypesSectionParser.cpp was initially added on branch |
| 3274 |
|
new_design. |
| 3275 |
|
|
| 3276 |
|
2004-11-22 15:55 tim |
| 3277 |
|
|
| 3278 |
< |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
| 3279 |
< |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
| 3278 |
> |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
| 3279 |
> |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
| 3280 |
|
branch new_design. |
| 3281 |
|
|
| 3282 |
|
2004-11-22 15:55 tim |
| 3283 |
|
|
| 3284 |
< |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
| 3285 |
< |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
| 3284 |
> |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
| 3285 |
> |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
| 3286 |
|
new_design. |
| 3287 |
|
|
| 3288 |
|
2004-11-22 15:55 tim |
| 3289 |
|
|
| 3290 |
< |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 3291 |
< |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
| 2788 |
< |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 2789 |
< |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
| 2790 |
< |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 2791 |
< |
io/ChargeAtomTypesSectionParser.hpp, |
| 2792 |
< |
io/DipoleAtomTypesSectionParser.cpp, |
| 2793 |
< |
io/DipoleAtomTypesSectionParser.hpp, |
| 2794 |
< |
io/DirectionalAtomTypesParser.hpp, |
| 2795 |
< |
io/DirectionalAtomTypesSectionParser.cpp, |
| 2796 |
< |
io/HarmonicBondTypesSectionParser.cpp, |
| 2797 |
< |
io/HarmonicBondTypesSectionParser.hpp, |
| 2798 |
< |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 2799 |
< |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 2800 |
< |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 2801 |
< |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
| 2802 |
< |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
| 2803 |
< |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
| 2804 |
< |
utils/GenericData.hpp: adding section parsers |
| 2805 |
< |
|
| 2806 |
< |
2004-11-22 15:55 tim |
| 2807 |
< |
|
| 2808 |
< |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
| 2809 |
< |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
| 3290 |
> |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
| 3291 |
> |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
| 3292 |
|
new_design. |
| 3293 |
|
|
| 3294 |
|
2004-11-22 15:55 tim |
| 3295 |
|
|
| 3296 |
< |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
| 2815 |
< |
added on branch new_design. |
| 2816 |
< |
|
| 2817 |
< |
2004-11-22 15:55 tim |
| 2818 |
< |
|
| 2819 |
< |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
| 3296 |
> |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
| 3297 |
|
was initially added on branch new_design. |
| 3298 |
|
|
| 3299 |
|
2004-11-22 15:55 tim |
| 3304 |
|
|
| 3305 |
|
2004-11-22 15:55 tim |
| 3306 |
|
|
| 3307 |
< |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
| 3308 |
< |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
| 3309 |
< |
branch new_design. |
| 3307 |
> |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
| 3308 |
> |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
| 3309 |
> |
new_design. |
| 3310 |
|
|
| 3311 |
|
2004-11-22 15:55 tim |
| 3312 |
|
|
| 3313 |
< |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
| 3314 |
< |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
| 3313 |
> |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
| 3314 |
> |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
| 3315 |
|
new_design. |
| 3316 |
|
|
| 3317 |
|
2004-11-22 15:55 tim |
| 3318 |
|
|
| 3319 |
< |
* src/io/AtomTypesSectionParser.hpp: file |
| 3320 |
< |
AtomTypesSectionParser.hpp was initially added on branch |
| 3319 |
> |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
| 3320 |
> |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
| 3321 |
> |
branch new_design. |
| 3322 |
> |
|
| 3323 |
> |
2004-11-22 15:55 tim |
| 3324 |
> |
|
| 3325 |
> |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
| 3326 |
> |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
| 3327 |
|
new_design. |
| 3328 |
|
|
| 3329 |
|
2004-11-22 15:55 tim |
| 3330 |
|
|
| 3331 |
< |
* src/io/StickyAtomTypesSectionParser.cpp: file |
| 3332 |
< |
StickyAtomTypesSectionParser.cpp was initially added on branch |
| 3331 |
> |
* src/io/StickyAtomTypesSectionParser.hpp: file |
| 3332 |
> |
StickyAtomTypesSectionParser.hpp was initially added on branch |
| 3333 |
|
new_design. |
| 3334 |
|
|
| 3335 |
|
2004-11-22 15:55 tim |
| 3339 |
|
|
| 3340 |
|
2004-11-22 15:55 tim |
| 3341 |
|
|
| 3342 |
< |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
| 3343 |
< |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
| 3342 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
| 3343 |
> |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
| 3344 |
> |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
| 3345 |
> |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
| 3346 |
> |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
| 3347 |
> |
io/ChargeAtomTypesSectionParser.hpp, |
| 3348 |
> |
io/DipoleAtomTypesSectionParser.cpp, |
| 3349 |
> |
io/DipoleAtomTypesSectionParser.hpp, |
| 3350 |
> |
io/DirectionalAtomTypesParser.hpp, |
| 3351 |
> |
io/DirectionalAtomTypesSectionParser.cpp, |
| 3352 |
> |
io/HarmonicBondTypesSectionParser.cpp, |
| 3353 |
> |
io/HarmonicBondTypesSectionParser.hpp, |
| 3354 |
> |
io/LennardJonesAtomTypesSectionParser.cpp, |
| 3355 |
> |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
| 3356 |
> |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
| 3357 |
> |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
| 3358 |
> |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
| 3359 |
> |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
| 3360 |
> |
utils/GenericData.hpp: adding section parsers |
| 3361 |
> |
|
| 3362 |
> |
2004-11-22 15:55 tim |
| 3363 |
> |
|
| 3364 |
> |
* src/io/DirectionalAtomTypesParser.hpp: file |
| 3365 |
> |
DirectionalAtomTypesParser.hpp was initially added on branch |
| 3366 |
|
new_design. |
| 3367 |
|
|
| 3368 |
|
2004-11-22 15:55 tim |
| 3369 |
|
|
| 3370 |
< |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
| 3370 |
> |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
| 3371 |
|
was initially added on branch new_design. |
| 3372 |
|
|
| 3373 |
|
2004-11-22 15:55 tim |
| 3374 |
|
|
| 3375 |
< |
* src/io/StickyAtomTypesSectionParser.hpp: file |
| 3376 |
< |
StickyAtomTypesSectionParser.hpp was initially added on branch |
| 2872 |
< |
new_design. |
| 3375 |
> |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
| 3376 |
> |
added on branch new_design. |
| 3377 |
|
|
| 3378 |
|
2004-11-19 17:12 tim |
| 3379 |
|
|
| 3380 |
+ |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
| 3381 |
+ |
added on branch new_design. |
| 3382 |
+ |
|
| 3383 |
+ |
2004-11-19 17:12 tim |
| 3384 |
+ |
|
| 3385 |
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
| 3386 |
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
| 3387 |
|
types/FixedBondType.hpp: remove more useless files |
| 3388 |
|
|
| 2880 |
– |
2004-11-19 17:12 tim |
| 2881 |
– |
|
| 2882 |
– |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
| 2883 |
– |
added on branch new_design. |
| 2884 |
– |
|
| 3389 |
|
2004-11-19 16:47 tim |
| 3390 |
|
|
| 3391 |
|
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
| 3394 |
|
|
| 3395 |
|
2004-11-19 16:38 tim |
| 3396 |
|
|
| 3397 |
< |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
| 3398 |
< |
branch new_design. |
| 3397 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3398 |
> |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
| 3399 |
> |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
| 3400 |
> |
integrators/NVT.hpp: refactory integrator |
| 3401 |
|
|
| 3402 |
|
2004-11-19 16:38 tim |
| 3403 |
|
|
| 3404 |
< |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
| 3405 |
< |
on branch new_design. |
| 3404 |
> |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
| 3405 |
> |
branch new_design. |
| 3406 |
|
|
| 3407 |
|
2004-11-19 16:38 tim |
| 3408 |
|
|
| 3409 |
< |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
| 3409 |
> |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
| 3410 |
|
branch new_design. |
| 3411 |
|
|
| 3412 |
|
2004-11-19 16:38 tim |
| 3413 |
|
|
| 3414 |
< |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
| 3414 |
> |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
| 3415 |
|
branch new_design. |
| 3416 |
|
|
| 3417 |
|
2004-11-19 16:38 tim |
| 3418 |
|
|
| 3419 |
< |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
| 3420 |
< |
branch new_design. |
| 3419 |
> |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
| 3420 |
> |
on branch new_design. |
| 3421 |
|
|
| 3422 |
|
2004-11-19 16:38 tim |
| 3423 |
|
|
| 3424 |
< |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3425 |
< |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
| 2920 |
< |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
| 2921 |
< |
integrators/NVT.hpp: refactory integrator |
| 3424 |
> |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
| 3425 |
> |
branch new_design. |
| 3426 |
|
|
| 3427 |
|
2004-11-19 15:37 tim |
| 3428 |
|
|
| 3430 |
|
|
| 3431 |
|
2004-11-19 15:23 tim |
| 3432 |
|
|
| 3433 |
+ |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
| 3434 |
+ |
branch new_design. |
| 3435 |
+ |
|
| 3436 |
+ |
2004-11-19 15:23 tim |
| 3437 |
+ |
|
| 3438 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
| 3439 |
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
| 3440 |
|
utils/TypeContainer.hpp: add EAM |
| 3444 |
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
| 3445 |
|
branch new_design. |
| 3446 |
|
|
| 2938 |
– |
2004-11-19 15:23 tim |
| 2939 |
– |
|
| 2940 |
– |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
| 2941 |
– |
branch new_design. |
| 2942 |
– |
|
| 3447 |
|
2004-11-19 13:02 tim |
| 3448 |
|
|
| 3449 |
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
| 3451 |
|
|
| 3452 |
|
2004-11-19 12:56 tim |
| 3453 |
|
|
| 3454 |
< |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
| 3454 |
> |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
| 3455 |
|
was initially added on branch new_design. |
| 3456 |
|
|
| 3457 |
|
2004-11-19 12:56 tim |
| 3458 |
|
|
| 3459 |
< |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
| 3459 |
> |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
| 3460 |
|
was initially added on branch new_design. |
| 3461 |
|
|
| 3462 |
|
2004-11-19 12:56 tim |
| 3481 |
|
|
| 3482 |
|
2004-11-18 18:26 tim |
| 3483 |
|
|
| 3484 |
+ |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
| 3485 |
+ |
initially added on branch new_design. |
| 3486 |
+ |
|
| 3487 |
+ |
2004-11-18 18:26 tim |
| 3488 |
+ |
|
| 3489 |
|
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
| 3490 |
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
| 3491 |
|
integrators/VelocityVerletIntegrator.cpp, |
| 3496 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
| 3497 |
|
DUFF parser |
| 3498 |
|
|
| 2990 |
– |
2004-11-18 18:26 tim |
| 2991 |
– |
|
| 2992 |
– |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
| 2993 |
– |
initially added on branch new_design. |
| 2994 |
– |
|
| 3499 |
|
2004-11-18 16:42 tim |
| 3500 |
|
|
| 3501 |
|
* forceFields/newDUFF.frc: adding new format DUFF force field |
| 3507 |
|
|
| 3508 |
|
2004-11-18 00:42 tim |
| 3509 |
|
|
| 3510 |
< |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
| 3510 |
> |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
| 3511 |
|
initially added on branch new_design. |
| 3512 |
|
|
| 3513 |
|
2004-11-18 00:42 tim |
| 3514 |
|
|
| 3515 |
< |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
| 3515 |
> |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
| 3516 |
|
initially added on branch new_design. |
| 3517 |
|
|
| 3518 |
|
2004-11-18 00:42 tim |
| 3555 |
|
|
| 3556 |
|
2004-11-17 16:47 tim |
| 3557 |
|
|
| 3558 |
+ |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
| 3559 |
+ |
was initially added on branch new_design. |
| 3560 |
+ |
|
| 3561 |
+ |
2004-11-17 16:47 tim |
| 3562 |
+ |
|
| 3563 |
|
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
| 3564 |
|
added on branch new_design. |
| 3565 |
|
|
| 3566 |
|
2004-11-17 16:47 tim |
| 3567 |
|
|
| 3568 |
+ |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
| 3569 |
+ |
added on branch new_design. |
| 3570 |
+ |
|
| 3571 |
+ |
2004-11-17 16:47 tim |
| 3572 |
+ |
|
| 3573 |
|
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
| 3574 |
|
initially added on branch new_design. |
| 3575 |
|
|
| 3576 |
|
2004-11-17 16:47 tim |
| 3577 |
|
|
| 3578 |
< |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
| 3578 |
> |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
| 3579 |
|
initially added on branch new_design. |
| 3580 |
|
|
| 3581 |
|
2004-11-17 16:47 tim |
| 3582 |
|
|
| 3583 |
< |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
| 3583 |
> |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
| 3584 |
|
initially added on branch new_design. |
| 3585 |
|
|
| 3586 |
|
2004-11-17 16:47 tim |
| 3600 |
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
| 3601 |
|
UreyBradleyBend and GhostBend |
| 3602 |
|
|
| 3089 |
– |
2004-11-17 16:47 tim |
| 3090 |
– |
|
| 3091 |
– |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
| 3092 |
– |
added on branch new_design. |
| 3093 |
– |
|
| 3094 |
– |
2004-11-17 16:47 tim |
| 3095 |
– |
|
| 3096 |
– |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
| 3097 |
– |
was initially added on branch new_design. |
| 3098 |
– |
|
| 3603 |
|
2004-11-17 13:58 tim |
| 3604 |
|
|
| 3605 |
|
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
| 3607 |
|
|
| 3608 |
|
2004-11-17 13:58 tim |
| 3609 |
|
|
| 3106 |
– |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
| 3107 |
– |
initially added on branch new_design. |
| 3108 |
– |
|
| 3109 |
– |
2004-11-17 13:58 tim |
| 3110 |
– |
|
| 3610 |
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
| 3611 |
|
was initially added on branch new_design. |
| 3612 |
|
|
| 3619 |
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
| 3620 |
|
stuff and Chebyshev Polynomial |
| 3621 |
|
|
| 3622 |
< |
2004-11-17 01:37 tim |
| 3622 |
> |
2004-11-17 13:58 tim |
| 3623 |
|
|
| 3624 |
< |
* src/types/PolynomialTorsionType.hpp: file |
| 3126 |
< |
PolynomialTorsionType.hpp was initially added on branch new_design. |
| 3127 |
< |
|
| 3128 |
< |
2004-11-17 01:37 tim |
| 3129 |
< |
|
| 3130 |
< |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
| 3624 |
> |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
| 3625 |
|
initially added on branch new_design. |
| 3626 |
|
|
| 3627 |
|
2004-11-17 01:37 tim |
| 3628 |
|
|
| 3629 |
< |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
| 3630 |
< |
initially added on branch new_design. |
| 3629 |
> |
* src/types/PolynomialTorsionType.hpp: file |
| 3630 |
> |
PolynomialTorsionType.hpp was initially added on branch new_design. |
| 3631 |
|
|
| 3632 |
|
2004-11-17 01:37 tim |
| 3633 |
|
|
| 3636 |
|
|
| 3637 |
|
2004-11-17 01:37 tim |
| 3638 |
|
|
| 3145 |
– |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
| 3146 |
– |
initially added on branch new_design. |
| 3147 |
– |
|
| 3148 |
– |
2004-11-17 01:37 tim |
| 3149 |
– |
|
| 3639 |
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
| 3640 |
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
| 3641 |
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
| 3648 |
|
CharmmTorsionType. Need to refine the design and add document for |
| 3649 |
|
them |
| 3650 |
|
|
| 3651 |
+ |
2004-11-17 01:37 tim |
| 3652 |
+ |
|
| 3653 |
+ |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
| 3654 |
+ |
initially added on branch new_design. |
| 3655 |
+ |
|
| 3656 |
+ |
2004-11-17 01:37 tim |
| 3657 |
+ |
|
| 3658 |
+ |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
| 3659 |
+ |
initially added on branch new_design. |
| 3660 |
+ |
|
| 3661 |
+ |
2004-11-17 01:37 tim |
| 3662 |
+ |
|
| 3663 |
+ |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
| 3664 |
+ |
initially added on branch new_design. |
| 3665 |
+ |
|
| 3666 |
|
2004-11-16 20:11 tim |
| 3667 |
|
|
| 3668 |
|
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
| 3675 |
|
|
| 3676 |
|
2004-11-16 18:20 tim |
| 3677 |
|
|
| 3174 |
– |
* src/math/Polynomial.hpp: Adding Polynomial class |
| 3175 |
– |
|
| 3176 |
– |
2004-11-16 18:20 tim |
| 3177 |
– |
|
| 3678 |
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
| 3679 |
|
on branch new_design. |
| 3680 |
|
|
| 3681 |
< |
2004-11-16 17:04 gezelter |
| 3681 |
> |
2004-11-16 18:20 tim |
| 3682 |
|
|
| 3683 |
< |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
| 3184 |
< |
initially added on branch new_design. |
| 3683 |
> |
* src/math/Polynomial.hpp: Adding Polynomial class |
| 3684 |
|
|
| 3685 |
|
2004-11-16 17:04 gezelter |
| 3686 |
|
|
| 3689 |
|
|
| 3690 |
|
2004-11-16 17:04 gezelter |
| 3691 |
|
|
| 3692 |
+ |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
| 3693 |
+ |
initially added on branch new_design. |
| 3694 |
+ |
|
| 3695 |
+ |
2004-11-16 17:04 gezelter |
| 3696 |
+ |
|
| 3697 |
|
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
| 3698 |
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
| 3699 |
|
|
| 3706 |
|
|
| 3707 |
|
2004-11-15 21:07 tim |
| 3708 |
|
|
| 3709 |
+ |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
| 3710 |
+ |
branch new_design. |
| 3711 |
+ |
|
| 3712 |
+ |
2004-11-15 21:07 tim |
| 3713 |
+ |
|
| 3714 |
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
| 3715 |
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
| 3716 |
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
| 3717 |
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
| 3718 |
|
|
| 3719 |
< |
2004-11-15 21:07 tim |
| 3719 |
> |
2004-11-15 18:00 tim |
| 3720 |
|
|
| 3721 |
< |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
| 3722 |
< |
branch new_design. |
| 3721 |
> |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 3722 |
> |
UseTheForce/ForceFieldFactory.cpp, |
| 3723 |
> |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
| 3724 |
> |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
| 3725 |
> |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
| 3726 |
|
|
| 3727 |
|
2004-11-15 18:00 tim |
| 3728 |
|
|
| 3731 |
|
|
| 3732 |
|
2004-11-15 18:00 tim |
| 3733 |
|
|
| 3734 |
< |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
| 3735 |
< |
branch new_design. |
| 3734 |
> |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
| 3735 |
> |
was initially added on branch new_design. |
| 3736 |
|
|
| 3737 |
|
2004-11-15 18:00 tim |
| 3738 |
|
|
| 3739 |
< |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
| 3740 |
< |
UseTheForce/ForceFieldFactory.cpp, |
| 3229 |
< |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
| 3230 |
< |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
| 3231 |
< |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
| 3739 |
> |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
| 3740 |
> |
branch new_design. |
| 3741 |
|
|
| 3742 |
< |
2004-11-15 18:00 tim |
| 3742 |
> |
2004-11-15 13:02 tim |
| 3743 |
|
|
| 3744 |
< |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
| 3745 |
< |
was initially added on branch new_design. |
| 3744 |
> |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
| 3745 |
> |
initially added on branch new_design. |
| 3746 |
|
|
| 3747 |
|
2004-11-15 13:02 tim |
| 3748 |
|
|
| 3756 |
|
|
| 3757 |
|
2004-11-15 13:02 tim |
| 3758 |
|
|
| 3250 |
– |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
| 3251 |
– |
initially added on branch new_design. |
| 3252 |
– |
|
| 3253 |
– |
2004-11-15 13:02 tim |
| 3254 |
– |
|
| 3759 |
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3760 |
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
| 3761 |
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
| 3879 |
|
|
| 3880 |
|
2004-11-09 18:11 tim |
| 3881 |
|
|
| 3882 |
+ |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
| 3883 |
+ |
added on branch new_design. |
| 3884 |
+ |
|
| 3885 |
+ |
2004-11-09 18:11 tim |
| 3886 |
+ |
|
| 3887 |
+ |
* src/integrators/VelocityVerletIntegrator.cpp: file |
| 3888 |
+ |
VelocityVerletIntegrator.cpp was initially added on branch |
| 3889 |
+ |
new_design. |
| 3890 |
+ |
|
| 3891 |
+ |
2004-11-09 18:11 tim |
| 3892 |
+ |
|
| 3893 |
|
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
| 3894 |
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 3895 |
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
| 3904 |
|
|
| 3905 |
|
2004-11-09 18:11 tim |
| 3906 |
|
|
| 3392 |
– |
* src/integrators/VelocityVerletIntegrator.cpp: file |
| 3393 |
– |
VelocityVerletIntegrator.cpp was initially added on branch |
| 3394 |
– |
new_design. |
| 3395 |
– |
|
| 3396 |
– |
2004-11-09 18:11 tim |
| 3397 |
– |
|
| 3907 |
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
| 3908 |
|
branch new_design. |
| 3909 |
|
|
| 3401 |
– |
2004-11-09 18:11 tim |
| 3402 |
– |
|
| 3403 |
– |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
| 3404 |
– |
added on branch new_design. |
| 3405 |
– |
|
| 3910 |
|
2004-11-08 20:08 tim |
| 3911 |
|
|
| 3912 |
|
* src/integrators/VelocityVerletIntegrator.hpp: file |
| 3915 |
|
|
| 3916 |
|
2004-11-08 20:08 tim |
| 3917 |
|
|
| 3918 |
+ |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
| 3919 |
+ |
branch new_design. |
| 3920 |
+ |
|
| 3921 |
+ |
2004-11-08 20:08 tim |
| 3922 |
+ |
|
| 3923 |
|
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
| 3924 |
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
| 3925 |
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
| 3926 |
|
utils/TypeContainer.hpp: More to break |
| 3927 |
|
|
| 3419 |
– |
2004-11-08 20:08 tim |
| 3420 |
– |
|
| 3421 |
– |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
| 3422 |
– |
branch new_design. |
| 3423 |
– |
|
| 3928 |
|
2004-11-06 00:21 tim |
| 3929 |
|
|
| 3930 |
|
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
| 3939 |
|
|
| 3940 |
|
2004-11-05 18:38 tim |
| 3941 |
|
|
| 3942 |
+ |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
| 3943 |
+ |
initially added on branch new_design. |
| 3944 |
+ |
|
| 3945 |
+ |
2004-11-05 18:38 tim |
| 3946 |
+ |
|
| 3947 |
|
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
| 3948 |
|
initially added on branch new_design. |
| 3949 |
|
|
| 3955 |
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
| 3956 |
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
| 3957 |
|
|
| 3449 |
– |
2004-11-05 18:38 tim |
| 3450 |
– |
|
| 3451 |
– |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
| 3452 |
– |
initially added on branch new_design. |
| 3453 |
– |
|
| 3958 |
|
2004-11-05 16:45 chrisfen |
| 3959 |
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|
| 3960 |
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* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
| 3992 |
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|
| 3993 |
|
2004-11-04 14:48 tim |
| 3994 |
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|
| 3491 |
– |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 3492 |
– |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 3493 |
– |
class |
| 3494 |
– |
|
| 3495 |
– |
2004-11-04 14:48 tim |
| 3496 |
– |
|
| 3995 |
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
| 3996 |
|
branch new_design. |
| 3997 |
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|
| 4000 |
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* src/brains/Stats.hpp: file Stats.hpp was initially added on |
| 4001 |
|
branch new_design. |
| 4002 |
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|
| 4003 |
+ |
2004-11-04 14:48 tim |
| 4004 |
+ |
|
| 4005 |
+ |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
| 4006 |
+ |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
| 4007 |
+ |
class |
| 4008 |
+ |
|
| 4009 |
|
2004-11-04 11:22 gezelter |
| 4010 |
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|
| 4011 |
|
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 4080 |
|
|
| 4081 |
|
2004-11-02 17:41 tim |
| 4082 |
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|
| 4083 |
< |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
| 4084 |
< |
branch new_design. |
| 4083 |
> |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 4084 |
> |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 4085 |
> |
Need unit test |
| 4086 |
|
|
| 4087 |
|
2004-11-02 17:41 tim |
| 4088 |
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|
| 4091 |
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|
| 4092 |
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2004-11-02 17:41 tim |
| 4093 |
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|
| 4094 |
< |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
| 4095 |
< |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
| 3591 |
< |
Need unit test |
| 4094 |
> |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
| 4095 |
> |
branch new_design. |
| 4096 |
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|
| 4097 |
|
2004-11-02 11:59 tim |
| 4098 |
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|
| 4099 |
< |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 4100 |
< |
SimSnapshotManager.hpp: SimModel in progress |
| 4099 |
> |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 4100 |
> |
branch new_design. |
| 4101 |
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|
| 4102 |
|
2004-11-02 11:59 tim |
| 4103 |
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|
| 4104 |
< |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
| 4105 |
< |
branch new_design. |
| 4104 |
> |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
| 4105 |
> |
SimSnapshotManager.hpp: SimModel in progress |
| 4106 |
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|
| 4107 |
|
2004-11-02 10:28 chrisfen |
| 4108 |
|
|
| 4112 |
|
|
| 4113 |
|
2004-11-02 10:27 tim |
| 4114 |
|
|
| 4115 |
< |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 4116 |
< |
added on branch new_design. |
| 4115 |
> |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 4116 |
> |
functions for dealing with memory issue |
| 4117 |
|
|
| 4118 |
|
2004-11-02 10:27 tim |
| 4119 |
|
|
| 4120 |
< |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
| 4121 |
< |
functions for dealing with memory issue |
| 4120 |
> |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
| 4121 |
> |
added on branch new_design. |
| 4122 |
|
|
| 4123 |
|
2004-11-02 10:23 tim |
| 4124 |
|
|
| 4147 |
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|
| 4148 |
|
2004-11-01 16:40 tim |
| 4149 |
|
|
| 4150 |
< |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 4151 |
< |
branch new_design. |
| 4150 |
> |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 4151 |
> |
on branch new_design. |
| 4152 |
|
|
| 4153 |
|
2004-11-01 16:40 tim |
| 4154 |
|
|
| 4155 |
< |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 4156 |
< |
version of Bond, Bend and Torsion. |
| 4155 |
> |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
| 4156 |
> |
branch new_design. |
| 4157 |
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|
| 4158 |
|
2004-11-01 16:40 tim |
| 4159 |
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|
| 4162 |
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|
| 4163 |
|
2004-11-01 16:40 tim |
| 4164 |
|
|
| 4165 |
< |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
| 4166 |
< |
on branch new_design. |
| 4165 |
> |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
| 4166 |
> |
version of Bond, Bend and Torsion. |
| 4167 |
|
|
| 4168 |
|
2004-11-01 16:37 tim |
| 4169 |
|
|
| 4172 |
|
|
| 4173 |
|
2004-11-01 16:37 tim |
| 4174 |
|
|
| 4175 |
< |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 4176 |
< |
branch new_design. |
| 4175 |
> |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 4176 |
> |
BondType, BendType, TorsionType |
| 4177 |
|
|
| 4178 |
|
2004-11-01 16:37 tim |
| 4179 |
|
|
| 4182 |
|
|
| 4183 |
|
2004-11-01 16:37 tim |
| 4184 |
|
|
| 4185 |
< |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
| 4186 |
< |
BondType, BendType, TorsionType |
| 4185 |
> |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
| 4186 |
> |
branch new_design. |
| 4187 |
|
|
| 4188 |
|
2004-11-01 15:15 tim |
| 4189 |
|
|
| 5015 |
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 5016 |
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 5017 |
|
directory |
| 5018 |
+ |
|
| 5019 |
+ |
2004-10-11 09:23 tim |
| 5020 |
+ |
|
| 5021 |
+ |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 5022 |
+ |
Makefile |
| 5023 |
|
|
| 5024 |
|
2004-10-09 01:01 tim |
| 5025 |
|
|
| 5026 |
< |
* samples/: alkane/Makefile.in, lipid/Makefile.in, |
| 5027 |
< |
metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in |
| 5026 |
> |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 5027 |
> |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 5028 |
> |
Remove some Makefile.in |
| 5029 |
|
|
| 5030 |
|
2004-10-08 18:15 tim |
| 5031 |
|
|
| 5041 |
|
|
| 5042 |
|
2004-10-08 17:04 tim |
| 5043 |
|
|
| 5044 |
< |
* samples/: alkane/Makefile, lipid/Makefile, metals/Makefile, |
| 5045 |
< |
minimizer/Makefile, water/Makefile.in, water/dimer/Makefile, |
| 5046 |
< |
water/dimer/Makefile.in, water/spce/Makefile, |
| 5044 |
> |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 5045 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 5046 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 5047 |
|
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 5048 |
|
water/ssde/Makefile, water/ssde/Makefile.in, |
| 5049 |
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 5206 |
|
|
| 5207 |
|
2004-09-29 12:56 gezelter |
| 5208 |
|
|
| 5209 |
< |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
| 4700 |
< |
make stuff |
| 5209 |
> |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 5210 |
|
|
| 5211 |
|
2004-09-29 12:46 tim |
| 5212 |
|
|
| 5472 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 5473 |
|
src/visitors/RigidBodyVisitor.cpp, |
| 5474 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 5475 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 4967 |
< |
make/_files/style.css, samples/Makefile.in, |
| 5475 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 5476 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 5477 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 5478 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 5520 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 5521 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 5522 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 5523 |
+ |
samples/argon/500.in, samples/argon/500.md, |
| 5524 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 5525 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 5526 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 5527 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 5528 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 5529 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 5647 |
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 5648 |
|
src/visitors/RigidBodyVisitor.cpp, |
| 5649 |
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 5650 |
< |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
| 5139 |
< |
make/_files/style.css, samples/Makefile.in, |
| 5650 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 5651 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 5652 |
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 5653 |
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 5695 |
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 5696 |
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 5697 |
|
samples/alkane/butane.in, samples/alkane/butane.md, |
| 5698 |
+ |
samples/argon/500.in, samples/argon/500.md, |
| 5699 |
+ |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 5700 |
+ |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 5701 |
+ |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 5702 |
|
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 5703 |
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 5704 |
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
