| 1 |
2004-06-09 11:16 tim |
| 2 |
|
| 3 |
* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
| 4 |
Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
| 5 |
Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
| 6 |
Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
| 7 |
Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
| 8 |
adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
| 9 |
Euler3) these classes use anonymous union and struct to support |
| 10 |
double[3], double[3][3] and double[4] 2. adding roll constraint |
| 11 |
algorithm |
| 12 |
|
| 13 |
2004-06-08 11:49 gezelter |
| 14 |
|
| 15 |
* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
| 16 |
Fixed a bug in NPTf (vScale was declared in the cpp file in |
| 17 |
addition to the declaration in Integrator.hpp file) |
| 18 |
|
| 19 |
2004-06-07 09:26 gezelter |
| 20 |
|
| 21 |
* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
| 22 |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
| 23 |
libmdtools/ConstraintIterator.hpp, |
| 24 |
libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
| 25 |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
| 26 |
libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
| 27 |
libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
| 28 |
libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
| 29 |
|
| 30 |
2004-06-07 09:09 chrisfen |
| 31 |
|
| 32 |
* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
| 33 |
bit... Got rid of some unnecessary lines of code in Thermo.cpp |
| 34 |
|
| 35 |
2004-06-04 16:00 gezelter |
| 36 |
|
| 37 |
* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
| 38 |
StuntDouble.cpp: small bugfixes |
| 39 |
|
| 40 |
2004-06-04 15:29 tim |
| 41 |
|
| 42 |
* libmdtools/Integrator.hpp: [no log message] |
| 43 |
|
| 44 |
2004-06-04 14:30 tim |
| 45 |
|
| 46 |
* ChangeLog, libmdtools/CallbackFunctor.cpp, |
| 47 |
libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
| 48 |
libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
| 49 |
libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
| 50 |
libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
| 51 |
libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
| 52 |
working |
| 53 |
|
| 54 |
2004-06-04 11:23 gezelter |
| 55 |
|
| 56 |
* forceFields/charmm27.vdw: Moved to SHAPES |
| 57 |
|
| 58 |
2004-06-04 11:23 gezelter |
| 59 |
|
| 60 |
* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
| 61 |
message] |
| 62 |
|
| 63 |
2004-06-04 09:59 gezelter |
| 64 |
|
| 65 |
* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
| 66 |
More work on Fortran side of error handler |
| 67 |
|
| 68 |
2004-06-04 09:59 gezelter |
| 69 |
|
| 70 |
* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
| 71 |
|
| 72 |
2004-06-04 09:35 gezelter |
| 73 |
|
| 74 |
* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
| 75 |
the error handlers |
| 76 |
|
| 77 |
2004-06-04 09:17 gezelter |
| 78 |
|
| 79 |
* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
| 80 |
|
| 81 |
2004-06-04 09:11 gezelter |
| 82 |
|
| 83 |
* libBASS/: config.h.in, fError.c: forgot to add these |
| 84 |
|
| 85 |
2004-06-03 22:15 tim |
| 86 |
|
| 87 |
* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 88 |
libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
| 89 |
libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
| 90 |
libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
| 91 |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
| 92 |
libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
| 93 |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
| 94 |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
| 95 |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 96 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 97 |
libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
| 98 |
libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
| 99 |
is working |
| 100 |
|
| 101 |
2004-06-03 21:38 gezelter |
| 102 |
|
| 103 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 104 |
libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
| 105 |
libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
| 106 |
libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
| 107 |
fortran access to SimError |
| 108 |
|
| 109 |
2004-06-03 16:51 tim |
| 110 |
|
| 111 |
* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
| 112 |
ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
| 113 |
ConstraintElement.cpp, ConstraintElement.hpp, |
| 114 |
ConstraintIterator.hpp, ConstraintManager.cpp, |
| 115 |
ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
| 116 |
Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
| 117 |
implementation of constraint |
| 118 |
|
| 119 |
2004-06-03 16:06 tim |
| 120 |
|
| 121 |
* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
| 122 |
first atom of a molecule |
| 123 |
|
| 124 |
2004-06-03 15:02 gezelter |
| 125 |
|
| 126 |
* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
| 127 |
|
| 128 |
2004-06-03 15:02 gezelter |
| 129 |
|
| 130 |
* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
| 131 |
autoconf |
| 132 |
|
| 133 |
2004-06-02 13:28 gezelter |
| 134 |
|
| 135 |
* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
| 136 |
have been in CVS |
| 137 |
|
| 138 |
2004-06-02 13:28 gezelter |
| 139 |
|
| 140 |
* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
| 141 |
in CVS? |
| 142 |
|
| 143 |
2004-06-02 13:27 gezelter |
| 144 |
|
| 145 |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
| 146 |
Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
| 147 |
|
| 148 |
2004-06-02 13:27 gezelter |
| 149 |
|
| 150 |
* libBASS/simError.h: starting fortran-usable version of simError |
| 151 |
|
| 152 |
2004-06-02 09:56 chrisfen |
| 153 |
|
| 154 |
* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
| 155 |
shouldn't be in CVS |
| 156 |
|
| 157 |
2004-06-02 09:56 chrisfen |
| 158 |
|
| 159 |
* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
| 160 |
Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
| 161 |
removed writeRaw |
| 162 |
|
| 163 |
2004-06-02 09:56 chrisfen |
| 164 |
|
| 165 |
* libBASS/simError.c: Formatting Changes |
| 166 |
|
| 167 |
2004-06-02 09:21 gezelter |
| 168 |
|
| 169 |
* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
| 170 |
severity levels in simError |
| 171 |
|
| 172 |
2004-06-01 16:45 gezelter |
| 173 |
|
| 174 |
* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
| 175 |
do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
| 176 |
simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
| 177 |
under MPI) |
| 178 |
|
| 179 |
2004-06-01 16:44 gezelter |
| 180 |
|
| 181 |
* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
| 182 |
|
| 183 |
2004-06-01 13:43 gezelter |
| 184 |
|
| 185 |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
| 186 |
|
| 187 |
2004-06-01 13:42 gezelter |
| 188 |
|
| 189 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 190 |
SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
| 191 |
mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
| 192 |
Cutoff Groups for MPI |
| 193 |
|
| 194 |
2004-06-01 13:07 chrisfen |
| 195 |
|
| 196 |
* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
| 197 |
useLiquidThermInt routine in ForceFields.cpp |
| 198 |
|
| 199 |
2004-06-01 12:15 chrisfen |
| 200 |
|
| 201 |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 202 |
SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
| 203 |
solid and liquid thermodynamic integration routines |
| 204 |
|
| 205 |
2004-06-01 10:57 tim |
| 206 |
|
| 207 |
* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
| 208 |
progress |
| 209 |
|
| 210 |
2004-06-01 09:27 chrisfen |
| 211 |
|
| 212 |
* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
| 213 |
keyword and changed useThermInt to useSolidThermInt |
| 214 |
|
| 215 |
2004-06-01 09:21 chrisfen |
| 216 |
|
| 217 |
* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
| 218 |
solid and liquid thermodynamic integration routines |
| 219 |
|
| 220 |
2004-05-28 10:21 gezelter |
| 221 |
|
| 222 |
* libmdtools/do_Forces.F90: bugfix starting |
| 223 |
|
| 224 |
2004-05-27 15:06 chrisfen |
| 225 |
|
| 226 |
* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
| 227 |
Integrator.cpp where it called writeRaw() when useThermInt = |
| 228 |
false... |
| 229 |
|
| 230 |
2004-05-27 14:51 tim |
| 231 |
|
| 232 |
* ChangeLog, libmdtools/do_Forces.F90, |
| 233 |
libmdtools/simulation_module.F90: Bug fix for SkipList |
| 234 |
|
| 235 |
2004-05-27 14:26 gezelter |
| 236 |
|
| 237 |
* libmdtools/SimSetup.cpp: bugfix in simsetup? |
| 238 |
|
| 239 |
2004-05-27 13:59 gezelter |
| 240 |
|
| 241 |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
| 242 |
InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
| 243 |
ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
| 244 |
mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
| 245 |
mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
| 246 |
Cutoff group changes under MPI |
| 247 |
|
| 248 |
2004-05-27 11:20 gezelter |
| 249 |
|
| 250 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
| 251 |
xlc++ |
| 252 |
|
| 253 |
2004-05-27 10:31 tim |
| 254 |
|
| 255 |
* libmdtools/SimInfo.cpp: groupList new bases on global index of |
| 256 |
atoms |
| 257 |
|
| 258 |
2004-05-27 10:21 gezelter |
| 259 |
|
| 260 |
* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
| 261 |
|
| 262 |
2004-05-27 10:21 gezelter |
| 263 |
|
| 264 |
* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
| 265 |
Fixed off-by-one error in groupStartRow and groupStartCol |
| 266 |
|
| 267 |
2004-05-26 19:48 tim |
| 268 |
|
| 269 |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
| 270 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 271 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 272 |
libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
| 273 |
libmdtools/calc_charge_charge.F90, |
| 274 |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
| 275 |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 276 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 277 |
libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
| 278 |
libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
| 279 |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 280 |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 281 |
libmdtools/simulation_module.F90: in the progress of fixing MPI |
| 282 |
version of cutoff group |
| 283 |
|
| 284 |
2004-05-26 11:41 gezelter |
| 285 |
|
| 286 |
* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
| 287 |
force loop into one. |
| 288 |
|
| 289 |
2004-05-24 17:24 gezelter |
| 290 |
|
| 291 |
* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
| 292 |
|
| 293 |
2004-05-24 16:23 chrisfen |
| 294 |
|
| 295 |
* libmdtools/Restraints.cpp: Removed unnecessary variables and |
| 296 |
changed error messages in Restraints.cpp |
| 297 |
|
| 298 |
2004-05-24 16:03 gezelter |
| 299 |
|
| 300 |
* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
| 301 |
calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 302 |
calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
| 303 |
for stress / pressure tensor by cutoff group |
| 304 |
|
| 305 |
2004-05-22 15:55 chrisfen |
| 306 |
|
| 307 |
* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
| 308 |
Too many arguements in a function call. |
| 309 |
|
| 310 |
2004-05-22 13:17 chrisfen |
| 311 |
|
| 312 |
* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
| 313 |
useThermInt. |
| 314 |
|
| 315 |
2004-05-22 13:16 chrisfen |
| 316 |
|
| 317 |
* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
| 318 |
ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
| 319 |
Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
| 320 |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
| 321 |
StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
| 322 |
code. |
| 323 |
|
| 324 |
2004-05-21 10:58 gezelter |
| 325 |
|
| 326 |
* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
| 327 |
to skipThisPair for efficiency |
| 328 |
|
| 329 |
2004-05-21 09:22 gezelter |
| 330 |
|
| 331 |
* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
| 332 |
forceFields/amber99.vdw, forceFields/charmm27.vdw, |
| 333 |
forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
| 334 |
samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
| 335 |
for SHAPES potential |
| 336 |
|
| 337 |
2004-05-20 15:27 chrisfen |
| 338 |
|
| 339 |
* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
| 340 |
included the bass keywords |
| 341 |
|
| 342 |
2004-05-20 15:24 chrisfen |
| 343 |
|
| 344 |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
| 345 |
Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
| 346 |
Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
| 347 |
additions... Restraints.cpp and .hpp were included for restraining |
| 348 |
particles in thermodynamic integration. By including these, |
| 349 |
changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
| 350 |
StatWriter, and possibly some other files. Two bass keywords were |
| 351 |
also added for performing thermodynamic integration: a lambda value |
| 352 |
one and a k power one. |
| 353 |
|
| 354 |
2004-05-13 16:08 gezelter |
| 355 |
|
| 356 |
* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
| 357 |
|
| 358 |
2004-05-12 17:01 tim |
| 359 |
|
| 360 |
* samples/: argon/Makefile, argon/argonEM.bass, |
| 361 |
argon/init_argon.eor, minimizer/argon/Makefile, |
| 362 |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
| 363 |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
| 364 |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
| 365 |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
| 366 |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
| 367 |
minimizer sample |
| 368 |
|
| 369 |
2004-05-12 16:54 gezelter |
| 370 |
|
| 371 |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
| 372 |
compilation |
| 373 |
|
| 374 |
2004-05-12 15:54 gezelter |
| 375 |
|
| 376 |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
| 377 |
for compilation under Mac OS X with IBM's xl compilers |
| 378 |
|
| 379 |
2004-05-12 15:14 gezelter |
| 380 |
|
| 381 |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
| 382 |
|
| 383 |
2004-05-12 15:14 gezelter |
| 384 |
|
| 385 |
* libmdtools/LJFF.cpp: Removed an extraneous write |
| 386 |
|
| 387 |
2004-05-12 15:13 gezelter |
| 388 |
|
| 389 |
* libBASS/simError.h: Starting to change the error model |
| 390 |
|
| 391 |
2004-05-12 14:45 gezelter |
| 392 |
|
| 393 |
* utils/Dump2XYZ.cpp: const char* fix |
| 394 |
|
| 395 |
2004-05-12 14:44 gezelter |
| 396 |
|
| 397 |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 398 |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
| 399 |
write statements |
| 400 |
|
| 401 |
2004-05-12 11:38 tim |
| 402 |
|
| 403 |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 404 |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 405 |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
| 406 |
massratio from simState, creat cutoff group forevery atom which |
| 407 |
does not belong to cutoff group defined at mdl file |
| 408 |
|
| 409 |
2004-05-12 10:58 gezelter |
| 410 |
|
| 411 |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
| 412 |
CutoffGroup |
| 413 |
|
| 414 |
2004-05-12 10:35 gezelter |
| 415 |
|
| 416 |
* samples/water/water.mdl: Added the cutoff Groups to the default |
| 417 |
water.mdl file |
| 418 |
|
| 419 |
2004-05-12 10:02 tim |
| 420 |
|
| 421 |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
| 422 |
fixed a bug in CutoffGroup::getCOM() |
| 423 |
|
| 424 |
2004-05-12 09:29 gezelter |
| 425 |
|
| 426 |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 427 |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 428 |
samples/water/ssd.bass: bug fixes for cutoffGroups |
| 429 |
|
| 430 |
2004-05-11 17:28 tim |
| 431 |
|
| 432 |
* utils/Vector3.hpp: adding generic Vector3 class |
| 433 |
|
| 434 |
2004-05-11 16:44 tim |
| 435 |
|
| 436 |
* libmdtools/Integrator.hpp: adding instantiation of |
| 437 |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
| 438 |
|
| 439 |
2004-05-11 16:31 gezelter |
| 440 |
|
| 441 |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
| 442 |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
| 443 |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
| 444 |
Fortran-side changes for group-based cutoffs |
| 445 |
|
| 446 |
2004-05-11 16:20 tim |
| 447 |
|
| 448 |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
| 449 |
|
| 450 |
2004-05-11 16:14 tim |
| 451 |
|
| 452 |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
| 453 |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
| 454 |
anoter one in CutoffGroup which causes seg fault |
| 455 |
|
| 456 |
2004-05-11 15:33 tim |
| 457 |
|
| 458 |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 459 |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 460 |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
| 461 |
into OOPSE |
| 462 |
|
| 463 |
2004-05-11 15:07 gezelter |
| 464 |
|
| 465 |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
| 466 |
|
| 467 |
2004-05-11 11:00 gezelter |
| 468 |
|
| 469 |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 470 |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
| 471 |
use the simplified cutoff stuff in the BASS library |
| 472 |
|
| 473 |
2004-05-10 23:21 gezelter |
| 474 |
|
| 475 |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
| 476 |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
| 477 |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 478 |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
| 479 |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 480 |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
| 481 |
Also restructured the plethora of cutoff radii into one |
| 482 |
cutoffRadius and one switchingRadius. Also removed the |
| 483 |
useMolecularCutoffs keyword |
| 484 |
|
| 485 |
2004-05-10 15:28 tim |
| 486 |
|
| 487 |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
| 488 |
DumpWriter |
| 489 |
|
| 490 |
2004-05-07 16:36 gezelter |
| 491 |
|
| 492 |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
| 493 |
for fortran group-based switching function |
| 494 |
|
| 495 |
2004-05-07 16:35 gezelter |
| 496 |
|
| 497 |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
| 498 |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
| 499 |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 500 |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
| 501 |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
| 502 |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
| 503 |
simulation_module.F90: Many changes to get group-based cutoffs to |
| 504 |
work |
| 505 |
|
| 506 |
2004-05-01 13:52 tim |
| 507 |
|
| 508 |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 509 |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
| 510 |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
| 511 |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
| 512 |
libmdtools/fortranWrapDefines.hpp, |
| 513 |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
| 514 |
|
| 515 |
2004-04-29 11:03 tim |
| 516 |
|
| 517 |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
| 518 |
calc_charge_charge when using molecular cutoff |
| 519 |
|
| 520 |
2004-04-28 21:11 tim |
| 521 |
|
| 522 |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
| 523 |
unmatched c/fortran interface |
| 524 |
|
| 525 |
2004-04-28 18:09 tim |
| 526 |
|
| 527 |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
| 528 |
keep the previous position of cantilever in SMD |
| 529 |
|
| 530 |
2004-04-28 17:34 tim |
| 531 |
|
| 532 |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
| 533 |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
| 534 |
in Molecule.cpp which initialize massRatio before creat the array. |
| 535 |
fix two bugs in ZconsVisitor |
| 536 |
|
| 537 |
2004-04-28 17:06 gezelter |
| 538 |
|
| 539 |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
| 540 |
Adding molecular cutoffs |
| 541 |
|
| 542 |
2004-04-28 16:39 gezelter |
| 543 |
|
| 544 |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
| 545 |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
| 546 |
molecular cutoffs |
| 547 |
|
| 548 |
2004-04-28 16:39 gezelter |
| 549 |
|
| 550 |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
| 551 |
Globals |
| 552 |
|
| 553 |
2004-04-27 11:26 tim |
| 554 |
|
| 555 |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 556 |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
| 557 |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
| 558 |
molecule and massRation into atom class |
| 559 |
|
| 560 |
2004-04-26 16:16 mmeineke |
| 561 |
|
| 562 |
* libBASS/Globals.cpp: modified the defaults for the system init |
| 563 |
time and system init state. |
| 564 |
|
| 565 |
2004-04-26 09:29 gezelter |
| 566 |
|
| 567 |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
| 568 |
calc_charge_charge.F90 |
| 569 |
|
| 570 |
2004-04-23 23:31 tim |
| 571 |
|
| 572 |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
| 573 |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
| 574 |
reaction field correction to charge-charge interaction |
| 575 |
|
| 576 |
2004-04-22 16:33 tim |
| 577 |
|
| 578 |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
| 579 |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
| 580 |
calculation of pressure tensor |
| 581 |
|
| 582 |
2004-04-22 09:55 tim |
| 583 |
|
| 584 |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
| 585 |
another bug in InitFromFile. MPI verion of OOPSE is working again |
| 586 |
|
| 587 |
2004-04-21 22:29 tim |
| 588 |
|
| 589 |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
| 590 |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
| 591 |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
| 592 |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
| 593 |
DumpWriter |
| 594 |
|
| 595 |
2004-04-21 00:32 tim |
| 596 |
|
| 597 |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
| 598 |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
| 599 |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
| 600 |
useless files |
| 601 |
|
| 602 |
2004-04-20 11:56 tim |
| 603 |
|
| 604 |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
| 605 |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
| 606 |
velocitize at thermo |
| 607 |
|
| 608 |
2004-04-20 00:39 tim |
| 609 |
|
| 610 |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
| 611 |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 612 |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
| 613 |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
| 614 |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 615 |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 616 |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
| 617 |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
| 618 |
|
| 619 |
2004-04-19 17:13 gezelter |
| 620 |
|
| 621 |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
| 622 |
Thermo.cpp: Fixed a charge bug |
| 623 |
|
| 624 |
2004-04-19 15:54 tim |
| 625 |
|
| 626 |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
| 627 |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 628 |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
| 629 |
a bug in CompositeVisitor which cause the double counting problem |
| 630 |
|
| 631 |
2004-04-19 12:44 tim |
| 632 |
|
| 633 |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 634 |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
| 635 |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
| 636 |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
| 637 |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
| 638 |
Dump2XYZ is almost working except atoms in rigidbody are double |
| 639 |
counted |
| 640 |
|
| 641 |
2004-04-18 22:52 tim |
| 642 |
|
| 643 |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
| 644 |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 645 |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
| 646 |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
| 647 |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 648 |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 649 |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
| 650 |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
| 651 |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 652 |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 653 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 654 |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 655 |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
| 656 |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
| 657 |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
| 658 |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
| 659 |
implement of quickLate using visitor and composite pattern |
| 660 |
|
| 661 |
2004-04-15 17:15 tim |
| 662 |
|
| 663 |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
| 664 |
exclude list |
| 665 |
|
| 666 |
2004-04-15 11:18 tim |
| 667 |
|
| 668 |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
| 669 |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
| 670 |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
| 671 |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 672 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 673 |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
| 674 |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
| 675 |
whole bunch of bugs :-) |
| 676 |
|
| 677 |
2004-04-14 12:20 chrisfen |
| 678 |
|
| 679 |
* forceFields/WATER.frc: Added the WATER.frc force field |
| 680 |
|
| 681 |
2004-04-14 11:32 gezelter |
| 682 |
|
| 683 |
* libmdtools/Molecule.cpp: fixed for get_potential |
| 684 |
|
| 685 |
2004-04-14 10:37 tim |
| 686 |
|
| 687 |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
| 688 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 689 |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
| 690 |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
| 691 |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
| 692 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 693 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 694 |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 695 |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
| 696 |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
| 697 |
Change DumpWriter and InitFromFile |
| 698 |
|
| 699 |
2004-04-13 11:26 gezelter |
| 700 |
|
| 701 |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
| 702 |
molecules can keep track of their own IntegrableObjects (and |
| 703 |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
| 704 |
RigidBodies (which was done incorrectly before). |
| 705 |
|
| 706 |
2004-04-13 11:25 gezelter |
| 707 |
|
| 708 |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
| 709 |
(will back out momentarily) |
| 710 |
|
| 711 |
2004-04-13 10:10 gezelter |
| 712 |
|
| 713 |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
| 714 |
Those were old. |
| 715 |
|
| 716 |
2004-04-13 10:09 gezelter |
| 717 |
|
| 718 |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
| 719 |
to add IntegrableObjects |
| 720 |
|
| 721 |
2004-04-12 16:02 gezelter |
| 722 |
|
| 723 |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
| 724 |
|
| 725 |
2004-04-12 15:32 gezelter |
| 726 |
|
| 727 |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
| 728 |
test run |
| 729 |
|
| 730 |
2004-04-12 15:32 gezelter |
| 731 |
|
| 732 |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
| 733 |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
| 734 |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
| 735 |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
| 736 |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
| 737 |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
| 738 |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
| 739 |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
| 740 |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
| 741 |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
| 742 |
(Somewhat extensive) |
| 743 |
|
| 744 |
2004-04-12 15:31 gezelter |
| 745 |
|
| 746 |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
| 747 |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
| 748 |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
| 749 |
Changes for RigidBody dynamics |
| 750 |
|
| 751 |
2004-03-17 09:22 tim |
| 752 |
|
| 753 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
| 754 |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
| 755 |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
| 756 |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
| 757 |
does not sound a good choice, next commit will seperate SMD and |
| 758 |
ZConstraint |
| 759 |
|
| 760 |
2004-03-16 14:22 tim |
| 761 |
|
| 762 |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 763 |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 764 |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
| 765 |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
| 766 |
now can support sequential moving. Refactorying is needed to |
| 767 |
support SMD in ZConstraint |
| 768 |
|
| 769 |
2004-03-02 15:32 tim |
| 770 |
|
| 771 |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
| 772 |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
| 773 |
support large file |
| 774 |
|
| 775 |
2004-03-01 16:17 tim |
| 776 |
|
| 777 |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
| 778 |
|
| 779 |
2004-03-01 15:01 tim |
| 780 |
|
| 781 |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
| 782 |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
| 783 |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
| 784 |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
| 785 |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
| 786 |
program which can be used to replace atom type for zconstraint into |
| 787 |
OOPSE |
| 788 |
|
| 789 |
2004-02-24 11:36 tim |
| 790 |
|
| 791 |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 792 |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
| 793 |
message] |
| 794 |
|
| 795 |
2004-02-24 10:49 tim |
| 796 |
|
| 797 |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 798 |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
| 799 |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 800 |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
| 801 |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
| 802 |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
| 803 |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
| 804 |
|
| 805 |
2004-02-24 10:44 tim |
| 806 |
|
| 807 |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
| 808 |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
| 809 |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
| 810 |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
| 811 |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
| 812 |
compose to implement Minimizer both versions are working |
| 813 |
|
| 814 |
2004-02-17 14:23 tim |
| 815 |
|
| 816 |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 817 |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 818 |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
| 819 |
libmdtools/MinimizerParameterSet.hpp, |
| 820 |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
| 821 |
to remove the constraint force along bond direction |
| 822 |
|
| 823 |
2004-02-10 16:33 tim |
| 824 |
|
| 825 |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 826 |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
| 827 |
single version of energy minimization is working. |
| 828 |
|
| 829 |
2004-02-09 15:38 mmeineke |
| 830 |
|
| 831 |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
| 832 |
the massive memory overusage by OOPSE |
| 833 |
|
| 834 |
2004-02-09 09:48 chrisfen |
| 835 |
|
| 836 |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
| 837 |
hardwired LJ_rcut |
| 838 |
|
| 839 |
2004-02-06 19:14 tim |
| 840 |
|
| 841 |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
| 842 |
message] |
| 843 |
|
| 844 |
2004-02-06 16:37 tim |
| 845 |
|
| 846 |
* ChangeLog, libBASS/Globals.cpp, |
| 847 |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
| 848 |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 849 |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
| 850 |
energy minimization for argon is working, need to add constraint |
| 851 |
|
| 852 |
2004-02-06 14:05 tim |
| 853 |
|
| 854 |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
| 855 |
one more file into Makefile.in |
| 856 |
|
| 857 |
2004-02-06 13:58 tim |
| 858 |
|
| 859 |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 860 |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
| 861 |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
| 862 |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
| 863 |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
| 864 |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
| 865 |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
| 866 |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 867 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 868 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
| 869 |
some lines into global.cpp to make it work with energy minimization |
| 870 |
|
| 871 |
2004-02-04 17:26 tim |
| 872 |
|
| 873 |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 874 |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 875 |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
| 876 |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
| 877 |
Single version of conjugate gradient with golden search linesearch |
| 878 |
pass a couple of functions test. Brent's algorithm is still broken |
| 879 |
|
| 880 |
2004-02-03 17:54 tim |
| 881 |
|
| 882 |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 883 |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
| 884 |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
| 885 |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
| 886 |
|
| 887 |
2004-02-03 15:47 tim |
| 888 |
|
| 889 |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
| 890 |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
| 891 |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
| 892 |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
| 893 |
SteepestDescent.hpp: [no log message] |
| 894 |
|
| 895 |
2004-02-03 15:43 tim |
| 896 |
|
| 897 |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
| 898 |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
| 899 |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 900 |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
| 901 |
constraint class |
| 902 |
|
| 903 |
2004-02-03 12:10 tim |
| 904 |
|
| 905 |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
| 906 |
|
| 907 |
2004-02-03 10:21 tim |
| 908 |
|
| 909 |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
| 910 |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
| 911 |
|
| 912 |
2004-02-02 15:29 tim |
| 913 |
|
| 914 |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
| 915 |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
| 916 |
Adding GoldenSection and Brent LineSearch Method |
| 917 |
|
| 918 |
2004-01-30 16:47 tim |
| 919 |
|
| 920 |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
| 921 |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 922 |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
| 923 |
MinimizerBase instead of a functor to do line seach |
| 924 |
|
| 925 |
2004-01-30 10:00 chrisfen |
| 926 |
|
| 927 |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
| 928 |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
| 929 |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 930 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 931 |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
| 932 |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
| 933 |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
| 934 |
has a working WATER.cpp forcefield and parser. This involved |
| 935 |
changes to WATER.cpp and ForceFields amoung other files. One |
| 936 |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
| 937 |
This will be removed on the next commit... |
| 938 |
|
| 939 |
2004-01-29 18:00 gezelter |
| 940 |
|
| 941 |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 942 |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 943 |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
| 944 |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
| 945 |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
| 946 |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
| 947 |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
| 948 |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
| 949 |
member list fixes for rigid bodies |
| 950 |
|
| 951 |
2004-01-29 16:44 tim |
| 952 |
|
| 953 |
* libmdtools/MinimizerParameterSet.hpp: Adding |
| 954 |
MinimizerParameterSet class. |
| 955 |
|
| 956 |
2004-01-28 17:44 tim |
| 957 |
|
| 958 |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
| 959 |
NLModel0 and NLModel1 |
| 960 |
|
| 961 |
2004-01-28 15:40 tim |
| 962 |
|
| 963 |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
| 964 |
of NLModel |
| 965 |
|
| 966 |
2004-01-27 15:34 gezelter |
| 967 |
|
| 968 |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
| 969 |
water.mdl file, updated ssd.bass to use new SSD name |
| 970 |
|
| 971 |
2004-01-27 15:34 gezelter |
| 972 |
|
| 973 |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 974 |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
| 975 |
stuff |
| 976 |
|
| 977 |
2004-01-27 14:39 gezelter |
| 978 |
|
| 979 |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
| 980 |
|
| 981 |
2004-01-27 14:39 gezelter |
| 982 |
|
| 983 |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
| 984 |
|
| 985 |
2004-01-27 14:38 gezelter |
| 986 |
|
| 987 |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
| 988 |
run time to test argon |
| 989 |
|
| 990 |
2004-01-27 14:38 gezelter |
| 991 |
|
| 992 |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
| 993 |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
| 994 |
morning |
| 995 |
|
| 996 |
2004-01-27 14:37 gezelter |
| 997 |
|
| 998 |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 999 |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 1000 |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
| 1001 |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
| 1002 |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
| 1003 |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
| 1004 |
do new rigidBody scheme |
| 1005 |
|
| 1006 |
2004-01-27 14:15 tim |
| 1007 |
|
| 1008 |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
| 1009 |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
| 1010 |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
| 1011 |
constraint for Nonlinear Optimization Model |
| 1012 |
|
| 1013 |
2004-01-26 17:01 gezelter |
| 1014 |
|
| 1015 |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
| 1016 |
Euler angles for orientation instead of unit vectors required |
| 1017 |
changes in MoLocator |
| 1018 |
|
| 1019 |
2004-01-26 16:53 gezelter |
| 1020 |
|
| 1021 |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
| 1022 |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
| 1023 |
water/water.mdl: Changed orientation lines from unit vectors to |
| 1024 |
euler angles |
| 1025 |
|
| 1026 |
2004-01-26 16:52 gezelter |
| 1027 |
|
| 1028 |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
| 1029 |
|
| 1030 |
2004-01-26 16:45 gezelter |
| 1031 |
|
| 1032 |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
| 1033 |
use Euler angles in the following order: phi, theta, psi Removed |
| 1034 |
the ability to set orientation using a unit vector |
| 1035 |
|
| 1036 |
2004-01-26 16:26 gezelter |
| 1037 |
|
| 1038 |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
| 1039 |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
| 1040 |
Euler angles in the following order: phi, theta, psi Removed the |
| 1041 |
ability to set orientation using a unit vector |
| 1042 |
|
| 1043 |
2004-01-26 13:52 gezelter |
| 1044 |
|
| 1045 |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 1046 |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
| 1047 |
|
| 1048 |
2004-01-22 12:34 chrisfen |
| 1049 |
|
| 1050 |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
| 1051 |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
| 1052 |
Corrected spelling in several directories, and stated WATER.cpp |
| 1053 |
|
| 1054 |
2004-01-21 17:16 tim |
| 1055 |
|
| 1056 |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
| 1057 |
NLOPModel.hpp: constraint class in energy minimization |
| 1058 |
|
| 1059 |
2004-01-20 15:34 tim |
| 1060 |
|
| 1061 |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
| 1062 |
|
| 1063 |
2004-01-20 15:32 tim |
| 1064 |
|
| 1065 |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
| 1066 |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
| 1067 |
|
| 1068 |
2004-01-19 16:17 gezelter |
| 1069 |
|
| 1070 |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
| 1071 |
more user-friendly |
| 1072 |
|
| 1073 |
2004-01-19 13:51 chrisfen |
| 1074 |
|
| 1075 |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
| 1076 |
|
| 1077 |
2004-01-19 13:36 tim |
| 1078 |
|
| 1079 |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
| 1080 |
time, status time, thermal time and reset time are not divisible by |
| 1081 |
dt |
| 1082 |
|
| 1083 |
2004-01-19 11:10 gezelter |
| 1084 |
|
| 1085 |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
| 1086 |
won't complain |
| 1087 |
|
| 1088 |
2004-01-19 11:10 gezelter |
| 1089 |
|
| 1090 |
* samples/lipid/5x5.bass: Fixed old bass file |
| 1091 |
|
| 1092 |
2004-01-19 11:09 gezelter |
| 1093 |
|
| 1094 |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
| 1095 |
required a change in how the MoleculeStamps are used by divideLabor |
| 1096 |
in mpiSimulation.cpp |
| 1097 |
|
| 1098 |
2004-01-19 11:08 gezelter |
| 1099 |
|
| 1100 |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 1101 |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
| 1102 |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
| 1103 |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
| 1104 |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 1105 |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
| 1106 |
|
| 1107 |
2004-01-16 16:55 tim |
| 1108 |
|
| 1109 |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
| 1110 |
eor file |
| 1111 |
|
| 1112 |
2004-01-16 16:51 mmeineke |
| 1113 |
|
| 1114 |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
| 1115 |
write eor files |
| 1116 |
|
| 1117 |
2004-01-16 10:01 mmeineke |
| 1118 |
|
| 1119 |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
| 1120 |
initialization of the AtomStruct |
| 1121 |
|
| 1122 |
2004-01-15 16:57 chuckv |
| 1123 |
|
| 1124 |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
| 1125 |
|
| 1126 |
2004-01-15 10:51 gezelter |
| 1127 |
|
| 1128 |
* ac-tools/aclocal.m4: Changes for altivec |
| 1129 |
|
| 1130 |
2004-01-15 09:22 gezelter |
| 1131 |
|
| 1132 |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
| 1133 |
|
| 1134 |
2004-01-14 23:33 gezelter |
| 1135 |
|
| 1136 |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
| 1137 |
|
| 1138 |
2004-01-14 20:14 gezelter |
| 1139 |
|
| 1140 |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 1141 |
notifyCutoffs.F90: More work for adding charges |
| 1142 |
|
| 1143 |
2004-01-14 17:41 gezelter |
| 1144 |
|
| 1145 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1146 |
src/Makefile.in: autoconf fixes |
| 1147 |
|
| 1148 |
2004-01-14 11:28 mmeineke |
| 1149 |
|
| 1150 |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
| 1151 |
|
| 1152 |
2004-01-14 10:48 gezelter |
| 1153 |
|
| 1154 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1155 |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
| 1156 |
changes for icc8 |
| 1157 |
|
| 1158 |
2004-01-13 18:01 gezelter |
| 1159 |
|
| 1160 |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
| 1161 |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
| 1162 |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
| 1163 |
Changes for adding direct charge-charge interactions (with |
| 1164 |
switching function) |
| 1165 |
|
| 1166 |
2004-01-13 17:34 gezelter |
| 1167 |
|
| 1168 |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
| 1169 |
oopseMPI_module.F90: Some changes for new MPI organization and |
| 1170 |
direct charge-charge interactions |
| 1171 |
|
| 1172 |
2004-01-13 17:11 tim |
| 1173 |
|
| 1174 |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
| 1175 |
|
| 1176 |
2004-01-13 16:22 tim |
| 1177 |
|
| 1178 |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
| 1179 |
|
| 1180 |
2004-01-13 15:35 tim |
| 1181 |
|
| 1182 |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
| 1183 |
eor file whenever it is used instead of rewinding it |
| 1184 |
|
| 1185 |
2004-01-13 15:04 tim |
| 1186 |
|
| 1187 |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
| 1188 |
of writeFrame |
| 1189 |
|
| 1190 |
2004-01-13 10:46 tim |
| 1191 |
|
| 1192 |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
| 1193 |
Merge the code of writeFinal and writeDump; |
| 1194 |
Adding sortingIndex into DumpWriter; |
| 1195 |
Fix a bug of writing last frame twice in integrator |
| 1196 |
|
| 1197 |
2004-01-12 17:54 tim |
| 1198 |
|
| 1199 |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
| 1200 |
a bug in copying string |
| 1201 |
|
| 1202 |
2004-01-12 15:37 tim |
| 1203 |
|
| 1204 |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
| 1205 |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
| 1206 |
Dumpwriter only write out the atoms on master nodes |
| 1207 |
|
| 1208 |
2004-01-10 04:46 tim |
| 1209 |
|
| 1210 |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
| 1211 |
roll it back fix a bug of copying string to a pointer Still have |
| 1212 |
Seg fault, it looks like a random MPI seg fault in totalview |
| 1213 |
|
| 1214 |
2004-01-09 21:15 tim |
| 1215 |
|
| 1216 |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
| 1217 |
|
| 1218 |
2004-01-09 15:29 gezelter |
| 1219 |
|
| 1220 |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
| 1221 |
|
| 1222 |
2004-01-08 17:25 chuckv |
| 1223 |
|
| 1224 |
* libmdtools/DumpWriter.cpp: A work in progress... |
| 1225 |
|
| 1226 |
2004-01-08 13:59 gezelter |
| 1227 |
|
| 1228 |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
| 1229 |
case |
| 1230 |
|
| 1231 |
2004-01-08 13:13 mmeineke |
| 1232 |
|
| 1233 |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
| 1234 |
state bug. |
| 1235 |
|
| 1236 |
2004-01-08 13:05 gezelter |
| 1237 |
|
| 1238 |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
| 1239 |
|
| 1240 |
2004-01-08 12:57 mmeineke |
| 1241 |
|
| 1242 |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
| 1243 |
exstended state bug |
| 1244 |
|
| 1245 |
2004-01-08 12:40 gezelter |
| 1246 |
|
| 1247 |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
| 1248 |
|
| 1249 |
2004-01-08 10:44 mmeineke |
| 1250 |
|
| 1251 |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
| 1252 |
XS state info flag |
| 1253 |
|
| 1254 |
2004-01-07 14:26 tim |
| 1255 |
|
| 1256 |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
| 1257 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
| 1258 |
samples/water/ssd.bass: Fixed a bug of sending message from master |
| 1259 |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
| 1260 |
|
| 1261 |
2004-01-06 14:49 chuckv |
| 1262 |
|
| 1263 |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
| 1264 |
performance fixes in the dipole dipole and reaction field code |
| 1265 |
|
| 1266 |
2004-01-06 13:54 chuckv |
| 1267 |
|
| 1268 |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
| 1269 |
little more sane |
| 1270 |
|
| 1271 |
2004-01-05 17:49 chuckv |
| 1272 |
|
| 1273 |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 1274 |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 1275 |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
| 1276 |
performance by reducing spurious function calls |
| 1277 |
|
| 1278 |
2004-01-05 17:18 chuckv |
| 1279 |
|
| 1280 |
* libmdtools/do_Forces.F90: mangling forces even further |
| 1281 |
|
| 1282 |
2004-01-05 17:18 chuckv |
| 1283 |
|
| 1284 |
* configure, ac-tools/configure.in: mpich mucking |
| 1285 |
|
| 1286 |
2004-01-05 17:12 chuckv |
| 1287 |
|
| 1288 |
* libmdtools/do_Forces.F90: mangled do_forces... |
| 1289 |
|
| 1290 |
2004-01-05 16:00 chuckv |
| 1291 |
|
| 1292 |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
| 1293 |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
| 1294 |
lookup |
| 1295 |
|
| 1296 |
2003-12-29 14:56 chuckv |
| 1297 |
|
| 1298 |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
| 1299 |
third-party directory for code not written by us. Also added |
| 1300 |
Mersenne Twister random number generator code. This will eventually |
| 1301 |
replace sprng as the random number generator used by OOPSE. |
| 1302 |
|
| 1303 |
2003-12-22 16:26 chuckv |
| 1304 |
|
| 1305 |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 1306 |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
| 1307 |
Fixes to profile code. |
| 1308 |
|
| 1309 |
2003-12-19 15:36 mmeineke |
| 1310 |
|
| 1311 |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
| 1312 |
timing.F90, timing.f90: More profiling fixes. |
| 1313 |
|
| 1314 |
2003-12-19 15:19 chuckv |
| 1315 |
|
| 1316 |
* libmdtools/timing.f90: Another change for MPI in timing. |
| 1317 |
|
| 1318 |
2003-12-19 15:17 chuckv |
| 1319 |
|
| 1320 |
* libmdtools/timing.f90: Small update to timing in MPI |
| 1321 |
|
| 1322 |
2003-12-19 13:53 mmeineke |
| 1323 |
|
| 1324 |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
| 1325 |
profiling commands work now. Will start adding PROFILE ifdefs into |
| 1326 |
the code |
| 1327 |
|
| 1328 |
2003-12-19 12:25 mmeineke |
| 1329 |
|
| 1330 |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
| 1331 |
some profiling routines |
| 1332 |
|
| 1333 |
2003-12-19 10:12 mmeineke |
| 1334 |
|
| 1335 |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
| 1336 |
and GofRomega |
| 1337 |
|
| 1338 |
additional work on randomBilayer |
| 1339 |
|
| 1340 |
2003-12-19 10:12 mmeineke |
| 1341 |
|
| 1342 |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
| 1343 |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
| 1344 |
GofRomega |
| 1345 |
|
| 1346 |
2003-12-18 16:47 mmeineke |
| 1347 |
|
| 1348 |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
| 1349 |
some profile functionality |
| 1350 |
|
| 1351 |
2003-12-18 15:46 chuckv |
| 1352 |
|
| 1353 |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
| 1354 |
Added functions for simple profiling in fortran. |
| 1355 |
|
| 1356 |
2003-12-17 15:13 chuckv |
| 1357 |
|
| 1358 |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
| 1359 |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
| 1360 |
rho_col were scattered into the same array. Unfortunately, MPI |
| 1361 |
zeros the array between scatters so half of the sum was being lost. |
| 1362 |
Fixed by added a temp array for column scatter, then sum loop over |
| 1363 |
nlocal. |
| 1364 |
|
| 1365 |
2003-12-16 15:49 mmeineke |
| 1366 |
|
| 1367 |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
| 1368 |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
| 1369 |
gofRomega. both need to be debugged and tested. |
| 1370 |
|
| 1371 |
2003-12-12 10:42 gezelter |
| 1372 |
|
| 1373 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1374 |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
| 1375 |
gradients (to do minimizations) |
| 1376 |
|
| 1377 |
2003-12-12 10:33 mmeineke |
| 1378 |
|
| 1379 |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
| 1380 |
header |
| 1381 |
|
| 1382 |
2003-12-10 11:52 mmeineke |
| 1383 |
|
| 1384 |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
| 1385 |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
| 1386 |
randomBilayer to the build. Also move the random bilayer builder |
| 1387 |
from bilayerSys to randomBilayer |
| 1388 |
|
| 1389 |
2003-11-25 10:44 mmeineke |
| 1390 |
|
| 1391 |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
| 1392 |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
| 1393 |
TB3 in DUFF.frc |
| 1394 |
|
| 1395 |
2003-11-21 15:09 mmeineke |
| 1396 |
|
| 1397 |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
| 1398 |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
| 1399 |
message in SimInfo. Added a more informative error message in |
| 1400 |
InitializeFromFile |
| 1401 |
|
| 1402 |
2003-11-21 15:07 mmeineke |
| 1403 |
|
| 1404 |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
| 1405 |
ing in the GofR,CosTheta |
| 1406 |
|
| 1407 |
2003-11-21 14:31 chrisfen |
| 1408 |
|
| 1409 |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
| 1410 |
a bug in SimInfo ordering of radii |
| 1411 |
|
| 1412 |
2003-11-11 12:20 mmeineke |
| 1413 |
|
| 1414 |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
| 1415 |
a min function. |
| 1416 |
|
| 1417 |
2003-11-10 16:50 mmeineke |
| 1418 |
|
| 1419 |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
| 1420 |
reordered the rcut/ecr/boxSize initialization |
| 1421 |
|
| 1422 |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
| 1423 |
now exit when it runs into rcut or ecr. |
| 1424 |
|
| 1425 |
2003-11-07 16:46 chuckv |
| 1426 |
|
| 1427 |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
| 1428 |
oopseMPI_module.F90: Added support for compiling fortran without |
| 1429 |
use of mpich modules. We use mpif.h instead.: |
| 1430 |
|
| 1431 |
2003-11-07 12:09 mmeineke |
| 1432 |
|
| 1433 |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
| 1434 |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
| 1435 |
the atom loop in the NPT family of integrators. |
| 1436 |
|
| 1437 |
2003-11-06 17:01 mmeineke |
| 1438 |
|
| 1439 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
| 1440 |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 1441 |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1442 |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
| 1443 |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
| 1444 |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
| 1445 |
* useIntiTime => useInitialTime |
| 1446 |
|
| 1447 |
2003-11-06 14:24 mmeineke |
| 1448 |
|
| 1449 |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
| 1450 |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
| 1451 |
parse_tree.h: fixed the includes in the Make.dep |
| 1452 |
|
| 1453 |
2003-11-06 14:11 mmeineke |
| 1454 |
|
| 1455 |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 1456 |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
| 1457 |
new-templateless branch to the main trunk. |
| 1458 |
|
| 1459 |
bug Fixes include: * fixed the switching function from ortho to |
| 1460 |
non-ortho box. !!!!! THis was responsible for all of the |
| 1461 |
sudden deaths we saw. * some formating in the string when we |
| 1462 |
write out the extended system state. * added NPT.cpp to the |
| 1463 |
makefile.in |
| 1464 |
|
| 1465 |
2003-11-06 13:20 mmeineke |
| 1466 |
|
| 1467 |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
| 1468 |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
| 1469 |
bug. The box was not switching between orthorhombic and |
| 1470 |
non-orthorhombic wrapping correctly. we added a fabs() to |
| 1471 |
the check.which should fix it. |
| 1472 |
|
| 1473 |
2003-11-05 14:16 mmeineke |
| 1474 |
|
| 1475 |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
| 1476 |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 1477 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 1478 |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
| 1479 |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 1480 |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
| 1481 |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
| 1482 |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
| 1483 |
some work on trying to find the compression bug |
| 1484 |
|
| 1485 |
2003-11-03 17:07 mmeineke |
| 1486 |
|
| 1487 |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
| 1488 |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
| 1489 |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
| 1490 |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
| 1491 |
most of standard template library from OOPSE. |
| 1492 |
|
| 1493 |
2003-10-31 16:06 mmeineke |
| 1494 |
|
| 1495 |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 1496 |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
| 1497 |
SimSetup.cpp: started work on template removal. |
| 1498 |
|
| 1499 |
2003-10-31 13:28 mmeineke |
| 1500 |
|
| 1501 |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
| 1502 |
added template stuff to the Maikefile template |
| 1503 |
|
| 1504 |
little changes to some printf format statements |
| 1505 |
|
| 1506 |
2003-10-31 13:28 mmeineke |
| 1507 |
|
| 1508 |
* libBASS/Makefile.in: added template stuff to the Maikefile |
| 1509 |
template |
| 1510 |
|
| 1511 |
2003-10-30 13:59 gezelter |
| 1512 |
|
| 1513 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 1514 |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
| 1515 |
rList problems |
| 1516 |
|
| 1517 |
2003-10-30 09:11 gezelter |
| 1518 |
|
| 1519 |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
| 1520 |
queried before q0 was allocated. |
| 1521 |
|
| 1522 |
2003-10-29 15:41 mmeineke |
| 1523 |
|
| 1524 |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
| 1525 |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
| 1526 |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
| 1527 |
in bass.l |
| 1528 |
|
| 1529 |
fixed a little bug in the first time step, regarding the setting of |
| 1530 |
ecr and est in fortran |
| 1531 |
|
| 1532 |
2003-10-29 15:40 mmeineke |
| 1533 |
|
| 1534 |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
| 1535 |
|
| 1536 |
2003-10-29 12:55 mmeineke |
| 1537 |
|
| 1538 |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1539 |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
| 1540 |
rcut is setup, as well as additional debugging comments. |
| 1541 |
|
| 1542 |
2003-10-29 09:28 gezelter |
| 1543 |
|
| 1544 |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
| 1545 |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
| 1546 |
templates |
| 1547 |
|
| 1548 |
2003-10-28 22:16 gezelter |
| 1549 |
|
| 1550 |
* src/Makefile.in: Refixed broken makefile |
| 1551 |
|
| 1552 |
2003-10-28 22:06 gezelter |
| 1553 |
|
| 1554 |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
| 1555 |
fixes |
| 1556 |
|
| 1557 |
2003-10-28 19:19 tim |
| 1558 |
|
| 1559 |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
| 1560 |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
| 1561 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 1562 |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 1563 |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 1564 |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
| 1565 |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
| 1566 |
and eta to the comment line of dump file. |
| 1567 |
|
| 1568 |
2003-10-28 17:25 mmeineke |
| 1569 |
|
| 1570 |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
| 1571 |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 1572 |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
| 1573 |
how c calls fortran. All function pointers and fortran calls are |
| 1574 |
rigidly typecast now. |
| 1575 |
|
| 1576 |
2003-10-28 15:42 gezelter |
| 1577 |
|
| 1578 |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1579 |
Portability fixes |
| 1580 |
|
| 1581 |
2003-10-28 15:09 gezelter |
| 1582 |
|
| 1583 |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
| 1584 |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
| 1585 |
src/Makefile.in: Compatibility fixes |
| 1586 |
|
| 1587 |
2003-10-28 12:08 mmeineke |
| 1588 |
|
| 1589 |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
| 1590 |
started work on template removal |
| 1591 |
|
| 1592 |
2003-10-28 12:04 gezelter |
| 1593 |
|
| 1594 |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
| 1595 |
trying to understand extern "C" stuff for pointers |
| 1596 |
|
| 1597 |
2003-10-28 11:20 gezelter |
| 1598 |
|
| 1599 |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
| 1600 |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
| 1601 |
|
| 1602 |
2003-10-28 11:03 gezelter |
| 1603 |
|
| 1604 |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
| 1605 |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
| 1606 |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
| 1607 |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
| 1608 |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 1609 |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
| 1610 |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
| 1611 |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
| 1612 |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
| 1613 |
more portable c header stuff Also, mod file fixes and portability |
| 1614 |
changes Some fortran changes will need to be reversed. |
| 1615 |
|
| 1616 |
2003-10-28 11:03 gezelter |
| 1617 |
|
| 1618 |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
| 1619 |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
| 1620 |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
| 1621 |
portable c header stuff Also, mod file fixes and portability |
| 1622 |
changes |
| 1623 |
|
| 1624 |
2003-10-28 11:02 gezelter |
| 1625 |
|
| 1626 |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
| 1627 |
stuff |
| 1628 |
|
| 1629 |
2003-10-27 18:00 gezelter |
| 1630 |
|
| 1631 |
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1632 |
ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1633 |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
| 1634 |
|
| 1635 |
2003-10-27 17:08 mmeineke |
| 1636 |
|
| 1637 |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1638 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
| 1639 |
added routines for the sysbuilder to work with simSetup |
| 1640 |
|
| 1641 |
remved the QuickBass routines, and had all parsing go through |
| 1642 |
SimSetup. LatticeBilayer is in complete working order now. |
| 1643 |
|
| 1644 |
2003-10-27 17:07 mmeineke |
| 1645 |
|
| 1646 |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
| 1647 |
routines for the sysbuilder to work with simSetup |
| 1648 |
|
| 1649 |
2003-10-27 11:20 gezelter |
| 1650 |
|
| 1651 |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
| 1652 |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
| 1653 |
|
| 1654 |
2003-10-24 17:17 mmeineke |
| 1655 |
|
| 1656 |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1657 |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
| 1658 |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
| 1659 |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
| 1660 |
overhauled latticeBilayer into its own program. Removed sysBuild |
| 1661 |
from the Makefile |
| 1662 |
|
| 1663 |
2003-10-24 12:36 gezelter |
| 1664 |
|
| 1665 |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
| 1666 |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
| 1667 |
builder |
| 1668 |
|
| 1669 |
2003-10-24 12:35 gezelter |
| 1670 |
|
| 1671 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
| 1672 |
merge problem |
| 1673 |
|
| 1674 |
2003-10-23 14:57 mmeineke |
| 1675 |
|
| 1676 |
* samples/metals/Makefile.in: added eam ForceField files to the |
| 1677 |
init |
| 1678 |
|
| 1679 |
fixed an eam mpi parmeter setup bug |
| 1680 |
|
| 1681 |
added the init file to the makefile |
| 1682 |
|
| 1683 |
2003-10-23 14:57 mmeineke |
| 1684 |
|
| 1685 |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
| 1686 |
to the init |
| 1687 |
|
| 1688 |
fixed an eam mpi parmeter setup bug |
| 1689 |
|
| 1690 |
2003-10-23 14:57 mmeineke |
| 1691 |
|
| 1692 |
* forceFields/Makefile.in: added eam ForceField files to the init |
| 1693 |
|
| 1694 |
2003-10-22 16:17 mmeineke |
| 1695 |
|
| 1696 |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
| 1697 |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
| 1698 |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
| 1699 |
no box skew allowed. |
| 1700 |
|
| 1701 |
2003-10-21 14:33 mmeineke |
| 1702 |
|
| 1703 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1704 |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
| 1705 |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
| 1706 |
* useInitTime = false: sets the origin time to 0.0 regardless |
| 1707 |
of the time stamp in the .init file * default=> useInitTime = |
| 1708 |
true; |
| 1709 |
|
| 1710 |
2003-10-17 16:19 mmeineke |
| 1711 |
|
| 1712 |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
| 1713 |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1714 |
staticProps.cpp, obj/placeholder: added the staticProps directory |
| 1715 |
to the build list for both configure and configure.in |
| 1716 |
|
| 1717 |
fixed a number of bugs in the staticProps code. gofr is now |
| 1718 |
working. |
| 1719 |
|
| 1720 |
2003-10-17 16:18 mmeineke |
| 1721 |
|
| 1722 |
* ac-tools/configure.in: added the staticProps directory to the |
| 1723 |
build list for both configure and configure.in |
| 1724 |
|
| 1725 |
2003-10-17 16:17 mmeineke |
| 1726 |
|
| 1727 |
* configure: added the staticProps directory to the build list |
| 1728 |
|
| 1729 |
2003-10-16 14:16 mmeineke |
| 1730 |
|
| 1731 |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
| 1732 |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
| 1733 |
use linked lists instead of a vector. |
| 1734 |
|
| 1735 |
Fixed the makefile to build DumpReader.cpp |
| 1736 |
|
| 1737 |
Removed a comment output in Exclude.cpp |
| 1738 |
|
| 1739 |
Modified DumpWriter and Integrator to write an eor file every time |
| 1740 |
a frame is written. This lets the .eor file represent the last |
| 1741 |
written frame of a simulation. |
| 1742 |
|
| 1743 |
2003-10-10 12:10 mmeineke |
| 1744 |
|
| 1745 |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
| 1746 |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
| 1747 |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1748 |
staticProps.cpp: removed the props directory, and moved everything |
| 1749 |
over to staticProps |
| 1750 |
|
| 1751 |
2003-10-09 17:09 mmeineke |
| 1752 |
|
| 1753 |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
| 1754 |
a position where it will compile and run first runs. |
| 1755 |
|
| 1756 |
2003-10-04 13:46 chuckv |
| 1757 |
|
| 1758 |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
| 1759 |
samples/metals/Au.bass: Fixed bug in calc_eam. |
| 1760 |
|
| 1761 |
2003-10-04 13:08 chuckv |
| 1762 |
|
| 1763 |
* samples/metals/init_au.in: added Au init file for eam. |
| 1764 |
|
| 1765 |
2003-10-03 17:11 mmeineke |
| 1766 |
|
| 1767 |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
| 1768 |
entahlpy from the statwriter and thermo. |
| 1769 |
|
| 1770 |
2003-10-03 17:02 mmeineke |
| 1771 |
|
| 1772 |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
| 1773 |
statements in simError |
| 1774 |
|
| 1775 |
added a function to get the maxCutoff |
| 1776 |
|
| 1777 |
2003-10-03 17:01 mmeineke |
| 1778 |
|
| 1779 |
* libBASS/simError.c: changed the formating ogf the error |
| 1780 |
statements in simError |
| 1781 |
|
| 1782 |
2003-09-30 11:00 mmeineke |
| 1783 |
|
| 1784 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
| 1785 |
f90Flags so they are no longer overwritten by the compiler. |
| 1786 |
|
| 1787 |
2003-09-29 17:06 mmeineke |
| 1788 |
|
| 1789 |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
| 1790 |
for conifig.in |
| 1791 |
|
| 1792 |
fixed wrappers to extern "C" |
| 1793 |
|
| 1794 |
2003-09-29 17:06 mmeineke |
| 1795 |
|
| 1796 |
* ac-tools/configure.in: added mpif90 mod check back same for |
| 1797 |
conifig.in |
| 1798 |
|
| 1799 |
2003-09-29 17:05 mmeineke |
| 1800 |
|
| 1801 |
* configure: added mpif90 mod check back |
| 1802 |
|
| 1803 |
2003-09-29 16:16 mmeineke |
| 1804 |
|
| 1805 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1806 |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
| 1807 |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
| 1808 |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
| 1809 |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
| 1810 |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
| 1811 |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
| 1812 |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
| 1813 |
found with SUN's SUNWspro.s1s7 |
| 1814 |
|
| 1815 |
2003-09-29 12:38 mmeineke |
| 1816 |
|
| 1817 |
* libmdtools/GenericData.hpp: light change in syntax. no |
| 1818 |
signifigant change. |
| 1819 |
|
| 1820 |
2003-09-25 16:17 mmeineke |
| 1821 |
|
| 1822 |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
| 1823 |
additional remarks from icc -w3 (extra verbose output) |
| 1824 |
|
| 1825 |
2003-09-25 14:27 mmeineke |
| 1826 |
|
| 1827 |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1828 |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
| 1829 |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
| 1830 |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
| 1831 |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
| 1832 |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
| 1833 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1834 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 1835 |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
| 1836 |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
| 1837 |
gcc -Wall and g++ -Wall |
| 1838 |
|
| 1839 |
2003-09-25 13:54 gezelter |
| 1840 |
|
| 1841 |
* configure, ac-tools/configure.in: fixed a bug in configure |
| 1842 |
|
| 1843 |
2003-09-25 11:42 gezelter |
| 1844 |
|
| 1845 |
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1846 |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
| 1847 |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1848 |
fixes for configure |
| 1849 |
|
| 1850 |
2003-09-24 14:34 mmeineke |
| 1851 |
|
| 1852 |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
| 1853 |
that it is called before the first Statistics are written. |
| 1854 |
|
| 1855 |
2003-09-23 15:36 gezelter |
| 1856 |
|
| 1857 |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
| 1858 |
bunch of Make.dep files to CVS |
| 1859 |
|
| 1860 |
2003-09-23 15:34 mmeineke |
| 1861 |
|
| 1862 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
| 1863 |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
| 1864 |
|
| 1865 |
Some small syntax cleaning in NPTfm and SimSetup |
| 1866 |
|
| 1867 |
2003-09-22 18:07 tim |
| 1868 |
|
| 1869 |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1870 |
SimInfo.hpp: fix bug in calculating maxCutoff |
| 1871 |
|
| 1872 |
2003-09-22 16:23 mmeineke |
| 1873 |
|
| 1874 |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
| 1875 |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
| 1876 |
Converted NPTf to work with the NPT base class. |
| 1877 |
|
| 1878 |
Removed NPTfm and NPTim from cvs |
| 1879 |
|
| 1880 |
2003-09-19 15:00 mmeineke |
| 1881 |
|
| 1882 |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 1883 |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
| 1884 |
class. NPTi is up to date. NPTf is not. |
| 1885 |
|
| 1886 |
2003-09-19 11:03 mmeineke |
| 1887 |
|
| 1888 |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
| 1889 |
makefile |
| 1890 |
|
| 1891 |
2003-09-19 11:01 gezelter |
| 1892 |
|
| 1893 |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
| 1894 |
|
| 1895 |
2003-09-19 11:01 gezelter |
| 1896 |
|
| 1897 |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
| 1898 |
(nearly) conserved quantities for both NPTi and NPTf |
| 1899 |
|
| 1900 |
2003-09-19 10:20 mmeineke |
| 1901 |
|
| 1902 |
* utils/Makefile.in: fixed a typo in the makefile. |
| 1903 |
|
| 1904 |
2003-09-19 09:55 gezelter |
| 1905 |
|
| 1906 |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
| 1907 |
samples/water/ssd.bass: [no log message] |
| 1908 |
|
| 1909 |
2003-09-19 09:22 tim |
| 1910 |
|
| 1911 |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
| 1912 |
|
| 1913 |
2003-09-17 09:22 mmeineke |
| 1914 |
|
| 1915 |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
| 1916 |
work with constraints. |
| 1917 |
|
| 1918 |
2003-09-16 15:02 tim |
| 1919 |
|
| 1920 |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
| 1921 |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
| 1922 |
|
| 1923 |
fixed conserved quantity in NPT (Still some small bug) |
| 1924 |
|
| 1925 |
NPTi appears very stable. |
| 1926 |
|
| 1927 |
2003-09-15 11:52 tim |
| 1928 |
|
| 1929 |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
| 1930 |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
| 1931 |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
| 1932 |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1933 |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
| 1934 |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
| 1935 |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
| 1936 |
statWriter fix bug of vector wrapping at NPTi |
| 1937 |
|
| 1938 |
2003-09-12 11:20 gezelter |
| 1939 |
|
| 1940 |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
| 1941 |
Makefile.in |
| 1942 |
|
| 1943 |
2003-09-12 11:20 gezelter |
| 1944 |
|
| 1945 |
* ChangeLog: Entered changes for configure into ChangeLog |
| 1946 |
|
| 1947 |
2003-09-09 15:35 mmeineke |
| 1948 |
|
| 1949 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
| 1950 |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
| 1951 |
|
| 1952 |
added two new NPT integrators, they still need work. |
| 1953 |
|
| 1954 |
2003-09-09 15:34 mmeineke |
| 1955 |
|
| 1956 |
* ChangeLog: updated the ChangeLog |
| 1957 |
|
| 1958 |
2003-09-05 17:45 gezelter |
| 1959 |
|
| 1960 |
* libmdtools/Make.dep: dependency on config.h |
| 1961 |
|
| 1962 |
2003-09-05 17:36 gezelter |
| 1963 |
|
| 1964 |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
| 1965 |
|
| 1966 |
2003-09-05 16:29 gezelter |
| 1967 |
|
| 1968 |
* samples/metals/Makefile.in: New Makefile for metals sample |
| 1969 |
|
| 1970 |
2003-09-05 16:27 gezelter |
| 1971 |
|
| 1972 |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
| 1973 |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
| 1974 |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1975 |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 1976 |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
| 1977 |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
| 1978 |
libmdtools/Makefile, libmdtools/Makefile.in, |
| 1979 |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
| 1980 |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
| 1981 |
libmdtools/fortranWrappers.cpp, |
| 1982 |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
| 1983 |
libmdtools/simulation_module.F90, samples/Makefile, |
| 1984 |
samples/Makefile.in, samples/alkane/Makefile, |
| 1985 |
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 1986 |
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 1987 |
samples/minimizer/argon/Makefile, |
| 1988 |
samples/minimizer/argon/Makefile.in, |
| 1989 |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
| 1990 |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
| 1991 |
samples/lipid/Makefile.in, samples/water/Makefile, |
| 1992 |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
| 1993 |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
| 1994 |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
| 1995 |
method of configuring OOPSE |
| 1996 |
|
| 1997 |
2003-09-04 16:48 mmeineke |
| 1998 |
|
| 1999 |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 2000 |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
| 2001 |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
| 2002 |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
| 2003 |
added resetTime to the Global namespace. |
| 2004 |
|
| 2005 |
added ability to reset the integrators in the NVT and NPT family. |
| 2006 |
|
| 2007 |
2003-09-04 16:48 mmeineke |
| 2008 |
|
| 2009 |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
| 2010 |
namespace. |
| 2011 |
|
| 2012 |
2003-09-02 09:30 tim |
| 2013 |
|
| 2014 |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
| 2015 |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
| 2016 |
PolicyByMass |
| 2017 |
|
| 2018 |
2003-08-28 16:09 tim |
| 2019 |
|
| 2020 |
* ChangeLog, libmdtools/GenericData.cpp, |
| 2021 |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
| 2022 |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
| 2023 |
|
| 2024 |
2003-08-27 14:23 tim |
| 2025 |
|
| 2026 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 2027 |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
| 2028 |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
| 2029 |
turn on the optimization flag, it causes a seg fault |
| 2030 |
|
| 2031 |
2003-08-27 11:25 gezelter |
| 2032 |
|
| 2033 |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 2034 |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
| 2035 |
stress tensor parallel bug. |
| 2036 |
|
| 2037 |
2003-08-27 11:16 tim |
| 2038 |
|
| 2039 |
* ChangeLog, libmdtools/DUFF.cpp, |
| 2040 |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
| 2041 |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
| 2042 |
molMembershipList use global index instead of local index |
| 2043 |
|
| 2044 |
2003-08-26 15:37 tim |
| 2045 |
|
| 2046 |
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
| 2047 |
mpiSimulation.cpp: set default force substraction policy to |
| 2048 |
PolicyByMass |
| 2049 |
|
| 2050 |
2003-08-26 15:29 tim |
| 2051 |
|
| 2052 |
* libmdtools/Integrator.cpp: [no log message] |
| 2053 |
|
| 2054 |
2003-08-26 15:13 mmeineke |
| 2055 |
|
| 2056 |
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
| 2057 |
Statwriter and Dumpwriter to handle files larger than 2 gb. |
| 2058 |
|
| 2059 |
commented out some print statements in Zconstraint |
| 2060 |
|
| 2061 |
hard coding some system init into bilayer.sys |
| 2062 |
|
| 2063 |
2003-08-26 15:12 mmeineke |
| 2064 |
|
| 2065 |
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
| 2066 |
added define statemewnt to Statwriter and Dumpwriter to handle |
| 2067 |
files larger than 2 gb. |
| 2068 |
|
| 2069 |
commented out some print statements in Zconstraint |
| 2070 |
|
| 2071 |
2003-08-26 15:02 tim |
| 2072 |
|
| 2073 |
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
| 2074 |
and check the seed which is specified by user at least contains 9 |
| 2075 |
digits |
| 2076 |
|
| 2077 |
2003-08-26 13:32 mmeineke |
| 2078 |
|
| 2079 |
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
| 2080 |
|
| 2081 |
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
| 2082 |
constucted in MPI. (The MPI struct had 6 doubles declared versus |
| 2083 |
the actual 11) |
| 2084 |
|
| 2085 |
2003-08-26 13:30 mmeineke |
| 2086 |
|
| 2087 |
* Makefile: changed the Makefiel a litle. |
| 2088 |
|
| 2089 |
2003-08-25 17:17 gezelter |
| 2090 |
|
| 2091 |
* utils/sysbuilder/Makefile: More FreeBSD fixes |
| 2092 |
|
| 2093 |
2003-08-25 16:51 gezelter |
| 2094 |
|
| 2095 |
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
| 2096 |
libmdtools/Makefile, src/Makefile: [no log message] |
| 2097 |
|
| 2098 |
2003-08-22 15:04 mmeineke |
| 2099 |
|
| 2100 |
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
| 2101 |
frequency of output dumps. |
| 2102 |
|
| 2103 |
2003-08-20 17:23 tim |
| 2104 |
|
| 2105 |
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
| 2106 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 2107 |
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
| 2108 |
if he does not specify any value for seed, oopse will take the |
| 2109 |
value of seconds of system time as seed |
| 2110 |
|
| 2111 |
2003-08-20 14:42 mmeineke |
| 2112 |
|
| 2113 |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 2114 |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
| 2115 |
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
| 2116 |
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
| 2117 |
|
| 2118 |
added some bug fixes for setting the random number generator seed |
| 2119 |
value. |
| 2120 |
|
| 2121 |
fixed a bug where ghostbend atom b was not being set. ( recent bug |
| 2122 |
from SimState conversion) |
| 2123 |
|
| 2124 |
2003-08-20 14:41 mmeineke |
| 2125 |
|
| 2126 |
* libBASS/Globals.hpp: updated the Changelog. |
| 2127 |
|
| 2128 |
added some bug fixes for setting the random number generator seed |
| 2129 |
value. |
| 2130 |
|
| 2131 |
2003-08-20 14:41 mmeineke |
| 2132 |
|
| 2133 |
* ChangeLog: updated the Changelog. |
| 2134 |
|
| 2135 |
2003-08-20 14:11 tim |
| 2136 |
|
| 2137 |
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
| 2138 |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
| 2139 |
bend class |
| 2140 |
|
| 2141 |
2003-08-20 10:13 mmeineke |
| 2142 |
|
| 2143 |
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
| 2144 |
make links. added -f to ln -s. |
| 2145 |
|
| 2146 |
2003-08-20 09:50 tim |
| 2147 |
|
| 2148 |
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
| 2149 |
|
| 2150 |
2003-08-20 09:34 tim |
| 2151 |
|
| 2152 |
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
| 2153 |
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
| 2154 |
printing |
| 2155 |
|
| 2156 |
2003-08-18 15:59 chuckv |
| 2157 |
|
| 2158 |
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 2159 |
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
| 2160 |
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
| 2161 |
Nanobuilder still broke. |
| 2162 |
|
| 2163 |
2003-08-15 14:24 tim |
| 2164 |
|
| 2165 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 2166 |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 2167 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 2168 |
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
| 2169 |
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
| 2170 |
Method |
| 2171 |
|
| 2172 |
2003-08-14 11:16 tim |
| 2173 |
|
| 2174 |
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
| 2175 |
with average force substraction strategy |
| 2176 |
|
| 2177 |
2003-08-13 16:20 chuckv |
| 2178 |
|
| 2179 |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
| 2180 |
profiling code -DPROFILE. |
| 2181 |
|
| 2182 |
2003-08-13 14:21 tim |
| 2183 |
|
| 2184 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 2185 |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 2186 |
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
| 2187 |
potential & z-contraint method |
| 2188 |
|
| 2189 |
2003-08-12 16:44 mmeineke |
| 2190 |
|
| 2191 |
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
| 2192 |
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 2193 |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 2194 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
| 2195 |
annoying bug in Directional Atom, where mu was getting written to |
| 2196 |
pseudorandom memory location. |
| 2197 |
|
| 2198 |
2003-08-12 14:56 tim |
| 2199 |
|
| 2200 |
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
| 2201 |
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
| 2202 |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 2203 |
libmdtools/SimSetup.cpp: debugging globals |
| 2204 |
|
| 2205 |
2003-08-12 13:40 gezelter |
| 2206 |
|
| 2207 |
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
| 2208 |
and new atypes in LJFF |
| 2209 |
|
| 2210 |
2003-08-12 13:15 gezelter |
| 2211 |
|
| 2212 |
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
| 2213 |
stuff... |
| 2214 |
|
| 2215 |
2003-08-12 13:14 chuckv |
| 2216 |
|
| 2217 |
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
| 2218 |
|
| 2219 |
2003-08-12 13:04 chuckv |
| 2220 |
|
| 2221 |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
| 2222 |
Missed del of files before. |
| 2223 |
|
| 2224 |
2003-08-12 13:03 chuckv |
| 2225 |
|
| 2226 |
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
| 2227 |
message] |
| 2228 |
|
| 2229 |
2003-08-12 13:01 chuckv |
| 2230 |
|
| 2231 |
* utils/sysbuilder/Makefile: commit makefile |
| 2232 |
|
| 2233 |
2003-08-12 12:51 tim |
| 2234 |
|
| 2235 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 2236 |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 2237 |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
| 2238 |
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
| 2239 |
harmonical potential to z-constraint method |
| 2240 |
|
| 2241 |
2003-08-11 17:31 chuckv |
| 2242 |
|
| 2243 |
* utils/Makefile: Changed makefile to only build quicklate. |
| 2244 |
|
| 2245 |
2003-08-11 17:25 chuckv |
| 2246 |
|
| 2247 |
* ac-tools/configure.in: added utils/sysbuilder to be built. |
| 2248 |
|
| 2249 |
2003-08-11 17:12 chuckv |
| 2250 |
|
| 2251 |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 2252 |
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
| 2253 |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
| 2254 |
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
| 2255 |
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
| 2256 |
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
| 2257 |
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
| 2258 |
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
| 2259 |
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
| 2260 |
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
| 2261 |
with new atom allocation in libmdtools. |
| 2262 |
|
| 2263 |
2003-08-11 14:41 tim |
| 2264 |
|
| 2265 |
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
| 2266 |
moving zconstraint molecules to specified positions |
| 2267 |
|
| 2268 |
2003-08-11 14:39 tim |
| 2269 |
|
| 2270 |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
| 2271 |
|
| 2272 |
2003-08-11 14:38 mmeineke |
| 2273 |
|
| 2274 |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 2275 |
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
| 2276 |
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
| 2277 |
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
| 2278 |
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
| 2279 |
libBASS/node_list.h, libBASS/parse_interface.h, |
| 2280 |
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
| 2281 |
into the BASS language syntax. |
| 2282 |
|
| 2283 |
2003-08-11 13:29 mmeineke |
| 2284 |
|
| 2285 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
| 2286 |
degrees of freedom to account for zConstreints |
| 2287 |
|
| 2288 |
2003-08-08 16:22 chuckv |
| 2289 |
|
| 2290 |
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
| 2291 |
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
| 2292 |
samples/metals/Au.bass: EAM works...... Neighbor list also |
| 2293 |
works..... |
| 2294 |
|
| 2295 |
2003-08-08 12:48 mmeineke |
| 2296 |
|
| 2297 |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
| 2298 |
instance of Atom::setZ and Atom::getZ in ZConstaint. |
| 2299 |
|
| 2300 |
2003-08-07 16:47 mmeineke |
| 2301 |
|
| 2302 |
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 2303 |
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
| 2304 |
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
| 2305 |
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
| 2306 |
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
| 2307 |
configuration from SimState rather than arrays from Atom |
| 2308 |
|
| 2309 |
2003-08-06 19:47 chuckv |
| 2310 |
|
| 2311 |
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
| 2312 |
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
| 2313 |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 2314 |
samples/metals/Au.bass: Bug fixes for eam... |
| 2315 |
|
| 2316 |
2003-08-01 11:18 tim |
| 2317 |
|
| 2318 |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
| 2319 |
Z-Constraint |
| 2320 |
|
| 2321 |
2003-07-31 14:59 tim |
| 2322 |
|
| 2323 |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 2324 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 2325 |
libmdtools/ZConstraint.cpp: add index range checking into |
| 2326 |
ZConstraint |
| 2327 |
|
| 2328 |
2003-07-31 10:38 tim |
| 2329 |
|
| 2330 |
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
| 2331 |
to the globals |
| 2332 |
|
| 2333 |
2003-07-31 10:35 tim |
| 2334 |
|
| 2335 |
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
| 2336 |
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
| 2337 |
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
| 2338 |
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
| 2339 |
Added Z constraint. |
| 2340 |
|
| 2341 |
2003-07-30 16:17 chuckv |
| 2342 |
|
| 2343 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
| 2344 |
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
| 2345 |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
| 2346 |
samples/metals/Au.bass: More bug fixes for eam. |
| 2347 |
|
| 2348 |
2003-07-29 11:32 mmeineke |
| 2349 |
|
| 2350 |
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
| 2351 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
| 2352 |
working on the props code |
| 2353 |
|
| 2354 |
2003-07-29 11:32 mmeineke |
| 2355 |
|
| 2356 |
* libBASS/Globals.cpp: [no log message] |
| 2357 |
|
| 2358 |
2003-07-25 15:05 chuckv |
| 2359 |
|
| 2360 |
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
| 2361 |
metals |
| 2362 |
|
| 2363 |
2003-07-25 15:00 chuckv |
| 2364 |
|
| 2365 |
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
| 2366 |
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
| 2367 |
|
| 2368 |
2003-07-24 16:22 chuckv |
| 2369 |
|
| 2370 |
* ac-tools/configure.in: Changed configure to look for both upper |
| 2371 |
and lower cass .mod files |
| 2372 |
|
| 2373 |
2003-07-24 14:57 chuckv |
| 2374 |
|
| 2375 |
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
| 2376 |
eam and do_forces. |
| 2377 |
|
| 2378 |
2003-07-23 17:13 chuckv |
| 2379 |
|
| 2380 |
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
| 2381 |
force_globals.F90, simulation_module.F90, status_module.F90: |
| 2382 |
Finished most code for eam.... |
| 2383 |
|
| 2384 |
2003-07-22 16:49 mmeineke |
| 2385 |
|
| 2386 |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
| 2387 |
function to the DumpReader. It should now save the start of each |
| 2388 |
frame in a vector. |
| 2389 |
|
| 2390 |
2003-07-22 15:05 mmeineke |
| 2391 |
|
| 2392 |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
| 2393 |
to read dump files |
| 2394 |
|
| 2395 |
2003-07-22 14:54 tim |
| 2396 |
|
| 2397 |
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
| 2398 |
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
| 2399 |
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
| 2400 |
message] |
| 2401 |
|
| 2402 |
2003-07-22 11:41 mmeineke |
| 2403 |
|
| 2404 |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 2405 |
SimSetup.cpp: Fixed a current time initialization bug in |
| 2406 |
InitFromFile. |
| 2407 |
|
| 2408 |
2003-07-21 16:27 mmeineke |
| 2409 |
|
| 2410 |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
| 2411 |
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
| 2412 |
friends to accomadate random file access |
| 2413 |
|
| 2414 |
2003-07-21 11:23 mmeineke |
| 2415 |
|
| 2416 |
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
| 2417 |
one sets it. |
| 2418 |
|
| 2419 |
2003-07-21 11:23 mmeineke |
| 2420 |
|
| 2421 |
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
| 2422 |
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
| 2423 |
from the time specified in the init file. |
| 2424 |
|
| 2425 |
2003-07-17 16:49 gezelter |
| 2426 |
|
| 2427 |
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 2428 |
DumpReader.cpp: Started work on a DumpReader |
| 2429 |
|
| 2430 |
2003-07-17 15:38 gezelter |
| 2431 |
|
| 2432 |
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
| 2433 |
|
| 2434 |
2003-07-17 15:32 gezelter |
| 2435 |
|
| 2436 |
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
| 2437 |
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
| 2438 |
Changes for SSD/E |
| 2439 |
|
| 2440 |
2003-07-17 14:38 mmeineke |
| 2441 |
|
| 2442 |
* libmdtools/do_Forces.F90: commented out an eam line |
| 2443 |
|
| 2444 |
2003-07-17 14:32 chuckv |
| 2445 |
|
| 2446 |
* libmdtools/atype_module.F90: fixed spelling issue |
| 2447 |
|
| 2448 |
2003-07-17 14:29 chuckv |
| 2449 |
|
| 2450 |
* libmdtools/: fInfo.c, status_module.F90: added info module |
| 2451 |
|
| 2452 |
2003-07-17 14:25 chuckv |
| 2453 |
|
| 2454 |
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
| 2455 |
atype_module.F90, calc_eam.F90, do_Forces.F90, |
| 2456 |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 2457 |
mpiSimulation_module.F90: Added massive changes for eam.... |
| 2458 |
|
| 2459 |
2003-07-16 16:49 chuckv |
| 2460 |
|
| 2461 |
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
| 2462 |
|
| 2463 |
2003-07-16 16:30 mmeineke |
| 2464 |
|
| 2465 |
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
| 2466 |
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 2467 |
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
| 2468 |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 2469 |
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
| 2470 |
wrappers.F90: Changed how cutoffs were handled from C. Now |
| 2471 |
notifyCutoffs in Fortran notifies those who need the information of |
| 2472 |
any changes to cutoffs. |
| 2473 |
|
| 2474 |
2003-07-16 12:35 gezelter |
| 2475 |
|
| 2476 |
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
| 2477 |
quickLate is now somewhat more intelligent about periodic |
| 2478 |
boundaries and wrapping. |
| 2479 |
|
| 2480 |
2003-07-16 11:40 chuckv |
| 2481 |
|
| 2482 |
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
| 2483 |
|
| 2484 |
2003-07-16 10:34 mmeineke |
| 2485 |
|
| 2486 |
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
| 2487 |
rebuilds on BoB |
| 2488 |
|
| 2489 |
2003-07-15 21:11 gezelter |
| 2490 |
|
| 2491 |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
| 2492 |
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
| 2493 |
fixes for box changes |
| 2494 |
|
| 2495 |
2003-07-15 17:29 mmeineke |
| 2496 |
|
| 2497 |
* libmdtools/simulation_module.F90: removed some debugging print |
| 2498 |
statements. |
| 2499 |
|
| 2500 |
2003-07-15 17:22 mmeineke |
| 2501 |
|
| 2502 |
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 2503 |
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
| 2504 |
do_forces. Rrf was not being used in the neighborlist correctly. |
| 2505 |
rcut was conssistently being set lowere than Rrf causing the dipole |
| 2506 |
cutoff region to be to small. Also led to the removal of the taper |
| 2507 |
region to buffer the dipole cutoff. |
| 2508 |
|
| 2509 |
2003-07-15 16:34 mmeineke |
| 2510 |
|
| 2511 |
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
| 2512 |
fixing ssd bug |
| 2513 |
|
| 2514 |
2003-07-15 14:56 gezelter |
| 2515 |
|
| 2516 |
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
| 2517 |
for the NPT ensembles |
| 2518 |
|
| 2519 |
2003-07-15 13:52 mmeineke |
| 2520 |
|
| 2521 |
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
| 2522 |
simSetup |
| 2523 |
|
| 2524 |
2003-07-15 12:57 mmeineke |
| 2525 |
|
| 2526 |
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
| 2527 |
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
| 2528 |
fixed some bugs, Changed entry_plug to info where appropriate |
| 2529 |
|
| 2530 |
2003-07-15 12:25 chuckv |
| 2531 |
|
| 2532 |
* utils/sysBuild.ggo: added more command line arguments |
| 2533 |
|
| 2534 |
2003-07-15 12:11 gezelter |
| 2535 |
|
| 2536 |
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
| 2537 |
Fixing force field line |
| 2538 |
|
| 2539 |
2003-07-15 12:10 gezelter |
| 2540 |
|
| 2541 |
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
| 2542 |
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 2543 |
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
| 2544 |
tensor |
| 2545 |
|
| 2546 |
2003-07-15 10:50 gezelter |
| 2547 |
|
| 2548 |
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
| 2549 |
|
| 2550 |
2003-07-15 10:42 gezelter |
| 2551 |
|
| 2552 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
| 2553 |
removed old outdated code |
| 2554 |
|
| 2555 |
2003-07-15 09:45 gezelter |
| 2556 |
|
| 2557 |
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
| 2558 |
|
| 2559 |
2003-07-15 09:28 gezelter |
| 2560 |
|
| 2561 |
* libmdtools/Molecule.cpp: removing get_vx |
| 2562 |
|
| 2563 |
2003-07-14 22:28 gezelter |
| 2564 |
|
| 2565 |
* libmdtools/NPTfm.cpp: Added NPTfm |
| 2566 |
|
| 2567 |
2003-07-14 22:27 gezelter |
| 2568 |
|
| 2569 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 2570 |
Bugfix in NPTim, fixes for NPTfm |
| 2571 |
|
| 2572 |
2003-07-14 22:08 gezelter |
| 2573 |
|
| 2574 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 2575 |
Checking in changes for NPTim |
| 2576 |
|
| 2577 |
2003-07-14 18:06 gezelter |
| 2578 |
|
| 2579 |
* utils/Makefile: Broken SysBuilder |
| 2580 |
|
| 2581 |
2003-07-14 18:06 gezelter |
| 2582 |
|
| 2583 |
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 2584 |
argon/init_argon.eor, minimizer/argon/argon.bass, |
| 2585 |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
| 2586 |
water/init_ssd.eor: Fixes for samples |
| 2587 |
|
| 2588 |
2003-07-14 18:06 gezelter |
| 2589 |
|
| 2590 |
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
| 2591 |
debugging write statements |
| 2592 |
|
| 2593 |
2003-07-14 17:38 gezelter |
| 2594 |
|
| 2595 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
| 2596 |
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
| 2597 |
|
| 2598 |
2003-07-14 16:48 mmeineke |
| 2599 |
|
| 2600 |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
| 2601 |
and set routines to Atom and DirectionalAtom |
| 2602 |
|
| 2603 |
2003-07-14 16:35 chuckv |
| 2604 |
|
| 2605 |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
| 2606 |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
| 2607 |
that takes different cmd line arguments. |
| 2608 |
|
| 2609 |
2003-07-14 16:28 mmeineke |
| 2610 |
|
| 2611 |
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
| 2612 |
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
| 2613 |
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
| 2614 |
were not being updated |
| 2615 |
|
| 2616 |
2003-07-14 10:04 gezelter |
| 2617 |
|
| 2618 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
| 2619 |
NPTim |
| 2620 |
|
| 2621 |
2003-07-14 09:55 mmeineke |
| 2622 |
|
| 2623 |
* forceFields/DUFF.frc: Switched the bond in the force field back |
| 2624 |
to constrained, to preserve energy |
| 2625 |
|
| 2626 |
2003-07-11 17:34 mmeineke |
| 2627 |
|
| 2628 |
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
| 2629 |
Integrator.hpp: working on som integrator bugs |
| 2630 |
|
| 2631 |
2003-07-11 10:26 gezelter |
| 2632 |
|
| 2633 |
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
| 2634 |
to worry about all the strtok() calls in our code |
| 2635 |
|
| 2636 |
2003-07-11 09:49 gezelter |
| 2637 |
|
| 2638 |
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
| 2639 |
|
| 2640 |
2003-07-10 20:15 gezelter |
| 2641 |
|
| 2642 |
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
| 2643 |
eor. |
| 2644 |
|
| 2645 |
2003-07-10 17:15 mmeineke |
| 2646 |
|
| 2647 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
| 2648 |
SimInfo.cpp, Thermo.cpp: fixed some bugs |
| 2649 |
|
| 2650 |
2003-07-10 14:53 chuckv |
| 2651 |
|
| 2652 |
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
| 2653 |
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
| 2654 |
nanoBuilder and a general Lattice builder. |
| 2655 |
|
| 2656 |
2003-07-10 12:10 gezelter |
| 2657 |
|
| 2658 |
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
| 2659 |
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
| 2660 |
|
| 2661 |
2003-07-09 17:14 mmeineke |
| 2662 |
|
| 2663 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 2664 |
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
| 2665 |
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
| 2666 |
caclulation of HmatInverse. |
| 2667 |
|
| 2668 |
2003-07-09 10:34 mmeineke |
| 2669 |
|
| 2670 |
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
| 2671 |
|
| 2672 |
2003-07-09 10:33 mmeineke |
| 2673 |
|
| 2674 |
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
| 2675 |
|
| 2676 |
2003-07-09 08:56 gezelter |
| 2677 |
|
| 2678 |
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
| 2679 |
|
| 2680 |
2003-07-09 08:56 gezelter |
| 2681 |
|
| 2682 |
* libBASS/Globals.cpp: Removed Qmass |
| 2683 |
|
| 2684 |
2003-07-08 21:15 gezelter |
| 2685 |
|
| 2686 |
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
| 2687 |
and NPTi |
| 2688 |
|
| 2689 |
2003-07-08 20:41 gezelter |
| 2690 |
|
| 2691 |
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
| 2692 |
|
| 2693 |
2003-07-08 16:10 gezelter |
| 2694 |
|
| 2695 |
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
| 2696 |
|
| 2697 |
2003-07-08 16:06 gezelter |
| 2698 |
|
| 2699 |
* libmdtools/NPTi.cpp: fixed box scaling |
| 2700 |
|
| 2701 |
2003-07-08 15:56 gezelter |
| 2702 |
|
| 2703 |
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
| 2704 |
SimInfo.hpp, Thermo.cpp: NPTi |
| 2705 |
|
| 2706 |
2003-07-03 14:41 mmeineke |
| 2707 |
|
| 2708 |
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
| 2709 |
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
| 2710 |
scripts in the makefiles |
| 2711 |
|
| 2712 |
2003-07-02 16:26 mmeineke |
| 2713 |
|
| 2714 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 2715 |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 2716 |
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
| 2717 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 2718 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 2719 |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
| 2720 |
utils/Makefile: fixed the bugs introduced by switching the periodic |
| 2721 |
box to a matrix |
| 2722 |
|
| 2723 |
2003-07-01 17:39 gezelter |
| 2724 |
|
| 2725 |
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
| 2726 |
|
| 2727 |
2003-07-01 17:29 gezelter |
| 2728 |
|
| 2729 |
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
| 2730 |
|
| 2731 |
2003-07-01 16:33 mmeineke |
| 2732 |
|
| 2733 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
| 2734 |
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
| 2735 |
the box matrix to everything. |
| 2736 |
|
| 2737 |
2003-06-30 17:03 mmeineke |
| 2738 |
|
| 2739 |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 2740 |
src/oopse.cpp: |
| 2741 |
Updated the ChangeLog, and Converted most of the SImInfo to use |
| 2742 |
non-Isotropic boxes. wrapVector needs to be finished. |
| 2743 |
|
| 2744 |
2003-06-25 16:12 mmeineke |
| 2745 |
|
| 2746 |
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
| 2747 |
to Harmonic bonds in the DUFF frc file |
| 2748 |
|
| 2749 |
fixed constraints. |
| 2750 |
|
| 2751 |
2003-06-25 16:11 mmeineke |
| 2752 |
|
| 2753 |
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
| 2754 |
the DUFF frc file |
| 2755 |
|
| 2756 |
2003-06-24 17:51 gezelter |
| 2757 |
|
| 2758 |
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
| 2759 |
|
| 2760 |
2003-06-24 14:57 mmeineke |
| 2761 |
|
| 2762 |
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
| 2763 |
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
| 2764 |
the DUFF forcefield and BondExtensions.cpp |
| 2765 |
|
| 2766 |
2003-06-23 16:24 mmeineke |
| 2767 |
|
| 2768 |
* libmdtools/Integrator.cpp: Doing some work to debug the |
| 2769 |
constraint code. |
| 2770 |
|
| 2771 |
2003-06-20 15:50 gezelter |
| 2772 |
|
| 2773 |
* libmdtools/Integrator.hpp: NPT fix |
| 2774 |
|
| 2775 |
2003-06-20 15:29 mmeineke |
| 2776 |
|
| 2777 |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 2778 |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 2779 |
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
| 2780 |
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
| 2781 |
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
| 2782 |
integrator and NVT seem to be working now. |
| 2783 |
|
| 2784 |
2003-06-20 11:49 gezelter |
| 2785 |
|
| 2786 |
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
| 2787 |
|
| 2788 |
2003-06-19 17:02 mmeineke |
| 2789 |
|
| 2790 |
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
| 2791 |
forceFields/LJ_FF.frc, forceFields/Makefile, |
| 2792 |
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
| 2793 |
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
| 2794 |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 2795 |
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
| 2796 |
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
| 2797 |
forcefield names. |
| 2798 |
|
| 2799 |
2003-06-19 14:21 mmeineke |
| 2800 |
|
| 2801 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
| 2802 |
finished the basics of the integrator and SimSetup.cpp |
| 2803 |
|
| 2804 |
2003-06-19 14:11 mmeineke |
| 2805 |
|
| 2806 |
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
| 2807 |
up / get it to work with the new Integrator. |
| 2808 |
|
| 2809 |
2003-06-18 17:20 mmeineke |
| 2810 |
|
| 2811 |
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
| 2812 |
output times. |
| 2813 |
|
| 2814 |
2003-06-17 16:56 mmeineke |
| 2815 |
|
| 2816 |
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
| 2817 |
fro the ghost Bend in TraPPE_Ex |
| 2818 |
|
| 2819 |
some work on the integrator. ( incomplete) |
| 2820 |
|
| 2821 |
2003-06-17 16:55 mmeineke |
| 2822 |
|
| 2823 |
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
| 2824 |
Bend in TraPPE_Ex |
| 2825 |
|
| 2826 |
2003-06-04 16:06 mmeineke |
| 2827 |
|
| 2828 |
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
| 2829 |
constrainB to the Symplectic integrator |
| 2830 |
|
| 2831 |
2003-05-30 16:32 mmeineke |
| 2832 |
|
| 2833 |
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
| 2834 |
the basic integrator. |
| 2835 |
|
| 2836 |
bilayerSys.cpp altered for building tb3. |
| 2837 |
|
| 2838 |
2003-05-30 16:31 mmeineke |
| 2839 |
|
| 2840 |
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
| 2841 |
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
| 2842 |
modifiying Symplectic to become the basic integrator. |
| 2843 |
|
| 2844 |
2003-05-30 15:19 mmeineke |
| 2845 |
|
| 2846 |
* libmdtools/Integrator.hpp: added some member variables for |
| 2847 |
position, velocity, etc. |
| 2848 |
|
| 2849 |
2003-05-30 14:07 mmeineke |
| 2850 |
|
| 2851 |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
| 2852 |
is now derived from Integrator |
| 2853 |
|
| 2854 |
2003-05-20 11:44 mmeineke |
| 2855 |
|
| 2856 |
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
| 2857 |
|
| 2858 |
2003-05-17 11:57 mmeineke |
| 2859 |
|
| 2860 |
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
| 2861 |
working |
| 2862 |
|
| 2863 |
2003-05-16 16:37 mmeineke |
| 2864 |
|
| 2865 |
* utils/bilayerSys.cpp: still working on the bilayer code |
| 2866 |
|
| 2867 |
2003-05-16 09:28 mmeineke |
| 2868 |
|
| 2869 |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
| 2870 |
work to overhaul sysbuild. |
| 2871 |
|
| 2872 |
2003-05-13 16:23 mmeineke |
| 2873 |
|
| 2874 |
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
| 2875 |
|
| 2876 |
2003-05-13 15:47 mmeineke |
| 2877 |
|
| 2878 |
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
| 2879 |
beadLipid/water.mdl: Added bead lipid model to the sample directory |
| 2880 |
|
| 2881 |
2003-05-13 15:34 mmeineke |
| 2882 |
|
| 2883 |
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
| 2884 |
the Trappe extended force field |
| 2885 |
|
| 2886 |
2003-05-13 12:01 mmeineke |
| 2887 |
|
| 2888 |
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
| 2889 |
TraPPe_Ex forceField |
| 2890 |
|
| 2891 |
2003-05-09 14:51 mmeineke |
| 2892 |
|
| 2893 |
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
| 2894 |
there were some duplicate entries |
| 2895 |
|
| 2896 |
added a two chain lipid to the lipid.mdl in sample |
| 2897 |
|
| 2898 |
2003-05-09 14:51 mmeineke |
| 2899 |
|
| 2900 |
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
| 2901 |
there were some duplicate entries |
| 2902 |
|
| 2903 |
2003-05-09 11:56 mmeineke |
| 2904 |
|
| 2905 |
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
| 2906 |
configure script |
| 2907 |
|
| 2908 |
added the CH branching group to the TraPPE_Ex fource field |
| 2909 |
|
| 2910 |
2003-05-09 11:55 mmeineke |
| 2911 |
|
| 2912 |
* ac-tools/configure.in: added the utils subdirectory to the |
| 2913 |
configure script |
| 2914 |
|
| 2915 |
2003-04-25 11:02 mmeineke |
| 2916 |
|
| 2917 |
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
| 2918 |
bilayer builder |
| 2919 |
|
| 2920 |
2003-04-24 21:00 mmeineke |
| 2921 |
|
| 2922 |
* libmdtools/f_verlet_constrained.F90: added a new test for |
| 2923 |
constraint failure |
| 2924 |
|
| 2925 |
2003-04-17 16:54 mmeineke |
| 2926 |
|
| 2927 |
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
| 2928 |
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 2929 |
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
| 2930 |
build our systems |
| 2931 |
|
| 2932 |
2003-04-16 16:11 mmeineke |
| 2933 |
|
| 2934 |
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
| 2935 |
|
| 2936 |
2003-04-15 16:47 mmeineke |
| 2937 |
|
| 2938 |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
| 2939 |
and sysBuild both will build now. woot! |
| 2940 |
|
| 2941 |
2003-04-15 16:20 mmeineke |
| 2942 |
|
| 2943 |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 2944 |
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
| 2945 |
|
| 2946 |
sysBuild still need to write the bass file. |
| 2947 |
|
| 2948 |
MoLocator.cpp is currently empty |
| 2949 |
|
| 2950 |
2003-04-15 15:40 chuckv |
| 2951 |
|
| 2952 |
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
| 2953 |
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
| 2954 |
forceFields/pdu3.eam, forceFields/ptu3.eam, |
| 2955 |
libmdtools/ForceFields.hpp: Added eam force files... |
| 2956 |
|
| 2957 |
2003-04-15 11:37 chuckv |
| 2958 |
|
| 2959 |
* libmdtools/EAM_FF.cpp: More eam work. |
| 2960 |
|
| 2961 |
2003-04-14 16:22 mmeineke |
| 2962 |
|
| 2963 |
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
| 2964 |
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
| 2965 |
working on the system builder |
| 2966 |
|
| 2967 |
2003-04-14 16:16 chuckv |
| 2968 |
|
| 2969 |
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
| 2970 |
ordering on NVT calculation in integrators. |
| 2971 |
|
| 2972 |
2003-04-14 14:51 mmeineke |
| 2973 |
|
| 2974 |
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
| 2975 |
obj/placeHolder: working on a system builder |
| 2976 |
|
| 2977 |
2003-04-14 14:04 mmeineke |
| 2978 |
|
| 2979 |
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
| 2980 |
|
| 2981 |
added sysBuild to the utils Makefile |
| 2982 |
|
| 2983 |
2003-04-14 14:03 mmeineke |
| 2984 |
|
| 2985 |
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
| 2986 |
Ghost bends to the TraPPE_Ex forceField |
| 2987 |
|
| 2988 |
2003-04-14 13:19 chuckv |
| 2989 |
|
| 2990 |
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
| 2991 |
|
| 2992 |
2003-04-11 13:46 mmeineke |
| 2993 |
|
| 2994 |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
| 2995 |
simulation_module.F90: fixed a memory bug in Fortran, where |
| 2996 |
molMembershipArray was declared nLocal instead of nGlobal. |
| 2997 |
|
| 2998 |
2003-04-11 10:16 gezelter |
| 2999 |
|
| 3000 |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 3001 |
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
| 3002 |
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
| 3003 |
for NPT |
| 3004 |
|
| 3005 |
2003-04-10 15:08 mmeineke |
| 3006 |
|
| 3007 |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
| 3008 |
globalIndex counter to Molecule |
| 3009 |
|
| 3010 |
2003-04-10 11:35 gezelter |
| 3011 |
|
| 3012 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
| 3013 |
ConstantStress |
| 3014 |
|
| 3015 |
2003-04-10 11:27 mmeineke |
| 3016 |
|
| 3017 |
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
| 3018 |
caused a miscalculation of nLocal. |
| 3019 |
|
| 3020 |
2003-04-10 11:21 mmeineke |
| 3021 |
|
| 3022 |
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
| 3023 |
do_Forces.F90: fixed a bug in symplectic, where presure was only |
| 3024 |
being calculated the first time through. |
| 3025 |
|
| 3026 |
2003-04-09 11:20 chuckv |
| 3027 |
|
| 3028 |
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
| 3029 |
file |
| 3030 |
|
| 3031 |
2003-04-09 08:59 gezelter |
| 3032 |
|
| 3033 |
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
| 3034 |
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
| 3035 |
|
| 3036 |
2003-04-08 23:06 gezelter |
| 3037 |
|
| 3038 |
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
| 3039 |
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 3040 |
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
| 3041 |
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 3042 |
calc_reaction_field.F90, calc_sticky_pair.F90, |
| 3043 |
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
| 3044 |
NVT |
| 3045 |
|
| 3046 |
2003-04-08 17:38 chuckv |
| 3047 |
|
| 3048 |
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
| 3049 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 3050 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 3051 |
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
| 3052 |
(kinda)... |
| 3053 |
|
| 3054 |
2003-04-08 16:35 gezelter |
| 3055 |
|
| 3056 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 3057 |
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
| 3058 |
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
| 3059 |
|
| 3060 |
2003-04-08 12:16 chuckv |
| 3061 |
|
| 3062 |
* libmdtools/: do_Forces.F90, neighborLists.F90, |
| 3063 |
simulation_module.F90: Moved expand neighborlist to init_FF. |
| 3064 |
|
| 3065 |
2003-04-08 10:20 chuckv |
| 3066 |
|
| 3067 |
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
| 3068 |
NVT |
| 3069 |
|
| 3070 |
2003-04-08 09:39 gezelter |
| 3071 |
|
| 3072 |
* libmdtools/Verlet.cpp: fixes for nvt / npt |
| 3073 |
|
| 3074 |
2003-04-08 09:34 gezelter |
| 3075 |
|
| 3076 |
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
| 3077 |
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
| 3078 |
|
| 3079 |
2003-04-08 07:50 gezelter |
| 3080 |
|
| 3081 |
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
| 3082 |
|
| 3083 |
2003-04-08 07:44 gezelter |
| 3084 |
|
| 3085 |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 3086 |
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
| 3087 |
NVT and NPT ensembles |
| 3088 |
|
| 3089 |
2003-04-07 16:42 gezelter |
| 3090 |
|
| 3091 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 3092 |
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
| 3093 |
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
| 3094 |
|
| 3095 |
2003-04-07 16:20 mmeineke |
| 3096 |
|
| 3097 |
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
| 3098 |
portion of SSD. |
| 3099 |
|
| 3100 |
2003-04-07 16:16 mmeineke |
| 3101 |
|
| 3102 |
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
| 3103 |
doing some testing in sticky through Symplectic. |
| 3104 |
|
| 3105 |
2003-04-07 15:51 gezelter |
| 3106 |
|
| 3107 |
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
| 3108 |
|
| 3109 |
2003-04-07 15:50 chuckv |
| 3110 |
|
| 3111 |
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
| 3112 |
tau and virial. |
| 3113 |
|
| 3114 |
2003-04-07 15:06 mmeineke |
| 3115 |
|
| 3116 |
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
| 3117 |
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
| 3118 |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
| 3119 |
src/Makefile: bug fixes |
| 3120 |
|
| 3121 |
2003-04-07 11:56 gezelter |
| 3122 |
|
| 3123 |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 3124 |
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
| 3125 |
Many fixes to add extended system |
| 3126 |
|
| 3127 |
2003-04-07 09:30 gezelter |
| 3128 |
|
| 3129 |
* src/Makefile: Fixed a bug caused by my experimentation |
| 3130 |
|
| 3131 |
2003-04-07 09:30 gezelter |
| 3132 |
|
| 3133 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
| 3134 |
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
| 3135 |
Added ExtendedSystem infrastructure for NPT and NVT calculations |
| 3136 |
|
| 3137 |
2003-04-07 09:30 gezelter |
| 3138 |
|
| 3139 |
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
| 3140 |
|
| 3141 |
2003-04-04 23:07 gezelter |
| 3142 |
|
| 3143 |
* src/Makefile: final mods to try a fortran compiler |
| 3144 |
|
| 3145 |
2003-04-04 22:39 gezelter |
| 3146 |
|
| 3147 |
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
| 3148 |
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
| 3149 |
|
| 3150 |
2003-04-04 21:56 gezelter |
| 3151 |
|
| 3152 |
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
| 3153 |
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
| 3154 |
|
| 3155 |
2003-04-04 21:45 gezelter |
| 3156 |
|
| 3157 |
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
| 3158 |
fixes to fortran wrappers |
| 3159 |
|
| 3160 |
2003-04-04 17:22 chuckv |
| 3161 |
|
| 3162 |
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 3163 |
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
| 3164 |
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 3165 |
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
| 3166 |
smarter, fortran gets dumber... |
| 3167 |
|
| 3168 |
2003-04-04 14:57 mmeineke |
| 3169 |
|
| 3170 |
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
| 3171 |
neighborLists.F90: fixed a memory read bug in neighborlist |
| 3172 |
|
| 3173 |
2003-04-04 14:47 gezelter |
| 3174 |
|
| 3175 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 3176 |
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
| 3177 |
|
| 3178 |
2003-04-04 14:16 gezelter |
| 3179 |
|
| 3180 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 3181 |
SimInfo.hpp: Fixes for ExtendedSystem |
| 3182 |
|
| 3183 |
2003-04-03 20:57 gezelter |
| 3184 |
|
| 3185 |
* libmdtools/ExtendedSystem.hpp: Added extended system header |
| 3186 |
|
| 3187 |
2003-04-03 20:57 gezelter |
| 3188 |
|
| 3189 |
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
| 3190 |
for extended system code |
| 3191 |
|
| 3192 |
2003-04-03 18:49 gezelter |
| 3193 |
|
| 3194 |
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
| 3195 |
extendedsystem |
| 3196 |
|
| 3197 |
2003-04-03 17:19 mmeineke |
| 3198 |
|
| 3199 |
* libmdtools/Molecule.hpp: added some little fixes here and there. |
| 3200 |
|
| 3201 |
2003-04-03 17:01 mmeineke |
| 3202 |
|
| 3203 |
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
| 3204 |
initialize bug. |
| 3205 |
|
| 3206 |
2003-04-03 16:12 mmeineke |
| 3207 |
|
| 3208 |
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
| 3209 |
little things like deleteing unused variables and such. |
| 3210 |
|
| 3211 |
2003-04-03 15:57 mmeineke |
| 3212 |
|
| 3213 |
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
| 3214 |
simError.h also some fixes to Molecule.hpp |
| 3215 |
|
| 3216 |
2003-04-03 15:57 mmeineke |
| 3217 |
|
| 3218 |
* libBASS/simError.h: a few fixes to simError.h |
| 3219 |
|
| 3220 |
2003-04-03 15:21 mmeineke |
| 3221 |
|
| 3222 |
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
| 3223 |
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
| 3224 |
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
| 3225 |
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
| 3226 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
| 3227 |
src/Makefile, src/oopse.cpp: fixed some small things with |
| 3228 |
simError.h |
| 3229 |
|
| 3230 |
2003-04-03 15:19 gezelter |
| 3231 |
|
| 3232 |
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
| 3233 |
|
| 3234 |
2003-04-03 14:58 gezelter |
| 3235 |
|
| 3236 |
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
| 3237 |
now) |
| 3238 |
|
| 3239 |
2003-04-03 08:42 gezelter |
| 3240 |
|
| 3241 |
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
| 3242 |
Changed Readme, added some files |
| 3243 |
|
| 3244 |
2003-04-02 17:19 mmeineke |
| 3245 |
|
| 3246 |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
| 3247 |
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
| 3248 |
dipoles mostly work, but there is a memory leak somewhere. |
| 3249 |
|
| 3250 |
2003-04-02 10:01 mmeineke |
| 3251 |
|
| 3252 |
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
| 3253 |
the proper atomIdents. |
| 3254 |
|
| 3255 |
2003-04-01 11:50 chuckv |
| 3256 |
|
| 3257 |
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 3258 |
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 3259 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
| 3260 |
bug fixes.... |
| 3261 |
|
| 3262 |
2003-04-01 11:49 mmeineke |
| 3263 |
|
| 3264 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
| 3265 |
DumpWriter to be more robust to errors. also added a little |
| 3266 |
namespace to InitFromFile to wrap it's helper functions in MPI |
| 3267 |
|
| 3268 |
2003-03-31 17:09 chuckv |
| 3269 |
|
| 3270 |
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
| 3271 |
not zeroed. |
| 3272 |
|
| 3273 |
2003-03-31 16:50 chuckv |
| 3274 |
|
| 3275 |
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
| 3276 |
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 3277 |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 3278 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 3279 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
| 3280 |
samples/alkane/butane.bass: Fixes in MPI force calc and in |
| 3281 |
Trappe_Ex parsing. |
| 3282 |
|
| 3283 |
2003-03-28 17:34 chuckv |
| 3284 |
|
| 3285 |
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
| 3286 |
|
| 3287 |
2003-03-28 16:45 chuckv |
| 3288 |
|
| 3289 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 3290 |
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
| 3291 |
routines. |
| 3292 |
|
| 3293 |
2003-03-28 14:33 mmeineke |
| 3294 |
|
| 3295 |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
| 3296 |
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
| 3297 |
bug where the Excludes were not being created properly |
| 3298 |
|
| 3299 |
2003-03-28 14:30 chuckv |
| 3300 |
|
| 3301 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 3302 |
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
| 3303 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
| 3304 |
and debugging mpi read write from file. |
| 3305 |
|
| 3306 |
2003-03-28 10:28 mmeineke |
| 3307 |
|
| 3308 |
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
| 3309 |
interactions in Trappe |
| 3310 |
|
| 3311 |
2003-03-27 18:33 chuckv |
| 3312 |
|
| 3313 |
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
| 3314 |
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
| 3315 |
|
| 3316 |
2003-03-27 17:16 mmeineke |
| 3317 |
|
| 3318 |
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
| 3319 |
excludes were not being initialized |
| 3320 |
|
| 3321 |
2003-03-27 16:52 mmeineke |
| 3322 |
|
| 3323 |
* src/Makefile: [no log message] |
| 3324 |
|
| 3325 |
2003-03-27 16:52 mmeineke |
| 3326 |
|
| 3327 |
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
| 3328 |
|
| 3329 |
2003-03-27 16:07 mmeineke |
| 3330 |
|
| 3331 |
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
| 3332 |
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
| 3333 |
Verlet.cpp: fixed the compile time bugs, Source builds and links |
| 3334 |
|
| 3335 |
2003-03-27 15:48 mmeineke |
| 3336 |
|
| 3337 |
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
| 3338 |
more bugs. |
| 3339 |
|
| 3340 |
2003-03-27 15:40 mmeineke |
| 3341 |
|
| 3342 |
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
| 3343 |
|
| 3344 |
2003-03-27 15:39 mmeineke |
| 3345 |
|
| 3346 |
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
| 3347 |
|
| 3348 |
2003-03-27 15:36 mmeineke |
| 3349 |
|
| 3350 |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 3351 |
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
| 3352 |
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
| 3353 |
|
| 3354 |
2003-03-27 15:12 mmeineke |
| 3355 |
|
| 3356 |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 3357 |
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
| 3358 |
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
| 3359 |
to. will now attempt to compile. |
| 3360 |
|
| 3361 |
2003-03-27 14:21 mmeineke |
| 3362 |
|
| 3363 |
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
| 3364 |
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
| 3365 |
updating SimSetup to initialize and use the new MPI division of |
| 3366 |
labour, and Molecule class |
| 3367 |
|
| 3368 |
2003-03-27 12:55 mmeineke |
| 3369 |
|
| 3370 |
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
| 3371 |
use Molecule |
| 3372 |
|
| 3373 |
2003-03-27 12:32 mmeineke |
| 3374 |
|
| 3375 |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
| 3376 |
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
| 3377 |
converted to the new Molecule model. TraPPE_Ex is currently being |
| 3378 |
updated. SimSetups routines are writtten, but not yet called. |
| 3379 |
|
| 3380 |
2003-03-27 10:07 gezelter |
| 3381 |
|
| 3382 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 3383 |
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
| 3384 |
numbering in MPI |
| 3385 |
|
| 3386 |
2003-03-27 09:30 mmeineke |
| 3387 |
|
| 3388 |
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
| 3389 |
|
| 3390 |
2003-03-26 20:49 gezelter |
| 3391 |
|
| 3392 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
| 3393 |
fileio for MPI |
| 3394 |
|
| 3395 |
2003-03-26 18:14 gezelter |
| 3396 |
|
| 3397 |
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
| 3398 |
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
| 3399 |
fixes many bug fixes |
| 3400 |
|
| 3401 |
2003-03-26 17:24 gezelter |
| 3402 |
|
| 3403 |
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
| 3404 |
sequence of atoms on the other processors. Node 0 now fires |
| 3405 |
potatoes at other processors to get them to send french fries back. |
| 3406 |
|
| 3407 |
2003-03-26 17:02 mmeineke |
| 3408 |
|
| 3409 |
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
| 3410 |
making the molecules is in place. ForceField needs to be updated |
| 3411 |
next. |
| 3412 |
|
| 3413 |
2003-03-26 16:54 mmeineke |
| 3414 |
|
| 3415 |
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
| 3416 |
the "static" bugs in Atom and Exclude |
| 3417 |
|
| 3418 |
2003-03-26 16:50 mmeineke |
| 3419 |
|
| 3420 |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
| 3421 |
SimSetup.cpp: still working on the SimSetup routine. also fixed |
| 3422 |
some things in Exclude.hpp |
| 3423 |
|
| 3424 |
2003-03-26 16:24 gezelter |
| 3425 |
|
| 3426 |
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
| 3427 |
|
| 3428 |
2003-03-26 16:23 gezelter |
| 3429 |
|
| 3430 |
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
| 3431 |
and Exclude list |
| 3432 |
|
| 3433 |
2003-03-26 16:04 gezelter |
| 3434 |
|
| 3435 |
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
| 3436 |
delete ranges of atoms |
| 3437 |
|
| 3438 |
2003-03-26 15:45 mmeineke |
| 3439 |
|
| 3440 |
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
| 3441 |
with static arrays similar to the Atom class |
| 3442 |
|
| 3443 |
2003-03-26 15:22 mmeineke |
| 3444 |
|
| 3445 |
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
| 3446 |
overhauling the molecule class to contain it's own bonds, bends, |
| 3447 |
and torsions. |
| 3448 |
|
| 3449 |
may god have mercy on my soul. |
| 3450 |
|
| 3451 |
2003-03-26 14:34 chuckv |
| 3452 |
|
| 3453 |
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
| 3454 |
|
| 3455 |
2003-03-26 13:02 gezelter |
| 3456 |
|
| 3457 |
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
| 3458 |
mpiSimulation.hpp: MPI stuff for passing out molecules |
| 3459 |
|
| 3460 |
2003-03-26 11:12 chuckv |
| 3461 |
|
| 3462 |
* libmdtools/mpiSimulation.cpp: working on load balancing |
| 3463 |
|
| 3464 |
2003-03-26 10:37 chuckv |
| 3465 |
|
| 3466 |
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3467 |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
| 3468 |
for Parallel thermalization |
| 3469 |
|
| 3470 |
2003-03-26 09:55 mmeineke |
| 3471 |
|
| 3472 |
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
| 3473 |
THermo.cpp |
| 3474 |
|
| 3475 |
2003-03-25 17:54 chuckv |
| 3476 |
|
| 3477 |
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
| 3478 |
of potential energy and temperature. |
| 3479 |
|
| 3480 |
2003-03-25 09:29 mmeineke |
| 3481 |
|
| 3482 |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
| 3483 |
src/MPIobj/dummy, src/obj/dummy: [no log message] |
| 3484 |
|
| 3485 |
2003-03-25 09:29 mmeineke |
| 3486 |
|
| 3487 |
* libBASS/MPIobj/dummy: added dummy files to keep the build |
| 3488 |
deirectories from being pruned. |
| 3489 |
|
| 3490 |
2003-03-24 20:07 gezelter |
| 3491 |
|
| 3492 |
* samples/Makefile: moving tests to samples |
| 3493 |
|
| 3494 |
2003-03-24 20:06 gezelter |
| 3495 |
|
| 3496 |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 3497 |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 3498 |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 3499 |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 3500 |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
| 3501 |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
| 3502 |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
| 3503 |
water/ssd.bass, water/water.mdl: moved tests to samples |
| 3504 |
|
| 3505 |
2003-03-24 19:51 gezelter |
| 3506 |
|
| 3507 |
* ac-tools/configure.in: Tests are becoming samples |
| 3508 |
|
| 3509 |
2003-03-24 19:46 gezelter |
| 3510 |
|
| 3511 |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 3512 |
|
| 3513 |
2003-03-24 16:55 gezelter |
| 3514 |
|
| 3515 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
| 3516 |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
| 3517 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
| 3518 |
libmdtools/calc_reaction_field.F90, |
| 3519 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 3520 |
libmdtools/simulation_module.F90: electrostatic changes for dipole |
| 3521 |
/ RF separation |
| 3522 |
|
| 3523 |
2003-03-24 13:33 mmeineke |
| 3524 |
|
| 3525 |
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 3526 |
do_Forces.F90: little bug fixes here and there |
| 3527 |
|
| 3528 |
2003-03-24 10:26 mmeineke |
| 3529 |
|
| 3530 |
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
| 3531 |
where short range interactions were not being calculated. |
| 3532 |
|
| 3533 |
removed some debug print statements |
| 3534 |
|
| 3535 |
2003-03-21 17:11 chuckv |
| 3536 |
|
| 3537 |
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
| 3538 |
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
| 3539 |
various write statements for debugging |
| 3540 |
|
| 3541 |
2003-03-21 16:26 chuckv |
| 3542 |
|
| 3543 |
* forceFields/Makefile: added links to the makefile in forceFields |
| 3544 |
|
| 3545 |
2003-03-21 15:52 gezelter |
| 3546 |
|
| 3547 |
* ac-tools/Make.conf.in, ac-tools/configure.in, |
| 3548 |
libmdtools/Makefile: Fixed F_MACH_DEP bug |
| 3549 |
|
| 3550 |
2003-03-21 15:37 gezelter |
| 3551 |
|
| 3552 |
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
| 3553 |
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
| 3554 |
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
| 3555 |
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
| 3556 |
autoconf fixes |
| 3557 |
|
| 3558 |
2003-03-21 14:58 gezelter |
| 3559 |
|
| 3560 |
* LICENSE: Added license file |
| 3561 |
|
| 3562 |
2003-03-21 14:55 gezelter |
| 3563 |
|
| 3564 |
* forceFields/Makefile: Fixed makefile |
| 3565 |
|
| 3566 |
2003-03-21 14:49 gezelter |
| 3567 |
|
| 3568 |
* forceFields/Makefile: Makefile for forceFields |
| 3569 |
|
| 3570 |
2003-03-21 14:42 gezelter |
| 3571 |
|
| 3572 |
* README: Readme changes |
| 3573 |
|
| 3574 |
2003-03-21 12:52 mmeineke |
| 3575 |
|
| 3576 |
* src/Makefile: [no log message] |
| 3577 |
|
| 3578 |
2003-03-21 12:52 mmeineke |
| 3579 |
|
| 3580 |
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
| 3581 |
|
| 3582 |
2003-03-21 12:42 mmeineke |
| 3583 |
|
| 3584 |
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 3585 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 3586 |
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 3587 |
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 3588 |
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 3589 |
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 3590 |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 3591 |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 3592 |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 3593 |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 3594 |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 3595 |
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 3596 |
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 3597 |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 3598 |
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 3599 |
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 3600 |
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 3601 |
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 3602 |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 3603 |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 3604 |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 3605 |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 3606 |
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 3607 |
utils/sfmakedepend, ac-tools/shtool, |
| 3608 |
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 3609 |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 3610 |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 3611 |
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 3612 |
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 3613 |
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 3614 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 3615 |
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 3616 |
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 3617 |
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 3618 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 3619 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 3620 |
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 3621 |
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3622 |
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 3623 |
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 3624 |
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 3625 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 3626 |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 3627 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 3628 |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 3629 |
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 3630 |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 3631 |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 3632 |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 3633 |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 3634 |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 3635 |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 3636 |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 3637 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 3638 |
revision |
| 3639 |
|
| 3640 |
2003-03-21 12:42 mmeineke |
| 3641 |
|
| 3642 |
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 3643 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 3644 |
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 3645 |
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 3646 |
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 3647 |
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 3648 |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 3649 |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 3650 |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 3651 |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 3652 |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 3653 |
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 3654 |
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 3655 |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 3656 |
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 3657 |
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 3658 |
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 3659 |
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 3660 |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 3661 |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 3662 |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 3663 |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 3664 |
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 3665 |
utils/sfmakedepend, ac-tools/shtool, |
| 3666 |
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 3667 |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 3668 |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 3669 |
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 3670 |
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 3671 |
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 3672 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 3673 |
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 3674 |
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 3675 |
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 3676 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 3677 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 3678 |
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 3679 |
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3680 |
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 3681 |
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 3682 |
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 3683 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 3684 |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 3685 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 3686 |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 3687 |
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 3688 |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 3689 |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 3690 |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 3691 |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 3692 |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 3693 |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 3694 |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 3695 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 3696 |
Tree |
| 3697 |
|
