| 1 |
2004-10-18 23:34 tim |
| 2 |
|
| 3 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
| 4 |
are fixed in Vector class |
| 5 |
|
| 6 |
2004-10-18 23:28 tim |
| 7 |
|
| 8 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
| 9 |
some bugs in RectMatrixTestCase |
| 10 |
|
| 11 |
2004-10-18 23:21 tim |
| 12 |
|
| 13 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
| 14 |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
| 15 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
| 16 |
test/math/VectorTestCase.hpp: implement more test cases |
| 17 |
|
| 18 |
2004-10-18 18:13 tim |
| 19 |
|
| 20 |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
| 21 |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
| 22 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
| 23 |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
| 24 |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
| 25 |
tests on math library |
| 26 |
|
| 27 |
2004-10-18 16:03 tim |
| 28 |
|
| 29 |
* test/math/: Makefile, QuaternionTestCase.cpp, |
| 30 |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
| 31 |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
| 32 |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
| 33 |
more testing units |
| 34 |
|
| 35 |
2004-10-18 12:07 tim |
| 36 |
|
| 37 |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
| 38 |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
| 39 |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
| 40 |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
| 41 |
|
| 42 |
2004-10-18 11:30 gezelter |
| 43 |
|
| 44 |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
| 45 |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
| 46 |
\phi) |
| 47 |
|
| 48 |
2004-10-18 11:29 gezelter |
| 49 |
|
| 50 |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
| 51 |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
| 52 |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
| 53 |
Shapes into OOPSE |
| 54 |
|
| 55 |
2004-10-18 10:21 gezelter |
| 56 |
|
| 57 |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
| 58 |
|
| 59 |
2004-10-18 00:23 tim |
| 60 |
|
| 61 |
* test/math/VectorTestCase.hpp: adding vector test case |
| 62 |
|
| 63 |
2004-10-18 00:23 tim |
| 64 |
|
| 65 |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
| 66 |
test case |
| 67 |
|
| 68 |
2004-10-16 20:19 tim |
| 69 |
|
| 70 |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
| 71 |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
| 72 |
progress |
| 73 |
|
| 74 |
2004-10-15 20:31 tim |
| 75 |
|
| 76 |
* src/math/Quaternion.hpp: add quaternion class |
| 77 |
|
| 78 |
2004-10-15 16:11 tim |
| 79 |
|
| 80 |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
| 81 |
IfstrstreamTestCase.hpp: adding test file |
| 82 |
|
| 83 |
2004-10-15 16:10 tim |
| 84 |
|
| 85 |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
| 86 |
|
| 87 |
2004-10-15 15:42 tim |
| 88 |
|
| 89 |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
| 90 |
|
| 91 |
2004-10-15 15:35 tim |
| 92 |
|
| 93 |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
| 94 |
|
| 95 |
2004-10-15 15:34 tim |
| 96 |
|
| 97 |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
| 98 |
namespace oopse |
| 99 |
|
| 100 |
2004-10-15 14:38 chuckv |
| 101 |
|
| 102 |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
| 103 |
XLF and XLC. |
| 104 |
|
| 105 |
2004-10-15 13:28 tim |
| 106 |
|
| 107 |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
| 108 |
adding ifstrstream test case |
| 109 |
|
| 110 |
2004-10-15 13:20 tim |
| 111 |
|
| 112 |
* src/io/basic_ifstrstream.hpp: fix include |
| 113 |
|
| 114 |
2004-10-15 13:18 tim |
| 115 |
|
| 116 |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
| 117 |
|
| 118 |
2004-10-15 13:17 tim |
| 119 |
|
| 120 |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
| 121 |
|
| 122 |
2004-10-15 13:16 tim |
| 123 |
|
| 124 |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
| 125 |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
| 126 |
|
| 127 |
2004-10-15 10:37 tim |
| 128 |
|
| 129 |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
| 130 |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
| 131 |
|
| 132 |
2004-10-15 10:20 tim |
| 133 |
|
| 134 |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
| 135 |
|
| 136 |
2004-10-15 10:19 tim |
| 137 |
|
| 138 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
| 139 |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
| 140 |
SquareMatrixTestCase class |
| 141 |
|
| 142 |
2004-10-15 02:52 tim |
| 143 |
|
| 144 |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
| 145 |
|
| 146 |
2004-10-14 18:28 tim |
| 147 |
|
| 148 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
| 149 |
Vector.hpp: math library in progress |
| 150 |
|
| 151 |
2004-10-14 18:27 tim |
| 152 |
|
| 153 |
* src/io/FileReader.hpp: FileReader in progress |
| 154 |
|
| 155 |
2004-10-13 18:53 tim |
| 156 |
|
| 157 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
| 158 |
test in isOrthogonal of SquareMatrix is failed by some reasons |
| 159 |
|
| 160 |
2004-10-13 17:28 tim |
| 161 |
|
| 162 |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
| 163 |
class |
| 164 |
|
| 165 |
2004-10-13 17:27 tim |
| 166 |
|
| 167 |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
| 168 |
RectMatrixTestCase.hpp: adding testing unit |
| 169 |
|
| 170 |
2004-10-13 17:24 tim |
| 171 |
|
| 172 |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
| 173 |
|
| 174 |
2004-10-13 01:51 tim |
| 175 |
|
| 176 |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
| 177 |
Vector3.hpp: refactory vector and matrix classes |
| 178 |
|
| 179 |
2004-10-13 01:50 tim |
| 180 |
|
| 181 |
* src/math/Vector3d.hpp: Remove some Makefile.in |
| 182 |
|
| 183 |
2004-10-12 18:57 tim |
| 184 |
|
| 185 |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
| 186 |
Matrix3x3d.hpp |
| 187 |
|
| 188 |
2004-10-12 14:08 tim |
| 189 |
|
| 190 |
* doc/: cppstyle.html, style.css: adding c++ coding style |
| 191 |
|
| 192 |
2004-10-11 17:15 tim |
| 193 |
|
| 194 |
* src/: constraints/AbstractClasses.hpp, |
| 195 |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
| 196 |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
| 197 |
|
| 198 |
2004-10-11 16:54 tim |
| 199 |
|
| 200 |
* scripts/filepp: fix a bug in filepp |
| 201 |
|
| 202 |
2004-10-11 16:13 tim |
| 203 |
|
| 204 |
* make/Makefile.in: using filepp to generate dependencies instead |
| 205 |
of compilers |
| 206 |
|
| 207 |
2004-10-11 16:10 tim |
| 208 |
|
| 209 |
* scripts/filepp: filepp can be used to generate dependencies for |
| 210 |
c/c++ now |
| 211 |
|
| 212 |
2004-10-11 13:40 tim |
| 213 |
|
| 214 |
* make/Makefile.in: remove -module from F90Options |
| 215 |
|
| 216 |
2004-10-11 13:01 tim |
| 217 |
|
| 218 |
* make/Makefile.in: adding rules to move fortran 90 module to |
| 219 |
target directory |
| 220 |
|
| 221 |
2004-10-11 10:43 gezelter |
| 222 |
|
| 223 |
* make/Makefile.in: fixed makefile.in |
| 224 |
|
| 225 |
2004-10-11 09:51 tim |
| 226 |
|
| 227 |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
| 228 |
machine |
| 229 |
|
| 230 |
2004-10-11 09:26 tim |
| 231 |
|
| 232 |
* forceFields/Makefile: add Makefile |
| 233 |
|
| 234 |
2004-10-11 09:23 tim |
| 235 |
|
| 236 |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
| 237 |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
| 238 |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
| 239 |
directory |
| 240 |
|
| 241 |
2004-10-11 09:23 tim |
| 242 |
|
| 243 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
| 244 |
Makefile |
| 245 |
|
| 246 |
2004-10-09 01:01 tim |
| 247 |
|
| 248 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
| 249 |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
| 250 |
Remove some Makefile.in |
| 251 |
|
| 252 |
2004-10-08 18:15 tim |
| 253 |
|
| 254 |
* make/Makefile.in: [no log message] |
| 255 |
|
| 256 |
2004-10-08 17:51 tim |
| 257 |
|
| 258 |
* make/Makefile.in: fix make install |
| 259 |
|
| 260 |
2004-10-08 17:10 tim |
| 261 |
|
| 262 |
* make/Makefile.in: adding make install |
| 263 |
|
| 264 |
2004-10-08 17:04 tim |
| 265 |
|
| 266 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
| 267 |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
| 268 |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
| 269 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
| 270 |
water/ssde/Makefile, water/ssde/Makefile.in, |
| 271 |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
| 272 |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
| 273 |
zcons/Makefile.in: add Makefile to sample directory |
| 274 |
|
| 275 |
2004-10-06 18:03 gezelter |
| 276 |
|
| 277 |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
| 278 |
stuff |
| 279 |
|
| 280 |
2004-10-06 18:03 gezelter |
| 281 |
|
| 282 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 283 |
make/Doxyfile, src/applications/getopt.c, |
| 284 |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
| 285 |
build fixes |
| 286 |
|
| 287 |
2004-10-06 17:20 tim |
| 288 |
|
| 289 |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
| 290 |
|
| 291 |
2004-10-06 17:19 tim |
| 292 |
|
| 293 |
* scripts/filepp: filepp can handle different fortran module case |
| 294 |
and suffix |
| 295 |
|
| 296 |
2004-10-06 16:27 gezelter |
| 297 |
|
| 298 |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
| 299 |
OOPSE-2.0 directory structure yet |
| 300 |
|
| 301 |
2004-10-06 16:27 gezelter |
| 302 |
|
| 303 |
* ChangeLog: Yeah yeah, we'lll get around to it later |
| 304 |
|
| 305 |
2004-10-06 16:22 gezelter |
| 306 |
|
| 307 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 308 |
make/Makefile.in: cleaning up build process |
| 309 |
|
| 310 |
2004-10-06 15:01 chrisfen |
| 311 |
|
| 312 |
* src/restraints/Restraints.cpp: made the file reading in |
| 313 |
restraints more intelligent - no longer gives uninformative seg |
| 314 |
faults |
| 315 |
|
| 316 |
2004-10-06 14:55 gezelter |
| 317 |
|
| 318 |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
| 319 |
|
| 320 |
2004-10-06 14:51 gezelter |
| 321 |
|
| 322 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
| 323 |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
| 324 |
|
| 325 |
2004-10-06 13:53 tim |
| 326 |
|
| 327 |
* make/: Makefile, Makefile.in: fix make statistics |
| 328 |
|
| 329 |
2004-10-06 13:18 tim |
| 330 |
|
| 331 |
* make/: Makefile, Makefile.in: adding GNU make functions to |
| 332 |
combine all of the static libraries to a big library |
| 333 |
|
| 334 |
2004-10-05 17:57 tim |
| 335 |
|
| 336 |
* make/: Makefile, Makefile.in: adding shared library flag |
| 337 |
|
| 338 |
2004-10-05 14:37 tim |
| 339 |
|
| 340 |
* src/: Makefile, UseTheForce/Makefile, |
| 341 |
UseTheForce/mpiSimulation_module.F90, |
| 342 |
UseTheForce/DarkSide/Makefile, |
| 343 |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
| 344 |
mpiSimulation_module to DarkSide |
| 345 |
|
| 346 |
2004-10-05 14:35 tim |
| 347 |
|
| 348 |
* make/: Makefile, Makefile.in: building MPI version;using static |
| 349 |
library instead of shared library |
| 350 |
|
| 351 |
2004-10-05 09:14 tim |
| 352 |
|
| 353 |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
| 354 |
to filepp |
| 355 |
|
| 356 |
2004-10-04 15:56 tim |
| 357 |
|
| 358 |
* make/: Makefile, Makefile.in: add make cvslog |
| 359 |
|
| 360 |
2004-10-04 11:24 gezelter |
| 361 |
|
| 362 |
* make/: Makefile, Makefile.in: more work on the parallel build |
| 363 |
|
| 364 |
2004-10-04 11:06 gezelter |
| 365 |
|
| 366 |
* make/: Makefile, Makefile.in: changes to backport declare flags |
| 367 |
|
| 368 |
2004-10-04 10:27 gezelter |
| 369 |
|
| 370 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
| 371 |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
| 372 |
shapes |
| 373 |
|
| 374 |
2004-10-01 23:40 tim |
| 375 |
|
| 376 |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
| 377 |
|
| 378 |
2004-10-01 23:22 tim |
| 379 |
|
| 380 |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
| 381 |
|
| 382 |
2004-10-01 16:59 tim |
| 383 |
|
| 384 |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
| 385 |
|
| 386 |
2004-10-01 16:22 gezelter |
| 387 |
|
| 388 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
| 389 |
few minor build changes |
| 390 |
|
| 391 |
2004-10-01 16:11 tim |
| 392 |
|
| 393 |
* scripts/filepp: adding fortran90 make dependency tool |
| 394 |
|
| 395 |
2004-09-30 10:41 tim |
| 396 |
|
| 397 |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
| 398 |
remove object files belong to current package. turn off silent |
| 399 |
mode |
| 400 |
|
| 401 |
2004-09-29 16:55 tim |
| 402 |
|
| 403 |
* src/: Makefile, UseTheForce/Makefile, |
| 404 |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
| 405 |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
| 406 |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
| 407 |
integrators/Makefile, io/Makefile, math/Makefile, |
| 408 |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
| 409 |
restraints/Makefile, types/Makefile, utils/Makefile, |
| 410 |
visitors/Makefile: define DEV_ROOT as relative path |
| 411 |
|
| 412 |
2004-09-29 16:54 tim |
| 413 |
|
| 414 |
* make/: Makefile, Makefile.in: get the relative path by shell |
| 415 |
script |
| 416 |
|
| 417 |
2004-09-29 16:32 tim |
| 418 |
|
| 419 |
* make/Makefile: eliminate DEV_ROOT by relative path |
| 420 |
|
| 421 |
2004-09-29 13:37 tim |
| 422 |
|
| 423 |
* make/Makefile.in: add PackageLibs; fix dependency rule |
| 424 |
|
| 425 |
2004-09-29 12:57 gezelter |
| 426 |
|
| 427 |
* configure, ac-tools/configure.in: updates |
| 428 |
|
| 429 |
2004-09-29 12:56 gezelter |
| 430 |
|
| 431 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
| 432 |
|
| 433 |
2004-09-29 12:46 tim |
| 434 |
|
| 435 |
* Makefile: If makefile does not exist, print error message |
| 436 |
|
| 437 |
2004-09-29 12:12 tim |
| 438 |
|
| 439 |
* make/: Make.conf.in, Makefile: fix dependencies rule |
| 440 |
|
| 441 |
2004-09-29 10:58 gezelter |
| 442 |
|
| 443 |
* Makefile, make/Makefile: still working on build process |
| 444 |
|
| 445 |
2004-09-29 10:00 tim |
| 446 |
|
| 447 |
* make/Makefile: add print statment to rules |
| 448 |
|
| 449 |
2004-09-29 09:59 tim |
| 450 |
|
| 451 |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
| 452 |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
| 453 |
applications/simpleBuilder/Makefile, brains/Makefile, |
| 454 |
constraints/Makefile, integrators/Makefile, io/Makefile, |
| 455 |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
| 456 |
profiling/Makefile, restraints/Makefile, types/Makefile, |
| 457 |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
| 458 |
|
| 459 |
2004-09-28 21:55 tim |
| 460 |
|
| 461 |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
| 462 |
which cause headache in bulding libutils |
| 463 |
|
| 464 |
2004-09-28 18:24 tim |
| 465 |
|
| 466 |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
| 467 |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
| 468 |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
| 469 |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
| 470 |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
| 471 |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
| 472 |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
| 473 |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
| 474 |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
| 475 |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
| 476 |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
| 477 |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
| 478 |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
| 479 |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
| 480 |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
| 481 |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
| 482 |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
| 483 |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
| 484 |
change directory structure of application. Every executable file is |
| 485 |
replaced in seperate directory |
| 486 |
|
| 487 |
2004-09-28 17:15 gezelter |
| 488 |
|
| 489 |
* lib/dummy: Keep that lib around, please. |
| 490 |
|
| 491 |
2004-09-28 17:14 gezelter |
| 492 |
|
| 493 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
| 494 |
starting a configure version |
| 495 |
|
| 496 |
2004-09-28 16:08 tim |
| 497 |
|
| 498 |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
| 499 |
UseTheForce/DarkSide/Makefile, |
| 500 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 501 |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
| 502 |
brains/Makefile, brains/simulation_module.F90: move fortran files |
| 503 |
around to solve dependency problem |
| 504 |
|
| 505 |
2004-09-28 15:43 tim |
| 506 |
|
| 507 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
| 508 |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
| 509 |
src/applications/Makedepend, src/applications/Makefile, |
| 510 |
src/brains/Makedepend, src/brains/simulation_module.F90, |
| 511 |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
| 512 |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
| 513 |
src/utils/Makefile: [no log message] |
| 514 |
|
| 515 |
2004-09-28 15:41 tim |
| 516 |
|
| 517 |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
| 518 |
problem |
| 519 |
|
| 520 |
2004-09-28 11:13 tim |
| 521 |
|
| 522 |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
| 523 |
src/io/Makefile: add yacc and lex rules |
| 524 |
|
| 525 |
2004-09-27 15:24 tim |
| 526 |
|
| 527 |
* make/Makefile: adding include path to F90Options |
| 528 |
|
| 529 |
2004-09-27 15:13 tim |
| 530 |
|
| 531 |
* make/Makefile: change suffix from .cc to .cpp |
| 532 |
|
| 533 |
2004-09-24 11:27 tim |
| 534 |
|
| 535 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
| 536 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
| 537 |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
| 538 |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
| 539 |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
| 540 |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
| 541 |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 542 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
| 543 |
UseTheForce/DarkSide/switch_module.F90, |
| 544 |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
| 545 |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
| 546 |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
| 547 |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
| 548 |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
| 549 |
applications/cmdline.c, applications/nanoBuilder.cpp, |
| 550 |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
| 551 |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
| 552 |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
| 553 |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
| 554 |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
| 555 |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
| 556 |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
| 557 |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
| 558 |
integrators/Integrator.hpp, integrators/NPT.cpp, |
| 559 |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
| 560 |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
| 561 |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
| 562 |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
| 563 |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
| 564 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
| 565 |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
| 566 |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
| 567 |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
| 568 |
math/MatVec3.h, math/randomSPRNG.cpp, |
| 569 |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
| 570 |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
| 571 |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
| 572 |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
| 573 |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
| 574 |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
| 575 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
| 576 |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
| 577 |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
| 578 |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
| 579 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
| 580 |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
| 581 |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
| 582 |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
| 583 |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
| 584 |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
| 585 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
| 586 |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
| 587 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
| 588 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
| 589 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
| 590 |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
| 591 |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
| 592 |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
| 593 |
utils/simError.c, visitors/AtomVisitor.cpp, |
| 594 |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
| 595 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
| 596 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
| 597 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
| 598 |
visitors/ZconsVisitor.hpp: change the #include in source files |
| 599 |
|
| 600 |
2004-09-23 23:16 gezelter |
| 601 |
|
| 602 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 603 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 604 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 605 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 606 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 607 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 608 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 609 |
src/UseTheForce/fForceField.h, |
| 610 |
src/UseTheForce/fSwitchingFunction.h, |
| 611 |
src/UseTheForce/fortranWrapDefines.hpp, |
| 612 |
src/UseTheForce/fortranWrappers.cpp, |
| 613 |
src/UseTheForce/fortranWrappers.hpp, |
| 614 |
src/UseTheForce/mpiComponentPlan.h, |
| 615 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 616 |
src/UseTheForce/mpiSimulation_module.F90, |
| 617 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 618 |
src/UseTheForce/DarkSide/atype_module.F90, |
| 619 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 620 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 621 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 622 |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 623 |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 624 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 625 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 626 |
src/UseTheForce/DarkSide/force_globals.F90, |
| 627 |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 628 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 629 |
src/UseTheForce/DarkSide/switch_module.F90, |
| 630 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 631 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 632 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 633 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 634 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 635 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 636 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 637 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 638 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 639 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 640 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 641 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 642 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 643 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 644 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 645 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 646 |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 647 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 648 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 649 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 650 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 651 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 652 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 653 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 654 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 655 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 656 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 657 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 658 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 659 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 660 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 661 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 662 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 663 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 664 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 665 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 666 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 667 |
src/minimizers/OOPSEMinimizer.cpp, |
| 668 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 669 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 670 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 671 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 672 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 673 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 674 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 675 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 676 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 677 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 678 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 679 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 680 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 681 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 682 |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 683 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 684 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 685 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 686 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 687 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 688 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 689 |
src/utils/simError.c, src/utils/simError.h, |
| 690 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 691 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 692 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 693 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 694 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 695 |
src/visitors/RigidBodyVisitor.cpp, |
| 696 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 697 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 698 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 699 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 700 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 701 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 702 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 703 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 704 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 705 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 706 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 707 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 708 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 709 |
src/applications/LatticeCreator.cpp, |
| 710 |
src/applications/LatticeCreator.hpp, |
| 711 |
src/applications/LatticeFactory.cpp, |
| 712 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 713 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 714 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 715 |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 716 |
src/applications/getopt.c, src/applications/getopt1.c, |
| 717 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 718 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 719 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 720 |
src/applications/simpleBuilder.ggo, |
| 721 |
src/applications/simpleBuilderCmd.c, |
| 722 |
src/integrators/AbstractClasses.hpp, |
| 723 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 724 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 725 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 726 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 727 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 728 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 729 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 730 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 731 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 732 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 733 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 734 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 735 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 736 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 737 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 738 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 739 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 740 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 741 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 742 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 743 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 744 |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 745 |
samples/argon/500.in, samples/argon/500.md, |
| 746 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 747 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 748 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 749 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 750 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 751 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 752 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 753 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 754 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 755 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 756 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 757 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 758 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 759 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 760 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 761 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 762 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 763 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 764 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 765 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 766 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 767 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 768 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 769 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 770 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 771 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 772 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 773 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
| 774 |
|
| 775 |
2004-09-23 23:16 gezelter |
| 776 |
|
| 777 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
| 778 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
| 779 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
| 780 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
| 781 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
| 782 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
| 783 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
| 784 |
src/UseTheForce/fForceField.h, |
| 785 |
src/UseTheForce/fSwitchingFunction.h, |
| 786 |
src/UseTheForce/fortranWrapDefines.hpp, |
| 787 |
src/UseTheForce/fortranWrappers.cpp, |
| 788 |
src/UseTheForce/fortranWrappers.hpp, |
| 789 |
src/UseTheForce/mpiComponentPlan.h, |
| 790 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
| 791 |
src/UseTheForce/mpiSimulation_module.F90, |
| 792 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
| 793 |
src/UseTheForce/DarkSide/atype_module.F90, |
| 794 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
| 795 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
| 796 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
| 797 |
src/UseTheForce/DarkSide/calc_eam.F90, |
| 798 |
src/UseTheForce/DarkSide/calc_gb.F90, |
| 799 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
| 800 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
| 801 |
src/UseTheForce/DarkSide/force_globals.F90, |
| 802 |
src/UseTheForce/DarkSide/neighborLists.F90, |
| 803 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
| 804 |
src/UseTheForce/DarkSide/switch_module.F90, |
| 805 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
| 806 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
| 807 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
| 808 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
| 809 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
| 810 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
| 811 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
| 812 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
| 813 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
| 814 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
| 815 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
| 816 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
| 817 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
| 818 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
| 819 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
| 820 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
| 821 |
src/types/MakeStamps.hpp, src/types/Makefile, |
| 822 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
| 823 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
| 824 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
| 825 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
| 826 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
| 827 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
| 828 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
| 829 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
| 830 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
| 831 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
| 832 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
| 833 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
| 834 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
| 835 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
| 836 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
| 837 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
| 838 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
| 839 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
| 840 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
| 841 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
| 842 |
src/minimizers/OOPSEMinimizer.cpp, |
| 843 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
| 844 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
| 845 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
| 846 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
| 847 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
| 848 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
| 849 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
| 850 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
| 851 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
| 852 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
| 853 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
| 854 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
| 855 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
| 856 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
| 857 |
src/utils/GenericData.hpp, src/utils/Makefile, |
| 858 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
| 859 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
| 860 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
| 861 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
| 862 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
| 863 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
| 864 |
src/utils/simError.c, src/utils/simError.h, |
| 865 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
| 866 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
| 867 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
| 868 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
| 869 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
| 870 |
src/visitors/RigidBodyVisitor.cpp, |
| 871 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
| 872 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
| 873 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
| 874 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
| 875 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
| 876 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
| 877 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
| 878 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
| 879 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
| 880 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
| 881 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
| 882 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
| 883 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
| 884 |
src/applications/LatticeCreator.cpp, |
| 885 |
src/applications/LatticeCreator.hpp, |
| 886 |
src/applications/LatticeFactory.cpp, |
| 887 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
| 888 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
| 889 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
| 890 |
src/applications/cmdline.c, src/applications/cmdline.h, |
| 891 |
src/applications/getopt.c, src/applications/getopt1.c, |
| 892 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
| 893 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
| 894 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
| 895 |
src/applications/simpleBuilder.ggo, |
| 896 |
src/applications/simpleBuilderCmd.c, |
| 897 |
src/integrators/AbstractClasses.hpp, |
| 898 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
| 899 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
| 900 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
| 901 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
| 902 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
| 903 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
| 904 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
| 905 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
| 906 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
| 907 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
| 908 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
| 909 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
| 910 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
| 911 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
| 912 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
| 913 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
| 914 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
| 915 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
| 916 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
| 917 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
| 918 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
| 919 |
samples/alkane/butane.in, samples/alkane/butane.md, |
| 920 |
samples/argon/500.in, samples/argon/500.md, |
| 921 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
| 922 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
| 923 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
| 924 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
| 925 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
| 926 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
| 927 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
| 928 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
| 929 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
| 930 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
| 931 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
| 932 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
| 933 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
| 934 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
| 935 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
| 936 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
| 937 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
| 938 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
| 939 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
| 940 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
| 941 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
| 942 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
| 943 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
| 944 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
| 945 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
| 946 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
| 947 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
| 948 |
forceFields/Pt.VC.funcfl: Initial revision |
| 949 |
|
