| 1 |
2003-08-27 14:23 tim |
| 2 |
|
| 3 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 4 |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
| 5 |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
| 6 |
turn on the optimization flag, it causes a seg fault |
| 7 |
|
| 8 |
2003-08-27 11:25 gezelter |
| 9 |
|
| 10 |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 11 |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
| 12 |
stress tensor parallel bug. |
| 13 |
|
| 14 |
2003-08-27 11:16 tim |
| 15 |
|
| 16 |
* ChangeLog, libmdtools/DUFF.cpp, |
| 17 |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
| 18 |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
| 19 |
molMembershipList use global index instead of local index |
| 20 |
|
| 21 |
2003-08-26 15:37 tim |
| 22 |
|
| 23 |
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
| 24 |
mpiSimulation.cpp: set default force substraction policy to |
| 25 |
PolicyByMass |
| 26 |
|
| 27 |
2003-08-26 15:29 tim |
| 28 |
|
| 29 |
* libmdtools/Integrator.cpp: [no log message] |
| 30 |
|
| 31 |
2003-08-26 15:13 mmeineke |
| 32 |
|
| 33 |
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
| 34 |
Statwriter and Dumpwriter to handle files larger than 2 gb. |
| 35 |
|
| 36 |
commented out some print statements in Zconstraint |
| 37 |
|
| 38 |
hard coding some system init into bilayer.sys |
| 39 |
|
| 40 |
2003-08-26 15:12 mmeineke |
| 41 |
|
| 42 |
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
| 43 |
added define statemewnt to Statwriter and Dumpwriter to handle |
| 44 |
files larger than 2 gb. |
| 45 |
|
| 46 |
commented out some print statements in Zconstraint |
| 47 |
|
| 48 |
2003-08-26 15:02 tim |
| 49 |
|
| 50 |
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
| 51 |
and check the seed which is specified by user at least contains 9 |
| 52 |
digits |
| 53 |
|
| 54 |
2003-08-26 13:32 mmeineke |
| 55 |
|
| 56 |
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
| 57 |
|
| 58 |
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
| 59 |
constucted in MPI. (The MPI struct had 6 doubles declared versus |
| 60 |
the actual 11) |
| 61 |
|
| 62 |
2003-08-26 13:30 mmeineke |
| 63 |
|
| 64 |
* Makefile: changed the Makefiel a litle. |
| 65 |
|
| 66 |
2003-08-25 17:17 gezelter |
| 67 |
|
| 68 |
* utils/sysbuilder/Makefile: More FreeBSD fixes |
| 69 |
|
| 70 |
2003-08-25 16:51 gezelter |
| 71 |
|
| 72 |
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
| 73 |
libmdtools/Makefile, src/Makefile: [no log message] |
| 74 |
|
| 75 |
2003-08-22 15:04 mmeineke |
| 76 |
|
| 77 |
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
| 78 |
frequency of output dumps. |
| 79 |
|
| 80 |
2003-08-20 17:23 tim |
| 81 |
|
| 82 |
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
| 83 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 84 |
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
| 85 |
if he does not specify any value for seed, oopse will take the |
| 86 |
value of seconds of system time as seed |
| 87 |
|
| 88 |
2003-08-20 14:42 mmeineke |
| 89 |
|
| 90 |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 91 |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
| 92 |
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
| 93 |
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
| 94 |
|
| 95 |
added some bug fixes for setting the random number generator seed |
| 96 |
value. |
| 97 |
|
| 98 |
fixed a bug where ghostbend atom b was not being set. ( recent bug |
| 99 |
from SimState conversion) |
| 100 |
|
| 101 |
2003-08-20 14:41 mmeineke |
| 102 |
|
| 103 |
* libBASS/Globals.hpp: updated the Changelog. |
| 104 |
|
| 105 |
added some bug fixes for setting the random number generator seed |
| 106 |
value. |
| 107 |
|
| 108 |
2003-08-20 14:41 mmeineke |
| 109 |
|
| 110 |
* ChangeLog: updated the Changelog. |
| 111 |
|
| 112 |
2003-08-20 14:11 tim |
| 113 |
|
| 114 |
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
| 115 |
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
| 116 |
bend class |
| 117 |
|
| 118 |
2003-08-20 10:13 mmeineke |
| 119 |
|
| 120 |
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
| 121 |
make links. added -f to ln -s. |
| 122 |
|
| 123 |
2003-08-20 09:50 tim |
| 124 |
|
| 125 |
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
| 126 |
|
| 127 |
2003-08-20 09:34 tim |
| 128 |
|
| 129 |
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
| 130 |
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
| 131 |
printing |
| 132 |
|
| 133 |
2003-08-18 15:59 chuckv |
| 134 |
|
| 135 |
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 136 |
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
| 137 |
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
| 138 |
Nanobuilder still broke. |
| 139 |
|
| 140 |
2003-08-15 14:24 tim |
| 141 |
|
| 142 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 143 |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 144 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 145 |
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
| 146 |
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
| 147 |
Method |
| 148 |
|
| 149 |
2003-08-14 11:16 tim |
| 150 |
|
| 151 |
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
| 152 |
with average force substraction strategy |
| 153 |
|
| 154 |
2003-08-13 16:20 chuckv |
| 155 |
|
| 156 |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
| 157 |
profiling code -DPROFILE. |
| 158 |
|
| 159 |
2003-08-13 14:21 tim |
| 160 |
|
| 161 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 162 |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 163 |
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
| 164 |
potential & z-contraint method |
| 165 |
|
| 166 |
2003-08-12 16:44 mmeineke |
| 167 |
|
| 168 |
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
| 169 |
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 170 |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 171 |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
| 172 |
annoying bug in Directional Atom, where mu was getting written to |
| 173 |
pseudorandom memory location. |
| 174 |
|
| 175 |
2003-08-12 14:56 tim |
| 176 |
|
| 177 |
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
| 178 |
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
| 179 |
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 180 |
libmdtools/SimSetup.cpp: debugging globals |
| 181 |
|
| 182 |
2003-08-12 13:40 gezelter |
| 183 |
|
| 184 |
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
| 185 |
and new atypes in LJFF |
| 186 |
|
| 187 |
2003-08-12 13:15 gezelter |
| 188 |
|
| 189 |
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
| 190 |
stuff... |
| 191 |
|
| 192 |
2003-08-12 13:14 chuckv |
| 193 |
|
| 194 |
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
| 195 |
|
| 196 |
2003-08-12 13:04 chuckv |
| 197 |
|
| 198 |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
| 199 |
Missed del of files before. |
| 200 |
|
| 201 |
2003-08-12 13:03 chuckv |
| 202 |
|
| 203 |
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
| 204 |
message] |
| 205 |
|
| 206 |
2003-08-12 13:01 chuckv |
| 207 |
|
| 208 |
* utils/sysbuilder/Makefile: commit makefile |
| 209 |
|
| 210 |
2003-08-12 12:51 tim |
| 211 |
|
| 212 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 213 |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 214 |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
| 215 |
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
| 216 |
harmonical potential to z-constraint method |
| 217 |
|
| 218 |
2003-08-11 17:31 chuckv |
| 219 |
|
| 220 |
* utils/Makefile: Changed makefile to only build quicklate. |
| 221 |
|
| 222 |
2003-08-11 17:25 chuckv |
| 223 |
|
| 224 |
* ac-tools/configure.in: added utils/sysbuilder to be built. |
| 225 |
|
| 226 |
2003-08-11 17:12 chuckv |
| 227 |
|
| 228 |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 229 |
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
| 230 |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
| 231 |
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
| 232 |
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
| 233 |
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
| 234 |
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
| 235 |
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
| 236 |
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
| 237 |
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
| 238 |
with new atom allocation in libmdtools. |
| 239 |
|
| 240 |
2003-08-11 14:41 tim |
| 241 |
|
| 242 |
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
| 243 |
moving zconstraint molecules to specified positions |
| 244 |
|
| 245 |
2003-08-11 14:39 tim |
| 246 |
|
| 247 |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
| 248 |
|
| 249 |
2003-08-11 14:38 mmeineke |
| 250 |
|
| 251 |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 252 |
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
| 253 |
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
| 254 |
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
| 255 |
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
| 256 |
libBASS/node_list.h, libBASS/parse_interface.h, |
| 257 |
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
| 258 |
into the BASS language syntax. |
| 259 |
|
| 260 |
2003-08-11 13:29 mmeineke |
| 261 |
|
| 262 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
| 263 |
degrees of freedom to account for zConstreints |
| 264 |
|
| 265 |
2003-08-08 16:22 chuckv |
| 266 |
|
| 267 |
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
| 268 |
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
| 269 |
samples/metals/Au.bass: EAM works...... Neighbor list also |
| 270 |
works..... |
| 271 |
|
| 272 |
2003-08-08 13:32 mmeineke |
| 273 |
|
| 274 |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
| 275 |
moved frameCount's functionality into DumpReader. also split props |
| 276 |
into staticProps and dynamicProps. (currently only have |
| 277 |
staticProps) |
| 278 |
|
| 279 |
2003-08-08 12:48 mmeineke |
| 280 |
|
| 281 |
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
| 282 |
instance of Atom::setZ and Atom::getZ in ZConstaint. |
| 283 |
|
| 284 |
2003-08-07 16:47 mmeineke |
| 285 |
|
| 286 |
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 287 |
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
| 288 |
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
| 289 |
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
| 290 |
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
| 291 |
configuration from SimState rather than arrays from Atom |
| 292 |
|
| 293 |
2003-08-06 19:47 chuckv |
| 294 |
|
| 295 |
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
| 296 |
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
| 297 |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 298 |
samples/metals/Au.bass: Bug fixes for eam... |
| 299 |
|
| 300 |
2003-08-01 11:18 tim |
| 301 |
|
| 302 |
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
| 303 |
Z-Constraint |
| 304 |
|
| 305 |
2003-07-31 14:59 tim |
| 306 |
|
| 307 |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 308 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 309 |
libmdtools/ZConstraint.cpp: add index range checking into |
| 310 |
ZConstraint |
| 311 |
|
| 312 |
2003-07-31 10:38 tim |
| 313 |
|
| 314 |
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
| 315 |
to the globals |
| 316 |
|
| 317 |
2003-07-31 10:35 tim |
| 318 |
|
| 319 |
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
| 320 |
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
| 321 |
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
| 322 |
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
| 323 |
Added Z constraint. |
| 324 |
|
| 325 |
2003-07-30 16:17 chuckv |
| 326 |
|
| 327 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
| 328 |
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
| 329 |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
| 330 |
samples/metals/Au.bass: More bug fixes for eam. |
| 331 |
|
| 332 |
2003-07-29 11:32 mmeineke |
| 333 |
|
| 334 |
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
| 335 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 336 |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
| 337 |
src/Makefile: working on the props code |
| 338 |
|
| 339 |
2003-07-29 11:32 mmeineke |
| 340 |
|
| 341 |
* libBASS/Globals.cpp: [no log message] |
| 342 |
|
| 343 |
2003-07-25 15:05 chuckv |
| 344 |
|
| 345 |
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
| 346 |
metals |
| 347 |
|
| 348 |
2003-07-25 15:00 chuckv |
| 349 |
|
| 350 |
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
| 351 |
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
| 352 |
|
| 353 |
2003-07-24 16:22 chuckv |
| 354 |
|
| 355 |
* ac-tools/configure.in: Changed configure to look for both upper |
| 356 |
and lower cass .mod files |
| 357 |
|
| 358 |
2003-07-24 14:57 chuckv |
| 359 |
|
| 360 |
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
| 361 |
eam and do_forces. |
| 362 |
|
| 363 |
2003-07-23 17:13 chuckv |
| 364 |
|
| 365 |
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
| 366 |
force_globals.F90, simulation_module.F90, status_module.F90: |
| 367 |
Finished most code for eam.... |
| 368 |
|
| 369 |
2003-07-22 16:49 mmeineke |
| 370 |
|
| 371 |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
| 372 |
function to the DumpReader. It should now save the start of each |
| 373 |
frame in a vector. |
| 374 |
|
| 375 |
2003-07-22 15:05 mmeineke |
| 376 |
|
| 377 |
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
| 378 |
to read dump files |
| 379 |
|
| 380 |
2003-07-22 14:54 tim |
| 381 |
|
| 382 |
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
| 383 |
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
| 384 |
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
| 385 |
message] |
| 386 |
|
| 387 |
2003-07-22 11:41 mmeineke |
| 388 |
|
| 389 |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 390 |
SimSetup.cpp: Fixed a current time initialization bug in |
| 391 |
InitFromFile. |
| 392 |
|
| 393 |
2003-07-21 16:27 mmeineke |
| 394 |
|
| 395 |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
| 396 |
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
| 397 |
friends to accomadate random file access |
| 398 |
|
| 399 |
2003-07-21 11:23 mmeineke |
| 400 |
|
| 401 |
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
| 402 |
one sets it. |
| 403 |
|
| 404 |
2003-07-21 11:23 mmeineke |
| 405 |
|
| 406 |
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
| 407 |
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
| 408 |
from the time specified in the init file. |
| 409 |
|
| 410 |
2003-07-17 16:49 gezelter |
| 411 |
|
| 412 |
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 413 |
DumpReader.cpp: Started work on a DumpReader |
| 414 |
|
| 415 |
2003-07-17 15:38 gezelter |
| 416 |
|
| 417 |
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
| 418 |
|
| 419 |
2003-07-17 15:32 gezelter |
| 420 |
|
| 421 |
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
| 422 |
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
| 423 |
Changes for SSD/E |
| 424 |
|
| 425 |
2003-07-17 14:38 mmeineke |
| 426 |
|
| 427 |
* libmdtools/do_Forces.F90: commented out an eam line |
| 428 |
|
| 429 |
2003-07-17 14:32 chuckv |
| 430 |
|
| 431 |
* libmdtools/atype_module.F90: fixed spelling issue |
| 432 |
|
| 433 |
2003-07-17 14:29 chuckv |
| 434 |
|
| 435 |
* libmdtools/: fInfo.c, status_module.F90: added info module |
| 436 |
|
| 437 |
2003-07-17 14:25 chuckv |
| 438 |
|
| 439 |
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
| 440 |
atype_module.F90, calc_eam.F90, do_Forces.F90, |
| 441 |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 442 |
mpiSimulation_module.F90: Added massive changes for eam.... |
| 443 |
|
| 444 |
2003-07-16 16:49 chuckv |
| 445 |
|
| 446 |
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
| 447 |
|
| 448 |
2003-07-16 16:30 mmeineke |
| 449 |
|
| 450 |
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
| 451 |
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 452 |
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
| 453 |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 454 |
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
| 455 |
wrappers.F90: Changed how cutoffs were handled from C. Now |
| 456 |
notifyCutoffs in Fortran notifies those who need the information of |
| 457 |
any changes to cutoffs. |
| 458 |
|
| 459 |
2003-07-16 12:35 gezelter |
| 460 |
|
| 461 |
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
| 462 |
quickLate is now somewhat more intelligent about periodic |
| 463 |
boundaries and wrapping. |
| 464 |
|
| 465 |
2003-07-16 11:40 chuckv |
| 466 |
|
| 467 |
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
| 468 |
|
| 469 |
2003-07-16 10:34 mmeineke |
| 470 |
|
| 471 |
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
| 472 |
rebuilds on BoB |
| 473 |
|
| 474 |
2003-07-15 21:11 gezelter |
| 475 |
|
| 476 |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
| 477 |
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
| 478 |
fixes for box changes |
| 479 |
|
| 480 |
2003-07-15 17:29 mmeineke |
| 481 |
|
| 482 |
* libmdtools/simulation_module.F90: removed some debugging print |
| 483 |
statements. |
| 484 |
|
| 485 |
2003-07-15 17:22 mmeineke |
| 486 |
|
| 487 |
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 488 |
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
| 489 |
do_forces. Rrf was not being used in the neighborlist correctly. |
| 490 |
rcut was conssistently being set lowere than Rrf causing the dipole |
| 491 |
cutoff region to be to small. Also led to the removal of the taper |
| 492 |
region to buffer the dipole cutoff. |
| 493 |
|
| 494 |
2003-07-15 16:34 mmeineke |
| 495 |
|
| 496 |
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
| 497 |
fixing ssd bug |
| 498 |
|
| 499 |
2003-07-15 14:56 gezelter |
| 500 |
|
| 501 |
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
| 502 |
for the NPT ensembles |
| 503 |
|
| 504 |
2003-07-15 13:52 mmeineke |
| 505 |
|
| 506 |
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
| 507 |
simSetup |
| 508 |
|
| 509 |
2003-07-15 12:57 mmeineke |
| 510 |
|
| 511 |
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
| 512 |
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
| 513 |
fixed some bugs, Changed entry_plug to info where appropriate |
| 514 |
|
| 515 |
2003-07-15 12:25 chuckv |
| 516 |
|
| 517 |
* utils/sysBuild.ggo: added more command line arguments |
| 518 |
|
| 519 |
2003-07-15 12:11 gezelter |
| 520 |
|
| 521 |
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
| 522 |
Fixing force field line |
| 523 |
|
| 524 |
2003-07-15 12:10 gezelter |
| 525 |
|
| 526 |
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
| 527 |
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 528 |
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
| 529 |
tensor |
| 530 |
|
| 531 |
2003-07-15 10:50 gezelter |
| 532 |
|
| 533 |
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
| 534 |
|
| 535 |
2003-07-15 10:42 gezelter |
| 536 |
|
| 537 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
| 538 |
removed old outdated code |
| 539 |
|
| 540 |
2003-07-15 09:45 gezelter |
| 541 |
|
| 542 |
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
| 543 |
|
| 544 |
2003-07-15 09:28 gezelter |
| 545 |
|
| 546 |
* libmdtools/Molecule.cpp: removing get_vx |
| 547 |
|
| 548 |
2003-07-14 22:28 gezelter |
| 549 |
|
| 550 |
* libmdtools/NPTfm.cpp: Added NPTfm |
| 551 |
|
| 552 |
2003-07-14 22:27 gezelter |
| 553 |
|
| 554 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 555 |
Bugfix in NPTim, fixes for NPTfm |
| 556 |
|
| 557 |
2003-07-14 22:08 gezelter |
| 558 |
|
| 559 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 560 |
Checking in changes for NPTim |
| 561 |
|
| 562 |
2003-07-14 18:06 gezelter |
| 563 |
|
| 564 |
* utils/Makefile: Broken SysBuilder |
| 565 |
|
| 566 |
2003-07-14 18:06 gezelter |
| 567 |
|
| 568 |
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 569 |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 570 |
for samples |
| 571 |
|
| 572 |
2003-07-14 18:06 gezelter |
| 573 |
|
| 574 |
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
| 575 |
debugging write statements |
| 576 |
|
| 577 |
2003-07-14 17:38 gezelter |
| 578 |
|
| 579 |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
| 580 |
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
| 581 |
|
| 582 |
2003-07-14 16:48 mmeineke |
| 583 |
|
| 584 |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
| 585 |
and set routines to Atom and DirectionalAtom |
| 586 |
|
| 587 |
2003-07-14 16:35 chuckv |
| 588 |
|
| 589 |
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
| 590 |
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
| 591 |
that takes different cmd line arguments. |
| 592 |
|
| 593 |
2003-07-14 16:28 mmeineke |
| 594 |
|
| 595 |
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
| 596 |
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
| 597 |
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
| 598 |
were not being updated |
| 599 |
|
| 600 |
2003-07-14 10:04 gezelter |
| 601 |
|
| 602 |
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
| 603 |
NPTim |
| 604 |
|
| 605 |
2003-07-14 09:55 mmeineke |
| 606 |
|
| 607 |
* forceFields/DUFF.frc: Switched the bond in the force field back |
| 608 |
to constrained, to preserve energy |
| 609 |
|
| 610 |
2003-07-11 17:34 mmeineke |
| 611 |
|
| 612 |
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
| 613 |
Integrator.hpp: working on som integrator bugs |
| 614 |
|
| 615 |
2003-07-11 10:26 gezelter |
| 616 |
|
| 617 |
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
| 618 |
to worry about all the strtok() calls in our code |
| 619 |
|
| 620 |
2003-07-11 09:49 gezelter |
| 621 |
|
| 622 |
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
| 623 |
|
| 624 |
2003-07-10 20:15 gezelter |
| 625 |
|
| 626 |
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
| 627 |
eor. |
| 628 |
|
| 629 |
2003-07-10 17:15 mmeineke |
| 630 |
|
| 631 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
| 632 |
SimInfo.cpp, Thermo.cpp: fixed some bugs |
| 633 |
|
| 634 |
2003-07-10 14:53 chuckv |
| 635 |
|
| 636 |
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
| 637 |
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
| 638 |
nanoBuilder and a general Lattice builder. |
| 639 |
|
| 640 |
2003-07-10 12:10 gezelter |
| 641 |
|
| 642 |
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
| 643 |
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
| 644 |
|
| 645 |
2003-07-09 17:14 mmeineke |
| 646 |
|
| 647 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 648 |
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
| 649 |
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
| 650 |
caclulation of HmatInverse. |
| 651 |
|
| 652 |
2003-07-09 10:34 mmeineke |
| 653 |
|
| 654 |
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
| 655 |
|
| 656 |
2003-07-09 10:33 mmeineke |
| 657 |
|
| 658 |
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
| 659 |
|
| 660 |
2003-07-09 08:56 gezelter |
| 661 |
|
| 662 |
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
| 663 |
|
| 664 |
2003-07-09 08:56 gezelter |
| 665 |
|
| 666 |
* libBASS/Globals.cpp: Removed Qmass |
| 667 |
|
| 668 |
2003-07-08 21:15 gezelter |
| 669 |
|
| 670 |
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
| 671 |
and NPTi |
| 672 |
|
| 673 |
2003-07-08 20:41 gezelter |
| 674 |
|
| 675 |
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
| 676 |
|
| 677 |
2003-07-08 16:10 gezelter |
| 678 |
|
| 679 |
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
| 680 |
|
| 681 |
2003-07-08 16:06 gezelter |
| 682 |
|
| 683 |
* libmdtools/NPTi.cpp: fixed box scaling |
| 684 |
|
| 685 |
2003-07-08 15:56 gezelter |
| 686 |
|
| 687 |
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
| 688 |
SimInfo.hpp, Thermo.cpp: NPTi |
| 689 |
|
| 690 |
2003-07-03 14:41 mmeineke |
| 691 |
|
| 692 |
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
| 693 |
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
| 694 |
scripts in the makefiles |
| 695 |
|
| 696 |
2003-07-02 16:26 mmeineke |
| 697 |
|
| 698 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 699 |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 700 |
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
| 701 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 702 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 703 |
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
| 704 |
utils/Makefile: fixed the bugs introduced by switching the periodic |
| 705 |
box to a matrix |
| 706 |
|
| 707 |
2003-07-01 17:39 gezelter |
| 708 |
|
| 709 |
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
| 710 |
|
| 711 |
2003-07-01 17:29 gezelter |
| 712 |
|
| 713 |
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
| 714 |
|
| 715 |
2003-07-01 16:33 mmeineke |
| 716 |
|
| 717 |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
| 718 |
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
| 719 |
the box matrix to everything. |
| 720 |
|
| 721 |
2003-06-30 17:03 mmeineke |
| 722 |
|
| 723 |
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 724 |
src/oopse.cpp: |
| 725 |
Updated the ChangeLog, and Converted most of the SImInfo to use |
| 726 |
non-Isotropic boxes. wrapVector needs to be finished. |
| 727 |
|
| 728 |
2003-06-25 16:12 mmeineke |
| 729 |
|
| 730 |
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
| 731 |
to Harmonic bonds in the DUFF frc file |
| 732 |
|
| 733 |
fixed constraints. |
| 734 |
|
| 735 |
2003-06-25 16:11 mmeineke |
| 736 |
|
| 737 |
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
| 738 |
the DUFF frc file |
| 739 |
|
| 740 |
2003-06-24 17:51 gezelter |
| 741 |
|
| 742 |
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
| 743 |
|
| 744 |
2003-06-24 14:57 mmeineke |
| 745 |
|
| 746 |
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
| 747 |
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
| 748 |
the DUFF forcefield and BondExtensions.cpp |
| 749 |
|
| 750 |
2003-06-23 16:24 mmeineke |
| 751 |
|
| 752 |
* libmdtools/Integrator.cpp: Doing some work to debug the |
| 753 |
constraint code. |
| 754 |
|
| 755 |
2003-06-20 15:50 gezelter |
| 756 |
|
| 757 |
* libmdtools/Integrator.hpp: NPT fix |
| 758 |
|
| 759 |
2003-06-20 15:29 mmeineke |
| 760 |
|
| 761 |
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 762 |
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 763 |
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
| 764 |
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
| 765 |
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
| 766 |
integrator and NVT seem to be working now. |
| 767 |
|
| 768 |
2003-06-20 11:49 gezelter |
| 769 |
|
| 770 |
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
| 771 |
|
| 772 |
2003-06-19 17:02 mmeineke |
| 773 |
|
| 774 |
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
| 775 |
forceFields/LJ_FF.frc, forceFields/Makefile, |
| 776 |
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
| 777 |
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
| 778 |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 779 |
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
| 780 |
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
| 781 |
forcefield names. |
| 782 |
|
| 783 |
2003-06-19 14:21 mmeineke |
| 784 |
|
| 785 |
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
| 786 |
finished the basics of the integrator and SimSetup.cpp |
| 787 |
|
| 788 |
2003-06-19 14:11 mmeineke |
| 789 |
|
| 790 |
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
| 791 |
up / get it to work with the new Integrator. |
| 792 |
|
| 793 |
2003-06-18 17:20 mmeineke |
| 794 |
|
| 795 |
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
| 796 |
output times. |
| 797 |
|
| 798 |
2003-06-17 16:56 mmeineke |
| 799 |
|
| 800 |
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
| 801 |
fro the ghost Bend in TraPPE_Ex |
| 802 |
|
| 803 |
some work on the integrator. ( incomplete) |
| 804 |
|
| 805 |
2003-06-17 16:55 mmeineke |
| 806 |
|
| 807 |
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
| 808 |
Bend in TraPPE_Ex |
| 809 |
|
| 810 |
2003-06-04 16:06 mmeineke |
| 811 |
|
| 812 |
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
| 813 |
constrainB to the Symplectic integrator |
| 814 |
|
| 815 |
2003-05-30 16:32 mmeineke |
| 816 |
|
| 817 |
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
| 818 |
the basic integrator. |
| 819 |
|
| 820 |
bilayerSys.cpp altered for building tb3. |
| 821 |
|
| 822 |
2003-05-30 16:31 mmeineke |
| 823 |
|
| 824 |
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
| 825 |
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
| 826 |
modifiying Symplectic to become the basic integrator. |
| 827 |
|
| 828 |
2003-05-30 15:19 mmeineke |
| 829 |
|
| 830 |
* libmdtools/Integrator.hpp: added some member variables for |
| 831 |
position, velocity, etc. |
| 832 |
|
| 833 |
2003-05-30 14:07 mmeineke |
| 834 |
|
| 835 |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
| 836 |
is now derived from Integrator |
| 837 |
|
| 838 |
2003-05-20 11:44 mmeineke |
| 839 |
|
| 840 |
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
| 841 |
|
| 842 |
2003-05-17 11:57 mmeineke |
| 843 |
|
| 844 |
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
| 845 |
working |
| 846 |
|
| 847 |
2003-05-16 16:37 mmeineke |
| 848 |
|
| 849 |
* utils/bilayerSys.cpp: still working on the bilayer code |
| 850 |
|
| 851 |
2003-05-16 09:28 mmeineke |
| 852 |
|
| 853 |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
| 854 |
work to overhaul sysbuild. |
| 855 |
|
| 856 |
2003-05-13 16:23 mmeineke |
| 857 |
|
| 858 |
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
| 859 |
|
| 860 |
2003-05-13 15:47 mmeineke |
| 861 |
|
| 862 |
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
| 863 |
beadLipid/water.mdl: Added bead lipid model to the sample directory |
| 864 |
|
| 865 |
2003-05-13 15:34 mmeineke |
| 866 |
|
| 867 |
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
| 868 |
the Trappe extended force field |
| 869 |
|
| 870 |
2003-05-13 12:01 mmeineke |
| 871 |
|
| 872 |
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
| 873 |
TraPPe_Ex forceField |
| 874 |
|
| 875 |
2003-05-09 14:51 mmeineke |
| 876 |
|
| 877 |
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
| 878 |
there were some duplicate entries |
| 879 |
|
| 880 |
added a two chain lipid to the lipid.mdl in sample |
| 881 |
|
| 882 |
2003-05-09 14:51 mmeineke |
| 883 |
|
| 884 |
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
| 885 |
there were some duplicate entries |
| 886 |
|
| 887 |
2003-05-09 11:56 mmeineke |
| 888 |
|
| 889 |
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
| 890 |
configure script |
| 891 |
|
| 892 |
added the CH branching group to the TraPPE_Ex fource field |
| 893 |
|
| 894 |
2003-05-09 11:55 mmeineke |
| 895 |
|
| 896 |
* ac-tools/configure.in: added the utils subdirectory to the |
| 897 |
configure script |
| 898 |
|
| 899 |
2003-04-25 11:02 mmeineke |
| 900 |
|
| 901 |
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
| 902 |
bilayer builder |
| 903 |
|
| 904 |
2003-04-24 21:00 mmeineke |
| 905 |
|
| 906 |
* libmdtools/f_verlet_constrained.F90: added a new test for |
| 907 |
constraint failure |
| 908 |
|
| 909 |
2003-04-17 16:54 mmeineke |
| 910 |
|
| 911 |
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
| 912 |
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 913 |
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
| 914 |
build our systems |
| 915 |
|
| 916 |
2003-04-16 16:11 mmeineke |
| 917 |
|
| 918 |
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
| 919 |
|
| 920 |
2003-04-15 16:47 mmeineke |
| 921 |
|
| 922 |
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
| 923 |
and sysBuild both will build now. woot! |
| 924 |
|
| 925 |
2003-04-15 16:20 mmeineke |
| 926 |
|
| 927 |
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 928 |
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
| 929 |
|
| 930 |
sysBuild still need to write the bass file. |
| 931 |
|
| 932 |
MoLocator.cpp is currently empty |
| 933 |
|
| 934 |
2003-04-15 15:40 chuckv |
| 935 |
|
| 936 |
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
| 937 |
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
| 938 |
forceFields/pdu3.eam, forceFields/ptu3.eam, |
| 939 |
libmdtools/ForceFields.hpp: Added eam force files... |
| 940 |
|
| 941 |
2003-04-15 11:37 chuckv |
| 942 |
|
| 943 |
* libmdtools/EAM_FF.cpp: More eam work. |
| 944 |
|
| 945 |
2003-04-14 16:22 mmeineke |
| 946 |
|
| 947 |
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
| 948 |
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
| 949 |
working on the system builder |
| 950 |
|
| 951 |
2003-04-14 16:16 chuckv |
| 952 |
|
| 953 |
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
| 954 |
ordering on NVT calculation in integrators. |
| 955 |
|
| 956 |
2003-04-14 14:51 mmeineke |
| 957 |
|
| 958 |
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
| 959 |
obj/placeHolder: working on a system builder |
| 960 |
|
| 961 |
2003-04-14 14:04 mmeineke |
| 962 |
|
| 963 |
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
| 964 |
|
| 965 |
added sysBuild to the utils Makefile |
| 966 |
|
| 967 |
2003-04-14 14:03 mmeineke |
| 968 |
|
| 969 |
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
| 970 |
Ghost bends to the TraPPE_Ex forceField |
| 971 |
|
| 972 |
2003-04-14 13:19 chuckv |
| 973 |
|
| 974 |
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
| 975 |
|
| 976 |
2003-04-11 13:46 mmeineke |
| 977 |
|
| 978 |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
| 979 |
simulation_module.F90: fixed a memory bug in Fortran, where |
| 980 |
molMembershipArray was declared nLocal instead of nGlobal. |
| 981 |
|
| 982 |
2003-04-11 10:16 gezelter |
| 983 |
|
| 984 |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 985 |
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
| 986 |
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
| 987 |
for NPT |
| 988 |
|
| 989 |
2003-04-10 15:08 mmeineke |
| 990 |
|
| 991 |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
| 992 |
globalIndex counter to Molecule |
| 993 |
|
| 994 |
2003-04-10 11:35 gezelter |
| 995 |
|
| 996 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
| 997 |
ConstantStress |
| 998 |
|
| 999 |
2003-04-10 11:27 mmeineke |
| 1000 |
|
| 1001 |
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
| 1002 |
caused a miscalculation of nLocal. |
| 1003 |
|
| 1004 |
2003-04-10 11:21 mmeineke |
| 1005 |
|
| 1006 |
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
| 1007 |
do_Forces.F90: fixed a bug in symplectic, where presure was only |
| 1008 |
being calculated the first time through. |
| 1009 |
|
| 1010 |
2003-04-09 11:20 chuckv |
| 1011 |
|
| 1012 |
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
| 1013 |
file |
| 1014 |
|
| 1015 |
2003-04-09 08:59 gezelter |
| 1016 |
|
| 1017 |
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
| 1018 |
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
| 1019 |
|
| 1020 |
2003-04-08 23:06 gezelter |
| 1021 |
|
| 1022 |
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
| 1023 |
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 1024 |
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
| 1025 |
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 1026 |
calc_reaction_field.F90, calc_sticky_pair.F90, |
| 1027 |
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
| 1028 |
NVT |
| 1029 |
|
| 1030 |
2003-04-08 17:38 chuckv |
| 1031 |
|
| 1032 |
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
| 1033 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 1034 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 1035 |
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
| 1036 |
(kinda)... |
| 1037 |
|
| 1038 |
2003-04-08 16:35 gezelter |
| 1039 |
|
| 1040 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1041 |
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
| 1042 |
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
| 1043 |
|
| 1044 |
2003-04-08 12:16 chuckv |
| 1045 |
|
| 1046 |
* libmdtools/: do_Forces.F90, neighborLists.F90, |
| 1047 |
simulation_module.F90: Moved expand neighborlist to init_FF. |
| 1048 |
|
| 1049 |
2003-04-08 10:20 chuckv |
| 1050 |
|
| 1051 |
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
| 1052 |
NVT |
| 1053 |
|
| 1054 |
2003-04-08 09:39 gezelter |
| 1055 |
|
| 1056 |
* libmdtools/Verlet.cpp: fixes for nvt / npt |
| 1057 |
|
| 1058 |
2003-04-08 09:34 gezelter |
| 1059 |
|
| 1060 |
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
| 1061 |
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
| 1062 |
|
| 1063 |
2003-04-08 07:50 gezelter |
| 1064 |
|
| 1065 |
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
| 1066 |
|
| 1067 |
2003-04-08 07:44 gezelter |
| 1068 |
|
| 1069 |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 1070 |
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
| 1071 |
NVT and NPT ensembles |
| 1072 |
|
| 1073 |
2003-04-07 16:42 gezelter |
| 1074 |
|
| 1075 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1076 |
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
| 1077 |
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
| 1078 |
|
| 1079 |
2003-04-07 16:20 mmeineke |
| 1080 |
|
| 1081 |
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
| 1082 |
portion of SSD. |
| 1083 |
|
| 1084 |
2003-04-07 16:16 mmeineke |
| 1085 |
|
| 1086 |
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
| 1087 |
doing some testing in sticky through Symplectic. |
| 1088 |
|
| 1089 |
2003-04-07 15:51 gezelter |
| 1090 |
|
| 1091 |
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
| 1092 |
|
| 1093 |
2003-04-07 15:50 chuckv |
| 1094 |
|
| 1095 |
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
| 1096 |
tau and virial. |
| 1097 |
|
| 1098 |
2003-04-07 15:06 mmeineke |
| 1099 |
|
| 1100 |
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
| 1101 |
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
| 1102 |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
| 1103 |
src/Makefile: bug fixes |
| 1104 |
|
| 1105 |
2003-04-07 11:56 gezelter |
| 1106 |
|
| 1107 |
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 1108 |
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
| 1109 |
Many fixes to add extended system |
| 1110 |
|
| 1111 |
2003-04-07 09:30 gezelter |
| 1112 |
|
| 1113 |
* src/Makefile: Fixed a bug caused by my experimentation |
| 1114 |
|
| 1115 |
2003-04-07 09:30 gezelter |
| 1116 |
|
| 1117 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
| 1118 |
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
| 1119 |
Added ExtendedSystem infrastructure for NPT and NVT calculations |
| 1120 |
|
| 1121 |
2003-04-07 09:30 gezelter |
| 1122 |
|
| 1123 |
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
| 1124 |
|
| 1125 |
2003-04-04 23:07 gezelter |
| 1126 |
|
| 1127 |
* src/Makefile: final mods to try a fortran compiler |
| 1128 |
|
| 1129 |
2003-04-04 22:39 gezelter |
| 1130 |
|
| 1131 |
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
| 1132 |
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
| 1133 |
|
| 1134 |
2003-04-04 21:56 gezelter |
| 1135 |
|
| 1136 |
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
| 1137 |
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
| 1138 |
|
| 1139 |
2003-04-04 21:45 gezelter |
| 1140 |
|
| 1141 |
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
| 1142 |
fixes to fortran wrappers |
| 1143 |
|
| 1144 |
2003-04-04 17:22 chuckv |
| 1145 |
|
| 1146 |
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 1147 |
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
| 1148 |
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
| 1149 |
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
| 1150 |
smarter, fortran gets dumber... |
| 1151 |
|
| 1152 |
2003-04-04 14:57 mmeineke |
| 1153 |
|
| 1154 |
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
| 1155 |
neighborLists.F90: fixed a memory read bug in neighborlist |
| 1156 |
|
| 1157 |
2003-04-04 14:47 gezelter |
| 1158 |
|
| 1159 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 1160 |
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
| 1161 |
|
| 1162 |
2003-04-04 14:16 gezelter |
| 1163 |
|
| 1164 |
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
| 1165 |
SimInfo.hpp: Fixes for ExtendedSystem |
| 1166 |
|
| 1167 |
2003-04-03 20:57 gezelter |
| 1168 |
|
| 1169 |
* libmdtools/ExtendedSystem.hpp: Added extended system header |
| 1170 |
|
| 1171 |
2003-04-03 20:57 gezelter |
| 1172 |
|
| 1173 |
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
| 1174 |
for extended system code |
| 1175 |
|
| 1176 |
2003-04-03 18:49 gezelter |
| 1177 |
|
| 1178 |
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
| 1179 |
extendedsystem |
| 1180 |
|
| 1181 |
2003-04-03 17:19 mmeineke |
| 1182 |
|
| 1183 |
* libmdtools/Molecule.hpp: added some little fixes here and there. |
| 1184 |
|
| 1185 |
2003-04-03 17:01 mmeineke |
| 1186 |
|
| 1187 |
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
| 1188 |
initialize bug. |
| 1189 |
|
| 1190 |
2003-04-03 16:12 mmeineke |
| 1191 |
|
| 1192 |
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
| 1193 |
little things like deleteing unused variables and such. |
| 1194 |
|
| 1195 |
2003-04-03 15:57 mmeineke |
| 1196 |
|
| 1197 |
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
| 1198 |
simError.h also some fixes to Molecule.hpp |
| 1199 |
|
| 1200 |
2003-04-03 15:57 mmeineke |
| 1201 |
|
| 1202 |
* libBASS/simError.h: a few fixes to simError.h |
| 1203 |
|
| 1204 |
2003-04-03 15:21 mmeineke |
| 1205 |
|
| 1206 |
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
| 1207 |
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
| 1208 |
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
| 1209 |
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
| 1210 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
| 1211 |
src/Makefile, src/oopse.cpp: fixed some small things with |
| 1212 |
simError.h |
| 1213 |
|
| 1214 |
2003-04-03 15:19 gezelter |
| 1215 |
|
| 1216 |
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
| 1217 |
|
| 1218 |
2003-04-03 14:58 gezelter |
| 1219 |
|
| 1220 |
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
| 1221 |
now) |
| 1222 |
|
| 1223 |
2003-04-03 08:42 gezelter |
| 1224 |
|
| 1225 |
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
| 1226 |
Changed Readme, added some files |
| 1227 |
|
| 1228 |
2003-04-02 17:19 mmeineke |
| 1229 |
|
| 1230 |
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
| 1231 |
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
| 1232 |
dipoles mostly work, but there is a memory leak somewhere. |
| 1233 |
|
| 1234 |
2003-04-02 10:01 mmeineke |
| 1235 |
|
| 1236 |
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
| 1237 |
the proper atomIdents. |
| 1238 |
|
| 1239 |
2003-04-01 11:50 chuckv |
| 1240 |
|
| 1241 |
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 1242 |
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 1243 |
samples/argon/argon.bass: more bug fixes.... |
| 1244 |
|
| 1245 |
2003-04-01 11:49 mmeineke |
| 1246 |
|
| 1247 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
| 1248 |
DumpWriter to be more robust to errors. also added a little |
| 1249 |
namespace to InitFromFile to wrap it's helper functions in MPI |
| 1250 |
|
| 1251 |
2003-03-31 17:09 chuckv |
| 1252 |
|
| 1253 |
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
| 1254 |
not zeroed. |
| 1255 |
|
| 1256 |
2003-03-31 16:50 chuckv |
| 1257 |
|
| 1258 |
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
| 1259 |
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 1260 |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 1261 |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 1262 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
| 1263 |
samples/alkane/butane.bass: Fixes in MPI force calc and in |
| 1264 |
Trappe_Ex parsing. |
| 1265 |
|
| 1266 |
2003-03-28 17:34 chuckv |
| 1267 |
|
| 1268 |
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
| 1269 |
|
| 1270 |
2003-03-28 16:45 chuckv |
| 1271 |
|
| 1272 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 1273 |
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
| 1274 |
routines. |
| 1275 |
|
| 1276 |
2003-03-28 14:33 mmeineke |
| 1277 |
|
| 1278 |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
| 1279 |
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
| 1280 |
bug where the Excludes were not being created properly |
| 1281 |
|
| 1282 |
2003-03-28 14:30 chuckv |
| 1283 |
|
| 1284 |
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 1285 |
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
| 1286 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
| 1287 |
and debugging mpi read write from file. |
| 1288 |
|
| 1289 |
2003-03-28 10:28 mmeineke |
| 1290 |
|
| 1291 |
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
| 1292 |
interactions in Trappe |
| 1293 |
|
| 1294 |
2003-03-27 18:33 chuckv |
| 1295 |
|
| 1296 |
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
| 1297 |
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
| 1298 |
|
| 1299 |
2003-03-27 17:16 mmeineke |
| 1300 |
|
| 1301 |
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
| 1302 |
excludes were not being initialized |
| 1303 |
|
| 1304 |
2003-03-27 16:52 mmeineke |
| 1305 |
|
| 1306 |
* src/Makefile: [no log message] |
| 1307 |
|
| 1308 |
2003-03-27 16:52 mmeineke |
| 1309 |
|
| 1310 |
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
| 1311 |
|
| 1312 |
2003-03-27 16:07 mmeineke |
| 1313 |
|
| 1314 |
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
| 1315 |
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
| 1316 |
Verlet.cpp: fixed the compile time bugs, Source builds and links |
| 1317 |
|
| 1318 |
2003-03-27 15:48 mmeineke |
| 1319 |
|
| 1320 |
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
| 1321 |
more bugs. |
| 1322 |
|
| 1323 |
2003-03-27 15:40 mmeineke |
| 1324 |
|
| 1325 |
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
| 1326 |
|
| 1327 |
2003-03-27 15:39 mmeineke |
| 1328 |
|
| 1329 |
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
| 1330 |
|
| 1331 |
2003-03-27 15:36 mmeineke |
| 1332 |
|
| 1333 |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 1334 |
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
| 1335 |
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
| 1336 |
|
| 1337 |
2003-03-27 15:12 mmeineke |
| 1338 |
|
| 1339 |
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
| 1340 |
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
| 1341 |
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
| 1342 |
to. will now attempt to compile. |
| 1343 |
|
| 1344 |
2003-03-27 14:21 mmeineke |
| 1345 |
|
| 1346 |
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
| 1347 |
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
| 1348 |
updating SimSetup to initialize and use the new MPI division of |
| 1349 |
labour, and Molecule class |
| 1350 |
|
| 1351 |
2003-03-27 12:55 mmeineke |
| 1352 |
|
| 1353 |
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
| 1354 |
use Molecule |
| 1355 |
|
| 1356 |
2003-03-27 12:32 mmeineke |
| 1357 |
|
| 1358 |
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
| 1359 |
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
| 1360 |
converted to the new Molecule model. TraPPE_Ex is currently being |
| 1361 |
updated. SimSetups routines are writtten, but not yet called. |
| 1362 |
|
| 1363 |
2003-03-27 10:07 gezelter |
| 1364 |
|
| 1365 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 1366 |
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
| 1367 |
numbering in MPI |
| 1368 |
|
| 1369 |
2003-03-27 09:30 mmeineke |
| 1370 |
|
| 1371 |
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
| 1372 |
|
| 1373 |
2003-03-26 20:49 gezelter |
| 1374 |
|
| 1375 |
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
| 1376 |
fileio for MPI |
| 1377 |
|
| 1378 |
2003-03-26 18:14 gezelter |
| 1379 |
|
| 1380 |
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
| 1381 |
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
| 1382 |
fixes many bug fixes |
| 1383 |
|
| 1384 |
2003-03-26 17:24 gezelter |
| 1385 |
|
| 1386 |
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
| 1387 |
sequence of atoms on the other processors. Node 0 now fires |
| 1388 |
potatoes at other processors to get them to send french fries back. |
| 1389 |
|
| 1390 |
2003-03-26 17:02 mmeineke |
| 1391 |
|
| 1392 |
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
| 1393 |
making the molecules is in place. ForceField needs to be updated |
| 1394 |
next. |
| 1395 |
|
| 1396 |
2003-03-26 16:54 mmeineke |
| 1397 |
|
| 1398 |
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
| 1399 |
the "static" bugs in Atom and Exclude |
| 1400 |
|
| 1401 |
2003-03-26 16:50 mmeineke |
| 1402 |
|
| 1403 |
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
| 1404 |
SimSetup.cpp: still working on the SimSetup routine. also fixed |
| 1405 |
some things in Exclude.hpp |
| 1406 |
|
| 1407 |
2003-03-26 16:24 gezelter |
| 1408 |
|
| 1409 |
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
| 1410 |
|
| 1411 |
2003-03-26 16:23 gezelter |
| 1412 |
|
| 1413 |
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
| 1414 |
and Exclude list |
| 1415 |
|
| 1416 |
2003-03-26 16:04 gezelter |
| 1417 |
|
| 1418 |
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
| 1419 |
delete ranges of atoms |
| 1420 |
|
| 1421 |
2003-03-26 15:45 mmeineke |
| 1422 |
|
| 1423 |
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
| 1424 |
with static arrays similar to the Atom class |
| 1425 |
|
| 1426 |
2003-03-26 15:22 mmeineke |
| 1427 |
|
| 1428 |
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
| 1429 |
overhauling the molecule class to contain it's own bonds, bends, |
| 1430 |
and torsions. |
| 1431 |
|
| 1432 |
may god have mercy on my soul. |
| 1433 |
|
| 1434 |
2003-03-26 14:34 chuckv |
| 1435 |
|
| 1436 |
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
| 1437 |
|
| 1438 |
2003-03-26 13:02 gezelter |
| 1439 |
|
| 1440 |
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
| 1441 |
mpiSimulation.hpp: MPI stuff for passing out molecules |
| 1442 |
|
| 1443 |
2003-03-26 11:12 chuckv |
| 1444 |
|
| 1445 |
* libmdtools/mpiSimulation.cpp: working on load balancing |
| 1446 |
|
| 1447 |
2003-03-26 10:37 chuckv |
| 1448 |
|
| 1449 |
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 1450 |
samples/argon/argon.bass: Fixes for Parallel thermalization |
| 1451 |
|
| 1452 |
2003-03-26 09:55 mmeineke |
| 1453 |
|
| 1454 |
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
| 1455 |
THermo.cpp |
| 1456 |
|
| 1457 |
2003-03-25 17:54 chuckv |
| 1458 |
|
| 1459 |
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
| 1460 |
of potential energy and temperature. |
| 1461 |
|
| 1462 |
2003-03-25 09:29 mmeineke |
| 1463 |
|
| 1464 |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
| 1465 |
src/MPIobj/dummy, src/obj/dummy: [no log message] |
| 1466 |
|
| 1467 |
2003-03-25 09:29 mmeineke |
| 1468 |
|
| 1469 |
* libBASS/MPIobj/dummy: added dummy files to keep the build |
| 1470 |
deirectories from being pruned. |
| 1471 |
|
| 1472 |
2003-03-24 20:07 gezelter |
| 1473 |
|
| 1474 |
* samples/Makefile: moving tests to samples |
| 1475 |
|
| 1476 |
2003-03-24 20:06 gezelter |
| 1477 |
|
| 1478 |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 1479 |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 1480 |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 1481 |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 1482 |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 1483 |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 1484 |
samples |
| 1485 |
|
| 1486 |
2003-03-24 19:51 gezelter |
| 1487 |
|
| 1488 |
* ac-tools/configure.in: Tests are becoming samples |
| 1489 |
|
| 1490 |
2003-03-24 19:46 gezelter |
| 1491 |
|
| 1492 |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 1493 |
|
| 1494 |
2003-03-24 16:55 gezelter |
| 1495 |
|
| 1496 |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
| 1497 |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
| 1498 |
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
| 1499 |
libmdtools/calc_reaction_field.F90, |
| 1500 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 1501 |
libmdtools/simulation_module.F90: electrostatic changes for dipole |
| 1502 |
/ RF separation |
| 1503 |
|
| 1504 |
2003-03-24 13:33 mmeineke |
| 1505 |
|
| 1506 |
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 1507 |
do_Forces.F90: little bug fixes here and there |
| 1508 |
|
| 1509 |
2003-03-24 10:26 mmeineke |
| 1510 |
|
| 1511 |
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
| 1512 |
where short range interactions were not being calculated. |
| 1513 |
|
| 1514 |
removed some debug print statements |
| 1515 |
|
| 1516 |
2003-03-21 17:11 chuckv |
| 1517 |
|
| 1518 |
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
| 1519 |
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
| 1520 |
various write statements for debugging |
| 1521 |
|
| 1522 |
2003-03-21 16:26 chuckv |
| 1523 |
|
| 1524 |
* forceFields/Makefile: added links to the makefile in forceFields |
| 1525 |
|
| 1526 |
2003-03-21 15:52 gezelter |
| 1527 |
|
| 1528 |
* ac-tools/Make.conf.in, ac-tools/configure.in, |
| 1529 |
libmdtools/Makefile: Fixed F_MACH_DEP bug |
| 1530 |
|
| 1531 |
2003-03-21 15:37 gezelter |
| 1532 |
|
| 1533 |
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
| 1534 |
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
| 1535 |
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
| 1536 |
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
| 1537 |
autoconf fixes |
| 1538 |
|
| 1539 |
2003-03-21 14:58 gezelter |
| 1540 |
|
| 1541 |
* LICENSE: Added license file |
| 1542 |
|
| 1543 |
2003-03-21 14:55 gezelter |
| 1544 |
|
| 1545 |
* forceFields/Makefile: Fixed makefile |
| 1546 |
|
| 1547 |
2003-03-21 14:49 gezelter |
| 1548 |
|
| 1549 |
* forceFields/Makefile: Makefile for forceFields |
| 1550 |
|
| 1551 |
2003-03-21 14:42 gezelter |
| 1552 |
|
| 1553 |
* README: Readme changes |
| 1554 |
|
| 1555 |
2003-03-21 12:52 mmeineke |
| 1556 |
|
| 1557 |
* src/Makefile: [no log message] |
| 1558 |
|
| 1559 |
2003-03-21 12:52 mmeineke |
| 1560 |
|
| 1561 |
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
| 1562 |
|
| 1563 |
2003-03-21 12:42 mmeineke |
| 1564 |
|
| 1565 |
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 1566 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1567 |
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 1568 |
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 1569 |
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 1570 |
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 1571 |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 1572 |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 1573 |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 1574 |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 1575 |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 1576 |
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 1577 |
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 1578 |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 1579 |
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 1580 |
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 1581 |
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 1582 |
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 1583 |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 1584 |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 1585 |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 1586 |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 1587 |
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 1588 |
utils/sfmakedepend, ac-tools/shtool, |
| 1589 |
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 1590 |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 1591 |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 1592 |
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 1593 |
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 1594 |
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 1595 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 1596 |
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 1597 |
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 1598 |
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 1599 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1600 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 1601 |
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 1602 |
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 1603 |
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 1604 |
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 1605 |
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 1606 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 1607 |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 1608 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 1609 |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 1610 |
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 1611 |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 1612 |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 1613 |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 1614 |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 1615 |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 1616 |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 1617 |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 1618 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 1619 |
Tree |
| 1620 |
|
| 1621 |
2003-03-21 12:42 mmeineke |
| 1622 |
|
| 1623 |
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
| 1624 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 1625 |
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
| 1626 |
ac-tools/install-sh, forceFields/DipoleTest.frc, |
| 1627 |
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
| 1628 |
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
| 1629 |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
| 1630 |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
| 1631 |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 1632 |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
| 1633 |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
| 1634 |
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
| 1635 |
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
| 1636 |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
| 1637 |
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
| 1638 |
libBASS/MakeStamps.hpp, libBASS/Makefile, |
| 1639 |
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
| 1640 |
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
| 1641 |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
| 1642 |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
| 1643 |
libBASS/parse_interface.h, libBASS/parse_me.h, |
| 1644 |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
| 1645 |
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
| 1646 |
utils/sfmakedepend, ac-tools/shtool, |
| 1647 |
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
| 1648 |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
| 1649 |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
| 1650 |
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
| 1651 |
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
| 1652 |
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
| 1653 |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 1654 |
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
| 1655 |
libmdtools/Makefile, libmdtools/Molecule.hpp, |
| 1656 |
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
| 1657 |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1658 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 1659 |
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
| 1660 |
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 1661 |
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
| 1662 |
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
| 1663 |
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
| 1664 |
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 1665 |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 1666 |
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 1667 |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
| 1668 |
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
| 1669 |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
| 1670 |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
| 1671 |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
| 1672 |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
| 1673 |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 1674 |
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 1675 |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 1676 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 1677 |
revision |
| 1678 |
|
