1 |
2006-10-10 10:08 chrisfen |
2 |
|
3 |
* src/applications/utilities/: affineScale, affineScale.in, |
4 |
solvator, solvator.in, waterBoxer, waterBoxer.in: who needs .in |
5 |
files for perl? using env |
6 |
|
7 |
2006-10-09 22:44 gezelter |
8 |
|
9 |
* src/: applications/randomBuilder/randomBuilder.cpp, |
10 |
applications/randomBuilder/randomBuilder.ggo, |
11 |
applications/randomBuilder/randomBuilderCmd.c, |
12 |
applications/randomBuilder/randomBuilderCmd.h, utils/MoLocator.cpp: |
13 |
fixing bugs in randomBuilder |
14 |
|
15 |
2006-10-09 18:16 gezelter |
16 |
|
17 |
* samples/argon/lj.md, |
18 |
src/applications/randomBuilder/randomBuilder.cpp, |
19 |
src/applications/simpleBuilder/Makefile, |
20 |
src/applications/simpleBuilder/randomBuilder.cpp, |
21 |
src/applications/simpleBuilder/randomBuilder.ggo, |
22 |
src/applications/simpleBuilder/randomBuilderCmd.c, |
23 |
src/applications/simpleBuilder/randomBuilderCmd.h: Fixing the |
24 |
builders to prepare for OOPSE-4 release |
25 |
|
26 |
2006-10-06 17:29 chuckv |
27 |
|
28 |
* src/applications/utilities/mdSplit: Added utility to split dump |
29 |
file frames into md files. |
30 |
|
31 |
2006-10-03 18:39 chrisfen |
32 |
|
33 |
* src/applications/utilities/Makefile: forgot to adjust the |
34 |
makefile |
35 |
|
36 |
2006-10-03 18:38 chrisfen |
37 |
|
38 |
* src/applications/utilities/: solvator.in, waterBoxer.in: added |
39 |
solvator and adjusted waterBoxer |
40 |
|
41 |
2006-10-02 19:54 chrisfen |
42 |
|
43 |
* src/applications/utilities/waterBoxer.in: improvements to |
44 |
waterBoxer |
45 |
|
46 |
2006-10-02 19:27 chrisfen |
47 |
|
48 |
* src/applications/utilities/waterBoxer.in: fixed a bug in |
49 |
waterBoxer for invalid water names |
50 |
|
51 |
2006-09-26 17:55 gezelter |
52 |
|
53 |
* AUTHORS, README: Starting cleanup for 4.0 release |
54 |
|
55 |
2006-09-26 12:08 gezelter |
56 |
|
57 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
58 |
BondOrderParameter.hpp: Cleaned up the code for BondOrderParameter |
59 |
and added a bunch of comments. Fixed a memory leak or ten. |
60 |
|
61 |
2006-09-26 10:33 gezelter |
62 |
|
63 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
64 |
BondOrderParameter.hpp: Some efficiency fixes (now computes Wigner |
65 |
3-j coefficients only once in the constructor). |
66 |
|
67 |
2006-09-25 21:30 gezelter |
68 |
|
69 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
70 |
BondOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
71 |
StaticPropsCmd.c, StaticPropsCmd.h: Mostly done with |
72 |
BondOrderParameter. Only a few performance tweaks remain |
73 |
|
74 |
2006-09-25 18:08 gezelter |
75 |
|
76 |
* src/: applications/staticProps/BondOrderParameter.cpp, |
77 |
applications/staticProps/BondOrderParameter.hpp, |
78 |
applications/staticProps/StaticProps.cpp, brains/SimCreator.cpp, |
79 |
math/SphericalHarmonic.cpp: fixing bond order parameter code |
80 |
|
81 |
2006-09-22 18:19 chrisfen |
82 |
|
83 |
* src/: UseTheForce/DarkSide/simulation.F90, brains/SimInfo.cpp, |
84 |
brains/fSimulation.h, io/ForceFieldOptions.cpp, |
85 |
io/ForceFieldOptions.hpp, io/Globals.cpp, io/Globals.hpp: refined |
86 |
the reaction field dielectric passing |
87 |
|
88 |
2006-09-21 21:41 gezelter |
89 |
|
90 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
91 |
BondOrderParameter.hpp: bug fixes (still broken, however) |
92 |
|
93 |
2006-09-21 21:36 gezelter |
94 |
|
95 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
96 |
BondOrderParameter.hpp: Following Rein ten Wolde article |
97 |
|
98 |
2006-09-21 17:47 gezelter |
99 |
|
100 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
101 |
BondOrderParameter.hpp: more bug fixes |
102 |
|
103 |
2006-09-21 16:43 gezelter |
104 |
|
105 |
* src/applications/staticProps/BondOrderParameter.cpp: more changes |
106 |
to BOP and SH |
107 |
|
108 |
2006-09-21 14:25 chrisfen |
109 |
|
110 |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
111 |
io/Globals.cpp: fixed the half self term for wolf electrostatics |
112 |
and OOPSE now chooses a cutoff radius dependent alpha for damped |
113 |
electrostatics |
114 |
|
115 |
2006-09-21 14:04 gezelter |
116 |
|
117 |
* src/applications/staticProps/BondOrderParameter.cpp: Fixed a bug |
118 |
in Wl code in BondOrderParameter |
119 |
|
120 |
2006-09-21 10:45 gezelter |
121 |
|
122 |
* src/: applications/staticProps/BondOrderParameter.cpp, |
123 |
math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: Bugfixes in |
124 |
BondOrderParameter and SphericalHarmonic |
125 |
|
126 |
2006-09-20 18:16 gezelter |
127 |
|
128 |
* src/: applications/staticProps/BondOrderParameter.cpp, |
129 |
math/Makefile, math/SphericalHarmonic.cpp, |
130 |
math/SphericalHarmonic.hpp: added SphericalHarmonics, fixed a few |
131 |
problems with BondOrderParameter |
132 |
|
133 |
2006-09-20 16:13 gezelter |
134 |
|
135 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
136 |
BondOrderParameter.hpp, GofAngle2.cpp, StaticProps.cpp, |
137 |
StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed bugs |
138 |
(mostly in BondOrderParameter) |
139 |
|
140 |
2006-09-19 17:20 gezelter |
141 |
|
142 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
143 |
BondOrderParameter.hpp: Adding BondOrderParameter to StaticProps |
144 |
|
145 |
2006-09-19 17:14 gezelter |
146 |
|
147 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
148 |
BondOrderParameter.hpp, Makefile, StaticProps.cpp, StaticProps.ggo, |
149 |
StaticPropsCmd.c, StaticPropsCmd.h: Working on BondOrderParameter |
150 |
|
151 |
2006-09-18 17:31 chuckv |
152 |
|
153 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
154 |
BondOrderParameter.hpp: Latest Version |
155 |
|
156 |
2006-09-08 12:13 gezelter |
157 |
|
158 |
* src/: brains/BlockSnapshotManager.cpp, io/DumpReader.cpp, |
159 |
utils/residentMem.c: fixed a DumpReader bug, took out extra |
160 |
printing statements in residentMem and BlockSnapshotManager |
161 |
|
162 |
2006-09-04 09:37 gezelter |
163 |
|
164 |
* configure, ac-tools/configure.in, |
165 |
src/applications/utilities/Makefile: changing configure script to |
166 |
process the new utilities |
167 |
|
168 |
2006-09-01 18:58 chrisfen |
169 |
|
170 |
* src/applications/utilities/waterBoxer.in: added some features to |
171 |
waterBoxer |
172 |
|
173 |
2006-09-01 17:08 chrisfen |
174 |
|
175 |
* src/applications/utilities/: Makefile, affineScale.in, |
176 |
waterBoxer.in: added the waterBoxer script |
177 |
|
178 |
2006-09-01 15:22 chrisfen |
179 |
|
180 |
* src/applications/utilities/affineScale.in: added comment info |
181 |
|
182 |
2006-09-01 15:16 gezelter |
183 |
|
184 |
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
185 |
brains/Register.cpp, integrators/Makefile, integrators/NgammaT.cpp, |
186 |
integrators/NgammaT.hpp, io/Globals.cpp: adding NgammaT integrator |
187 |
|
188 |
2006-09-01 14:29 chrisfen |
189 |
|
190 |
* src/applications/utilities/affineScale.in: modified affineScale |
191 |
to work with the new OOPSE files |
192 |
|
193 |
2006-09-01 10:15 chrisfen |
194 |
|
195 |
* src/io/: RestReader.cpp, RestWriter.cpp: fixed TI MPI bug |
196 |
|
197 |
2006-08-31 18:34 chrisfen |
198 |
|
199 |
* src/: integrators/VelocityVerletIntegrator.cpp, |
200 |
restraints/ThermoIntegrationForceManager.cpp: fixes to zang writing |
201 |
|
202 |
2006-08-31 16:12 chrisfen |
203 |
|
204 |
* samples/alkane/butane.in, samples/alkane/butane.md, |
205 |
samples/argon/500.in, samples/argon/500.md, samples/argon/ar864.in, |
206 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
207 |
samples/argon/argonNVT.md, samples/cutoff/GB-Ar-max.md, |
208 |
samples/cutoff/GB-Ar-mix.md, samples/cutoff/GB-Ar-traditional.md, |
209 |
samples/cutoff/cutoff_test.in, samples/cutoff/cutoff_test.md, |
210 |
samples/cutoff/gb-ar.in, samples/cutoff/max.md, |
211 |
samples/cutoff/mix.md, samples/cutoff/traditional.md, |
212 |
samples/dipole/splitInWater.in, samples/dipole/splitInWater.md, |
213 |
samples/dipole/split_SSD.in, samples/dipole/split_SSD.md, |
214 |
samples/dipole/twoSplitDipole.in, samples/dipole/twoSplitDipole.md, |
215 |
samples/gbljtest/2gb.in, samples/gbljtest/2gb.md, |
216 |
samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
217 |
samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
218 |
samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
219 |
samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
220 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
221 |
samples/metals/EAM/Au_bulk.in, samples/metals/EAM/Au_bulk_FBD.md, |
222 |
samples/metals/EAM/Au_bulk_voter.md, |
223 |
samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.in, |
224 |
samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.md, |
225 |
samples/metals/EAM/nanoparticle/Au_nanoparticle.in, |
226 |
samples/metals/EAM/nanoparticle/Au_nanoparticle.md, |
227 |
samples/metals/EAM/nanorod/Au_nanoparticle.in, |
228 |
samples/metals/EAM/nanorod/Au_nanoparticle_FCC.md, |
229 |
samples/metals/Sutton-Chen/Au_bulk.in, |
230 |
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
231 |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
232 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
233 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.md, |
234 |
samples/thermoIntegration/liquid/ssde.in, |
235 |
samples/thermoIntegration/liquid/ssde.md, |
236 |
samples/thermoIntegration/solid/ssde.in, |
237 |
samples/thermoIntegration/solid/ssde.md, samples/water/dimer/cl.in, |
238 |
samples/water/dimer/cl.md, samples/water/dimer/mix.in, |
239 |
samples/water/dimer/mix.md, samples/water/dimer/mix2.in, |
240 |
samples/water/dimer/mix2.md, samples/water/dimer/ssd.in, |
241 |
samples/water/dimer/ssd.md, samples/water/dimer/tap.in, |
242 |
samples/water/dimer/tap.md, samples/water/dimer/two.in, |
243 |
samples/water/dimer/two.md, samples/water/spce/spce.in, |
244 |
samples/water/spce/spce.md, samples/water/ssd/ssd.in, |
245 |
samples/water/ssd/ssd.md, samples/water/ssd-ion/ssd-ion.md, |
246 |
samples/water/ssd-ion/ssdCl.in, samples/water/ssd-ion/ssdCl.md, |
247 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
248 |
samples/water/ssdrf/ssdrf.in, samples/water/ssdrf/ssdrf.md, |
249 |
samples/water/tap/tap.in, samples/water/tap/tap.md, |
250 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
251 |
samples/water/tip4p/tp4.in, samples/water/tip4p/tp4.md, |
252 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
253 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
254 |
src/restraints/ThermoIntegrationForceManager.cpp: converted samples |
255 |
over to the OOPSE-4 file format |
256 |
|
257 |
Fixed an MPI bug in thermodynamic integration |
258 |
|
259 |
2006-08-30 17:13 gezelter |
260 |
|
261 |
* src/applications/hydrodynamics/Hydro.cpp: removed extra file in |
262 |
Hydro.cpp |
263 |
|
264 |
2006-08-30 17:04 gezelter |
265 |
|
266 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
267 |
applications/dynamicProps/DynamicProps.cpp, |
268 |
applications/staticProps/StaticProps.cpp, |
269 |
applications/utilities/dumpConverter, openbabel/oopseformat.cpp: |
270 |
Changing utility programs to use the new file format |
271 |
|
272 |
2006-08-30 16:33 gezelter |
273 |
|
274 |
* src/: brains/SimCreator.cpp, io/DumpReader.cpp, |
275 |
io/DumpWriter.cpp: fixed some bugs in DumpWriter, eliminated some |
276 |
extra printing of debugging information |
277 |
|
278 |
2006-08-30 14:42 tim |
279 |
|
280 |
* configure, ac-tools/OOPSE.m4, forceFields/Au.u3.funcfl, |
281 |
forceFields/Ni.u3.funcfl, samples/argon/lj.md, |
282 |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
283 |
src/brains/SimCreator.hpp, src/brains/SimInfo.cpp, |
284 |
src/brains/SimInfo.hpp, src/io/DumpReader.cpp, |
285 |
src/io/DumpReader.hpp, src/io/DumpWriter.cpp, |
286 |
src/io/DumpWriter.hpp, src/io/Globals.cpp, src/io/Globals.hpp, |
287 |
src/mdParser/SimplePreprocessor.hpp, src/openbabel/Makefile, |
288 |
src/openbabel/oopseformat.cpp, src/primitives/StuntDouble.cpp, |
289 |
src/primitives/StuntDouble.hpp, src/utils/StringUtils.cpp, |
290 |
src/utils/StringUtils.hpp: Massive changes preparing for release of |
291 |
OOPSE-4: The main difference is that the new MD file format (.md, |
292 |
.dump, .eor) now contains meta-data information along with the |
293 |
configuration information. |
294 |
|
295 |
2006-08-24 13:42 xsun |
296 |
|
297 |
* src/io/Globals.cpp: change the globals.cpp to make sure we can |
298 |
set targetPressure and surfaceTension to be negative. |
299 |
|
300 |
2006-08-14 16:32 chrisfen |
301 |
|
302 |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed an ordering |
303 |
issue in quadrupole-charge interactions |
304 |
|
305 |
2006-08-02 15:40 gezelter |
306 |
|
307 |
* make/Makefile.in, samples/water/ssde/ssde.md, src/config.h.in, |
308 |
src/antlr/Makefile, src/applications/atom2md/atom2md.cpp, |
309 |
src/brains/Snapshot.cpp, src/brains/Snapshot.hpp, |
310 |
src/openbabel/Makefile, src/openbabel/oopseformat.cpp, |
311 |
src/openbabel/oopseformat.hpp: starting change of file formats |
312 |
|
313 |
2006-08-02 14:06 gezelter |
314 |
|
315 |
* src/applications/: atom2md/Makefile, atom2md/atom2md.cpp, |
316 |
atom2mdin/Makefile, atom2mdin/atom2mdin.cpp: Changing atom2mdin |
317 |
into atom2md to reflect new unified file format |
318 |
|
319 |
2006-07-27 17:02 chrisfen |
320 |
|
321 |
* src/applications/utilities/dumpConverter: fixed a pvf bug |
322 |
|
323 |
2006-07-27 16:36 tim |
324 |
|
325 |
* src/applications/utilities/dumpConverter: fixed dumpConverter |
326 |
problems |
327 |
|
328 |
2006-07-27 15:05 gezelter |
329 |
|
330 |
* src/applications/utilities/dumpConverter: added dumpConverter |
331 |
|
332 |
2006-07-26 17:45 gezelter |
333 |
|
334 |
* make/Makefile.in: removed shapes sample |
335 |
|
336 |
2006-07-26 17:45 gezelter |
337 |
|
338 |
* src/applications/utilities/affineScale.in: fixed a spelling bug |
339 |
|
340 |
2006-07-26 17:01 gezelter |
341 |
|
342 |
* configure: added perl interpreter to affineScale script |
343 |
|
344 |
2006-07-26 17:01 gezelter |
345 |
|
346 |
* ac-tools/configure.in: added perl substitution for affineScale |
347 |
script |
348 |
|
349 |
2006-07-26 17:00 gezelter |
350 |
|
351 |
* make/Makefile.in: added install target for scripts |
352 |
|
353 |
2006-07-26 17:00 gezelter |
354 |
|
355 |
* src/applications/utilities/: Makefile, affineScale.in: Adding a |
356 |
directory for scripts Adding affineScale script |
357 |
|
358 |
2006-07-24 10:51 xsun |
359 |
|
360 |
* src/UseTheForce/DarkSide/gb.F90: fixed a getSigma bug |
361 |
|
362 |
2006-07-19 08:46 chrisfen |
363 |
|
364 |
* samples/: thermoIntegration/liquid/water.md, |
365 |
thermoIntegration/solid/water.md, water/dimer/water.md, |
366 |
water/spce/water.md, water/ssd/water.md, water/ssd-ion/water.md, |
367 |
water/ssde/water.md, water/ssdrf/water.md, water/tap/water.md, |
368 |
water/tip3p_ice/water.md, water/tip4p/water.md: Added tred to |
369 |
sample water.md files |
370 |
|
371 |
2006-07-19 08:35 chrisfen |
372 |
|
373 |
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp, |
374 |
RigidBodyVisitor.cpp, RigidBodyVisitor.hpp: Added TRED water |
375 |
visitor for Dump2XYZ visualization |
376 |
|
377 |
2006-07-19 08:33 chrisfen |
378 |
|
379 |
* forceFields/DUFF2.frc: Added TRED parameters to forcefield |
380 |
|
381 |
2006-07-17 14:13 xsun |
382 |
|
383 |
* src/UseTheForce/DarkSide/gb.F90: fixed d / sigma0 confusion |
384 |
|
385 |
2006-07-15 22:48 gezelter |
386 |
|
387 |
* src/io/ForceFieldOptions.cpp: testing commit logger |
388 |
|
389 |
2006-07-15 22:46 gezelter |
390 |
|
391 |
* src/io/ForceFieldOptions.cpp: removed printing of GBN and GBM |
392 |
from previous debugging |
393 |
|
394 |
2006-07-14 10:47 xsun |
395 |
|
396 |
* configure, ac-tools/OOPSE.m4: Fixed a bug in the fftw part of the |
397 |
configure script. |
398 |
|
399 |
2006-07-07 15:44 gezelter |
400 |
|
401 |
* configure, ac-tools/configure.in, samples/gbljtest/2gb.md, |
402 |
src/UseTheForce/DarkSide/gb.F90: removed icc from C++ search lines, |
403 |
did some formatting work on GB module, mucked around with a GB |
404 |
example |
405 |
|
406 |
2006-07-07 10:18 chuckv |
407 |
|
408 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
409 |
BondOrderParameter.hpp: Adding more changes to orientational bond |
410 |
order parameter. |
411 |
|
412 |
2006-07-03 15:40 chuckv |
413 |
|
414 |
* src/math/Wigner3jm.F90: Added utility function to winger3jm from |
415 |
slatac. |
416 |
|
417 |
2006-07-03 10:06 chrisfen |
418 |
|
419 |
* src/UseTheForce/DarkSide/mpole.F90: Added the multipole |
420 |
interaction routine. It doesn't work yet, so it's not included in |
421 |
the build. |
422 |
|
423 |
2006-07-03 09:18 chrisfen |
424 |
|
425 |
* src/: UseTheForce/doForces.F90, |
426 |
UseTheForce/doForces_interface.F90, |
427 |
UseTheForce/doForces_interface.h, |
428 |
UseTheForce/DarkSide/electrostatic.F90, |
429 |
UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp, |
430 |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
431 |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
432 |
brains/fSimulation.h, integrators/VelocityVerletIntegrator.cpp, |
433 |
io/Globals.cpp, io/Globals.hpp, |
434 |
restraints/ThermoIntegrationForceManager.cpp: Added simulation box |
435 |
dipole moment accumulation for the purposes of calculating |
436 |
dielectric constants |
437 |
|
438 |
2006-07-01 18:27 kdaily |
439 |
|
440 |
* src/UseTheForce/DarkSide/gb.F90: fixed forces and torques for GB |
441 |
|
442 |
2006-06-28 10:35 chrisfen |
443 |
|
444 |
* src/io/: DumpReader.cpp, RestReader.cpp, RestReader.hpp: more |
445 |
efficient file reading for thermodynamic integration, and fixed |
446 |
some formatting |
447 |
|
448 |
2006-06-27 12:36 chuckv |
449 |
|
450 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
451 |
BondOrderParameter.hpp: Beginnings of a order parameter. |
452 |
|
453 |
2006-06-27 12:19 chuckv |
454 |
|
455 |
* src/applications/staticProps/: BondOrderParameter.cpp, |
456 |
BondOrderParameter.hpp: Adding code for bond orientational |
457 |
parameters. |
458 |
|
459 |
2006-06-22 11:21 chrisfen |
460 |
|
461 |
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
462 |
integrators/VelocityVerletIntegrator.cpp, io/RestWriter.cpp, |
463 |
io/RestWriter.hpp, restraints/ThermoIntegrationForceManager.cpp: |
464 |
MPI thermodynamic integration works now. |
465 |
|
466 |
2006-06-21 14:28 chrisfen |
467 |
|
468 |
* src/visitors/AtomVisitor.cpp: fixed a build problem... |
469 |
GB_12b_ratio no longer exists (replaced with BG_l). |
470 |
|
471 |
2006-06-19 13:55 chuckv |
472 |
|
473 |
* src/math/: Makefile, Wigner3jm.F90, Wigner3jm_interface.h: Added |
474 |
support for Winger3jm coefficients. |
475 |
|
476 |
2006-06-18 21:36 chrisfen |
477 |
|
478 |
* src/: io/RestReader.cpp, io/RestWriter.cpp, |
479 |
restraints/ThermoIntegrationForceManager.cpp: fixes for mpi |
480 |
thermodynamic integration, close to fully working... |
481 |
|
482 |
2006-06-17 13:02 tim |
483 |
|
484 |
* src/visitors/AtomVisitor.cpp: output the principle axis of GB |
485 |
|
486 |
2006-06-15 14:38 gezelter |
487 |
|
488 |
* configure, ac-tools/OOPSE.m4, ac-tools/configure.in, |
489 |
samples/water/tip4p/tp4.md: added mpi compilers, demoted pg |
490 |
compilers after pathscale |
491 |
|
492 |
2006-06-09 14:26 chrisfen |
493 |
|
494 |
* src/UseTheForce/DarkSide/electrostatic.F90: reformulated some of |
495 |
the electrostatics |
496 |
|
497 |
2006-06-07 18:49 chrisfen |
498 |
|
499 |
* samples/water/ssd/ssd.md, |
500 |
src/UseTheForce/DarkSide/electrostatic.F90: damping now works for |
501 |
charge-quadrupole and dipole-dipole |
502 |
|
503 |
2006-06-07 14:05 chrisfen |
504 |
|
505 |
* src/: UseTheForce/DarkSide/simParallel.F90, io/RestReader.cpp: |
506 |
Fixed a spelling error and a bug in MPI Thermodynamic Integration |
507 |
on file read-in |
508 |
|
509 |
2006-06-06 14:26 chrisfen |
510 |
|
511 |
* src/io/: DumpReader.cpp, MultipoleAtomTypesSectionParser.cpp: |
512 |
fixed some typos |
513 |
|
514 |
2006-06-06 13:43 gezelter |
515 |
|
516 |
* forceFields/DUFF2.frc, samples/gbljtest/2gb.in, |
517 |
samples/gbljtest/2gb.md, samples/gbljtest/gb.md, |
518 |
samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md, |
519 |
samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md, |
520 |
samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md, |
521 |
samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md, |
522 |
src/UseTheForce/DarkSide/gb.F90, |
523 |
src/integrators/LDForceManager.cpp, |
524 |
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
525 |
src/utils/interpolation.F90, src/visitors/AtomVisitor.hpp: testing |
526 |
GB, removing CM drift in Langevin Dynamics, fixing a memory leak, |
527 |
adding a visitor |
528 |
|
529 |
2006-06-05 14:44 gezelter |
530 |
|
531 |
* src/UseTheForce/DarkSide/: fForceOptions.F90, gb.F90: Added |
532 |
methods to access GB_mu and GB_nu from the force field options |
533 |
|
534 |
2006-06-05 14:24 gezelter |
535 |
|
536 |
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
537 |
src/UseTheForce/doForces.F90, src/UseTheForce/fForceOptions.h, |
538 |
src/UseTheForce/DarkSide/gb.F90, |
539 |
src/UseTheForce/DarkSide/gb_interface.F90, |
540 |
src/UseTheForce/DarkSide/gb_interface.h, |
541 |
src/applications/hydrodynamics/AnalyticalModel.cpp, |
542 |
src/applications/hydrodynamics/ApproximationModel.cpp, |
543 |
src/applications/hydrodynamics/ApproximationModel.hpp, |
544 |
src/applications/hydrodynamics/CompositeShape.cpp, |
545 |
src/applications/hydrodynamics/CompositeShape.hpp, |
546 |
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
547 |
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
548 |
src/applications/hydrodynamics/ShapeBuilder.cpp, |
549 |
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
550 |
src/hydrodynamics/HydroProp.cpp, src/hydrodynamics/HydroProp.hpp, |
551 |
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
552 |
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
553 |
src/integrators/LDForceManager.cpp, |
554 |
src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp, |
555 |
src/io/ForceFieldOptions.hpp, |
556 |
src/io/GayBerneAtomTypesSectionParser.cpp, |
557 |
src/io/GayBerneAtomTypesSectionParser.hpp, |
558 |
src/types/DirectionalAtomType.cpp, |
559 |
src/types/DirectionalAtomType.hpp, src/utils/HydroProps.hpp: |
560 |
Massive changes for GB code with multiple ellipsoid types (a la |
561 |
Cleaver's paper). |
562 |
|
563 |
Also, changes in hydrodynamics code to make HydroProp a somewhat |
564 |
smarter class (rather than just a struct). |
565 |
|
566 |
2006-06-01 14:06 xsun |
567 |
|
568 |
* src/applications/staticProps/: Makefile, RippleOP.cpp, |
569 |
RippleOP.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
570 |
StaticPropsCmd.h: Add the RippleOP to calculate the orderparameter |
571 |
of the ripples. |
572 |
|
573 |
2006-05-25 17:40 chrisfen |
574 |
|
575 |
* forceFields/DUFF2.frc, samples/thermoIntegration/liquid/water.md, |
576 |
samples/thermoIntegration/solid/water.md, |
577 |
samples/water/dimer/water.md, samples/water/spce/water.md, |
578 |
samples/water/ssd/water.md, samples/water/ssd-ion/water.md, |
579 |
samples/water/ssde/water.md, samples/water/ssdrf/water.md, |
580 |
samples/water/tap/water.md, samples/water/tip3p_ice/water.md, |
581 |
samples/water/tip4p/water.md, src/io/Globals.cpp: Added TIP5P-E and |
582 |
fixed a bug for Thermodynamic integration (you can now have a |
583 |
lambda of 0) |
584 |
|
585 |
2006-05-25 13:02 tim |
586 |
|
587 |
* src/applications/hydrodynamics/ApproximationModel.cpp: Fix a type |
588 |
promotion problem |
589 |
|
590 |
2006-05-25 12:27 tim |
591 |
|
592 |
* src/applications/hydrodynamics/: AnalyticalModel.hpp, |
593 |
ApproximationModel.cpp, Hydro.cpp, HydrodynamicsModel.hpp: replace |
594 |
double with RealType |
595 |
|
596 |
2006-05-25 11:27 gezelter |
597 |
|
598 |
* configure: What? |
599 |
|
600 |
2006-05-25 11:24 gezelter |
601 |
|
602 |
* ac-tools/OOPSE.m4: more changes |
603 |
|
604 |
2006-05-25 11:19 gezelter |
605 |
|
606 |
* configure, ac-tools/OOPSE.m4: more changes for MPICH with |
607 |
profiling libraries required |
608 |
|
609 |
2006-05-25 10:54 gezelter |
610 |
|
611 |
* configure, ac-tools/OOPSE.m4: MPI stuff |
612 |
|
613 |
2006-05-24 14:31 gezelter |
614 |
|
615 |
* configure, ac-tools/OOPSE.m4, src/config.h.in, |
616 |
src/applications/hydrodynamics/AnalyticalModel.cpp, |
617 |
src/applications/hydrodynamics/AnalyticalModel.hpp, |
618 |
src/applications/hydrodynamics/ApproximationModel.cpp, |
619 |
src/applications/hydrodynamics/ApproximationModel.hpp, |
620 |
src/applications/hydrodynamics/CompositeShape.cpp, |
621 |
src/applications/hydrodynamics/CompositeShape.hpp, |
622 |
src/applications/hydrodynamics/Ellipsoid.cpp, |
623 |
src/applications/hydrodynamics/Ellipsoid.hpp, |
624 |
src/applications/hydrodynamics/Hydro.cpp, |
625 |
src/applications/hydrodynamics/HydrodynamicsModel.cpp, |
626 |
src/applications/hydrodynamics/HydrodynamicsModel.hpp, |
627 |
src/applications/hydrodynamics/RoughShell.cpp, |
628 |
src/applications/hydrodynamics/RoughShell.hpp, |
629 |
src/applications/hydrodynamics/Shape.hpp, |
630 |
src/applications/hydrodynamics/ShapeBuilder.cpp, |
631 |
src/applications/hydrodynamics/ShapeBuilder.hpp, |
632 |
src/applications/hydrodynamics/Spheric.cpp, |
633 |
src/applications/hydrodynamics/Spheric.hpp: fixes for Hydrodynamics |
634 |
|
635 |
2006-05-24 12:18 tim |
636 |
|
637 |
* src/integrators/LDForceManager.cpp: fix a bug in parsing |
638 |
HydroProp file |
639 |
|
640 |
2006-05-24 11:24 gezelter |
641 |
|
642 |
* src/integrators/LDForceManager.cpp: Fixed a bug when spherical |
643 |
boundary conditions were off. |
644 |
|
645 |
2006-05-23 17:12 xsun |
646 |
|
647 |
* src/applications/staticProps/Hxy.cpp: fixed an initialization bug |
648 |
of Hxy.cpp. |
649 |
|
650 |
2006-05-23 14:46 tim |
651 |
|
652 |
* src/applications/dump2Xyz/Dump2XYZ.cpp: wrapping back to PBC by |
653 |
molecule instead of by individual atom |
654 |
|
655 |
2006-05-22 11:30 xsun |
656 |
|
657 |
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, StaticProps.ggo, |
658 |
StaticPropsCmd.c, StaticPropsCmd.h: fixed the bugs of Hxy.cpp. |
659 |
|
660 |
2006-05-19 17:26 chrisfen |
661 |
|
662 |
* ChangeLog, src/io/DumpWriter.cpp: Last bug showed up in 2 places, |
663 |
fixed the other one. |
664 |
|
665 |
2006-05-19 16:45 tim |
666 |
|
667 |
* src/io/DumpWriter.cpp: Fix a bug of printing empty line in |
668 |
DumpWriter |
669 |
|
670 |
2006-05-19 11:11 tim |
671 |
|
672 |
* make/Makefile.in: change the order of include path and library |
673 |
path |
674 |
|
675 |
2006-05-17 17:51 tim |
676 |
|
677 |
* ChangeLog, samples/water/ssd/ssd.md, src/config.h.in, |
678 |
src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp, |
679 |
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
680 |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
681 |
src/UseTheForce/doForces_interface.h, |
682 |
src/UseTheForce/fForceOptions.h, |
683 |
src/UseTheForce/DarkSide/eam_interface.h, |
684 |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
685 |
src/UseTheForce/DarkSide/gb_interface.h, |
686 |
src/UseTheForce/DarkSide/lj_interface.h, |
687 |
src/UseTheForce/DarkSide/shapes_interface.h, |
688 |
src/UseTheForce/DarkSide/simulation_interface.h, |
689 |
src/UseTheForce/DarkSide/sticky_interface.h, |
690 |
src/UseTheForce/DarkSide/suttonchen_interface.h, |
691 |
src/applications/dynamicProps/CrossTimeCorrFunc.cpp, |
692 |
src/applications/dynamicProps/CrossTimeCorrFunc.hpp, |
693 |
src/applications/dynamicProps/DipoleCorrFunc.cpp, |
694 |
src/applications/dynamicProps/DipoleCorrFunc.hpp, |
695 |
src/applications/dynamicProps/LegendreCorrFunc.cpp, |
696 |
src/applications/dynamicProps/LegendreCorrFunc.hpp, |
697 |
src/applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
698 |
src/applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
699 |
src/applications/dynamicProps/RCorrFunc.cpp, |
700 |
src/applications/dynamicProps/RCorrFunc.hpp, |
701 |
src/applications/dynamicProps/TimeCorrFunc.hpp, |
702 |
src/applications/dynamicProps/VCorrFunc.cpp, |
703 |
src/applications/dynamicProps/VCorrFunc.hpp, |
704 |
src/applications/hydrodynamics/Makefile, |
705 |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
706 |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
707 |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
708 |
src/applications/randomBuilder/randomBuilder.cpp, |
709 |
src/applications/simpleBuilder/randomBuilder.cpp, |
710 |
src/applications/staticProps/DensityPlot.cpp, |
711 |
src/applications/staticProps/DensityPlot.hpp, |
712 |
src/applications/staticProps/GofAngle2.cpp, |
713 |
src/applications/staticProps/GofAngle2.hpp, |
714 |
src/applications/staticProps/GofR.cpp, |
715 |
src/applications/staticProps/GofR.hpp, |
716 |
src/applications/staticProps/GofRAngle.cpp, |
717 |
src/applications/staticProps/GofRAngle.hpp, |
718 |
src/applications/staticProps/GofXyz.cpp, |
719 |
src/applications/staticProps/GofXyz.hpp, |
720 |
src/applications/staticProps/Hxy.cpp, |
721 |
src/applications/staticProps/Hxy.hpp, |
722 |
src/applications/staticProps/P2OrderParameter.cpp, |
723 |
src/applications/staticProps/P2OrderParameter.hpp, |
724 |
src/applications/staticProps/RhoZ.cpp, |
725 |
src/applications/staticProps/RhoZ.hpp, |
726 |
src/applications/staticProps/SCDOrderParameter.cpp, |
727 |
src/applications/staticProps/SCDOrderParameter.hpp, |
728 |
src/applications/staticProps/StaticProps.cpp, |
729 |
src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp, |
730 |
src/brains/DataStorage.hpp, src/brains/ForceManager.cpp, |
731 |
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
732 |
src/brains/SimInfo.hpp, src/brains/Snapshot.cpp, |
733 |
src/brains/Snapshot.hpp, src/brains/Stats.hpp, |
734 |
src/brains/Thermo.cpp, src/brains/Thermo.hpp, |
735 |
src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp, |
736 |
src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp, |
737 |
src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp, |
738 |
src/constraints/ZconstraintForceManager.cpp, |
739 |
src/constraints/ZconstraintForceManager.hpp, |
740 |
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
741 |
src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp, |
742 |
src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp, |
743 |
src/integrators/DLM.hpp, src/integrators/Integrator.hpp, |
744 |
src/integrators/LDForceManager.cpp, |
745 |
src/integrators/LDForceManager.hpp, |
746 |
src/integrators/LangevinDynamics.cpp, |
747 |
src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp, |
748 |
src/integrators/NPAT.hpp, src/integrators/NPT.cpp, |
749 |
src/integrators/NPT.hpp, src/integrators/NPTf.cpp, |
750 |
src/integrators/NPTf.hpp, src/integrators/NPTi.cpp, |
751 |
src/integrators/NPTi.hpp, src/integrators/NPTxyz.cpp, |
752 |
src/integrators/NPTxyz.hpp, src/integrators/NPrT.cpp, |
753 |
src/integrators/NPrT.hpp, src/integrators/NVE.cpp, |
754 |
src/integrators/NVE.hpp, src/integrators/NVT.cpp, |
755 |
src/integrators/NVT.hpp, src/integrators/RotationAlgorithm.hpp, |
756 |
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
757 |
src/integrators/VelocityVerletIntegrator.cpp, |
758 |
src/integrators/VelocityVerletIntegrator.hpp, |
759 |
src/io/AtomTypesSectionParser.cpp, |
760 |
src/io/BendTypesSectionParser.cpp, |
761 |
src/io/BondTypesSectionParser.cpp, |
762 |
src/io/ChargeAtomTypesSectionParser.cpp, |
763 |
src/io/DirectionalAtomTypesSectionParser.cpp, |
764 |
src/io/DumpReader.cpp, src/io/DumpWriter.cpp, |
765 |
src/io/EAMAtomTypesSectionParser.cpp, |
766 |
src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp, |
767 |
src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp, |
768 |
src/io/RestReader.cpp, src/io/RestReader.hpp, |
769 |
src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp, |
770 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
771 |
src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp, |
772 |
src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp, |
773 |
src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp, |
774 |
src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp, |
775 |
src/math/CholeskyDecomposition.hpp, |
776 |
src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp, |
777 |
src/math/MatVec3.c, src/math/MatVec3.h, |
778 |
src/math/MersenneTwister.hpp, src/math/Polynomial.hpp, |
779 |
src/math/Quaternion.hpp, src/math/RandNumGen.hpp, |
780 |
src/math/RealSphericalHarmonic.cpp, |
781 |
src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp, |
782 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
783 |
src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp, |
784 |
src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp, |
785 |
src/minimizers/CGFamilyMinimizer.cpp, |
786 |
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp, |
787 |
src/minimizers/Minimizer.hpp, |
788 |
src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp, |
789 |
src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp, |
790 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
791 |
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
792 |
src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp, |
793 |
src/primitives/DirectionalAtom.cpp, |
794 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
795 |
src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp, |
796 |
src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp, |
797 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
798 |
src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp, |
799 |
src/primitives/Torsion.cpp, src/primitives/Torsion.hpp, |
800 |
src/primitives/UreyBradleyBend.cpp, |
801 |
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
802 |
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
803 |
src/restraints/ThermoIntegrationForceManager.hpp, |
804 |
src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp, |
805 |
src/selection/SelectionEvaluator.cpp, |
806 |
src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp, |
807 |
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
808 |
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
809 |
src/types/BendType.hpp, src/types/BondType.hpp, |
810 |
src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp, |
811 |
src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp, |
812 |
src/types/DirectionalAtomType.cpp, |
813 |
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
814 |
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
815 |
src/types/MorseBondType.hpp, src/types/OplsTorsionType.hpp, |
816 |
src/types/PolynomialBendType.hpp, src/types/PolynomialBondType.hpp, |
817 |
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
818 |
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
819 |
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
820 |
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
821 |
src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp, |
822 |
src/utils/GenericData.hpp, src/utils/MoLocator.cpp, |
823 |
src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp, |
824 |
src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp, |
825 |
src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp, |
826 |
src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h, |
827 |
src/utils/residentMem.c, src/utils/residentMem.h, |
828 |
src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp: |
829 |
Adding single precision capabilities to c++ side |
830 |
|
831 |
2006-05-17 15:54 gezelter |
832 |
|
833 |
* configure, ac-tools/configure.in, make/Makefile.in, |
834 |
src/UseTheForce/doForces.F90, |
835 |
src/UseTheForce/DarkSide/neighborLists.F90, |
836 |
src/UseTheForce/DarkSide/shapes.F90, |
837 |
src/UseTheForce/DarkSide/simParallel.F90, |
838 |
src/UseTheForce/DarkSide/simulation_interface.F90, |
839 |
src/utils/definitions.F90: Adding single precision capabilities to |
840 |
the fortran side |
841 |
|
842 |
2006-05-17 12:10 gezelter |
843 |
|
844 |
* configure, ac-tools/configure.in, src/config.h.in: adding |
845 |
--enable-single to configure script |
846 |
|
847 |
2006-05-17 11:37 gezelter |
848 |
|
849 |
* ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, |
850 |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
851 |
src/UseTheForce/DarkSide/electrostatic.F90, |
852 |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
853 |
src/UseTheForce/DarkSide/gb.F90, |
854 |
src/UseTheForce/DarkSide/lj_interface.F90, |
855 |
src/UseTheForce/DarkSide/shapes.F90, |
856 |
src/UseTheForce/DarkSide/sticky.F90, |
857 |
src/UseTheForce/DarkSide/suttonchen.F90, |
858 |
src/UseTheForce/DarkSide/suttonchen_interface.F90, |
859 |
src/UseTheForce/DarkSide/switcheroo.F90, src/math/derfc.F90, |
860 |
src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran |
861 |
side prepped for single precision... |
862 |
|
863 |
2006-05-17 10:03 chrisfen |
864 |
|
865 |
* samples/water/ssd-ion/ssdCl.md, |
866 |
src/UseTheForce/DarkSide/electrostatic.F90: electrostatic |
867 |
refinement |
868 |
|
869 |
2006-05-16 23:03 gezelter |
870 |
|
871 |
* configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes |
872 |
|
873 |
2006-05-16 16:38 gezelter |
874 |
|
875 |
* configure, ac-tools/OOPSE.m4, ac-tools/config.guess, |
876 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, |
877 |
ac-tools/missing, ac-tools/mkinstalldirs, make/Makefile.in, |
878 |
src/config.h.in, src/applications/staticProps/Hxy.cpp, |
879 |
src/applications/staticProps/Hxy.hpp, |
880 |
src/applications/staticProps/StaticProps.cpp: Autoconf fixes for |
881 |
FFTW. Multiple FFTW version support. |
882 |
|
883 |
2006-05-15 22:06 gezelter |
884 |
|
885 |
* README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
886 |
make/Makefile.in, src/config.h.in, |
887 |
src/applications/hydrodynamics/AnalyticalModel.cpp, |
888 |
src/applications/hydrodynamics/AnalyticalModel.hpp, |
889 |
src/applications/staticProps/Hxy.cpp, |
890 |
src/applications/staticProps/Hxy.hpp, |
891 |
src/applications/staticProps/StaticProps.cpp, |
892 |
src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, |
893 |
src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp, |
894 |
src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp, |
895 |
src/integrators/LDForceManager.cpp, |
896 |
src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, |
897 |
src/utils/HydroProps.hpp: [no log message] |
898 |
|
899 |
2006-05-12 17:34 xsun |
900 |
|
901 |
* src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, |
902 |
StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to |
903 |
calculate undulation spectrum |
904 |
|
905 |
2006-05-09 21:44 tim |
906 |
|
907 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
908 |
applications/dump2Xyz/Dump2XYZ.ggo, |
909 |
applications/dump2Xyz/Dump2XYZCmd.c, |
910 |
applications/dump2Xyz/Dump2XYZCmd.h, |
911 |
applications/hydrodynamics/ApproximationModel.cpp, |
912 |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a |
913 |
gay-berne switch to Dump2XYZ |
914 |
|
915 |
2006-05-05 13:58 gezelter |
916 |
|
917 |
* src/UseTheForce/DarkSide/qpole.F90: Adding qpole |
918 |
|
919 |
2006-05-05 10:34 tim |
920 |
|
921 |
* ac-tools/aclocal.m4: finding ifort arguments that won't die under |
922 |
two different versions of the intel fortran compiler |
923 |
|
924 |
2006-05-03 09:15 chrisfen |
925 |
|
926 |
* src/applications/randomBuilder/Makefile: missing makefile was |
927 |
hanging up 'make clean' |
928 |
|
929 |
2006-04-25 18:59 chuckv |
930 |
|
931 |
* src/applications/randomBuilder/: randomBuilder.cpp, |
932 |
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added |
933 |
random builder to cvs. |
934 |
|
935 |
2006-04-25 18:54 chuckv |
936 |
|
937 |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
938 |
Change in siminfo used in nanoparticleBuilder. |
939 |
|
940 |
2006-04-25 18:30 chuckv |
941 |
|
942 |
* make/Makefile.in: Added random builder |
943 |
|
944 |
2006-04-25 18:29 chuckv |
945 |
|
946 |
* src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, |
947 |
randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a |
948 |
random builder to oopse. |
949 |
|
950 |
2006-04-25 09:35 gezelter |
951 |
|
952 |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
953 |
ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table |
954 |
to pick vdw radii for hydrodynamics if the LJ sigma can't be found. |
955 |
|
956 |
2006-04-24 22:09 gezelter |
957 |
|
958 |
* configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, |
959 |
src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, |
960 |
src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, |
961 |
src/brains/SimInfo.hpp, src/brains/Thermo.cpp, |
962 |
src/brains/Thermo.hpp, src/integrators/LDForceManager.cpp, |
963 |
src/integrators/LDForceManager.hpp, |
964 |
src/integrators/LangevinDynamics.cpp, src/io/Globals.cpp, |
965 |
src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding |
966 |
spherical boundary conditions to LD integrator |
967 |
|
968 |
2006-04-24 22:06 gezelter |
969 |
|
970 |
* src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: |
971 |
Added EAM atom types to Hydro models |
972 |
|
973 |
2006-04-21 16:02 chrisfen |
974 |
|
975 |
* src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the |
976 |
EAM module |
977 |
|
978 |
2006-04-21 15:32 chrisfen |
979 |
|
980 |
* ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, |
981 |
samples/shape/C60.shape, samples/shape/C70.shape, |
982 |
samples/shape/Makefile, samples/shape/Shapes.frc, |
983 |
samples/shape/cholesterol.shape, samples/shape/ethylBenzene.shape, |
984 |
samples/shape/linear.in, samples/shape/linear.md, |
985 |
samples/shape/linear.shape, samples/shape/toluene.shape, |
986 |
samples/thermoIntegration/liquid/ssde.md, |
987 |
samples/thermoIntegration/solid/ssde.md, |
988 |
samples/water/spce/spce.md, samples/water/ssd/ssd.md, |
989 |
samples/water/ssd-ion/ssdCl.md, samples/water/ssde/ssde.md, |
990 |
samples/water/ssdrf/ssdrf.md, samples/water/tip3p_ice/tp3.md, |
991 |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90, |
992 |
src/UseTheForce/DarkSide/LJ.F90: Removed sqrt splines and shape |
993 |
stuff (doesn't work, so why was it in there?). Changed some of the |
994 |
water samples to use shifted_force. Probably should set the |
995 |
defaults to use the damped version now that we sped it up. |
996 |
|
997 |
2006-04-20 23:19 chrisfen |
998 |
|
999 |
* samples/water/spce/spce.md, |
1000 |
src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... |
1001 |
|
1002 |
2006-04-20 17:02 chrisfen |
1003 |
|
1004 |
* samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, |
1005 |
src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky |
1006 |
|
1007 |
2006-04-20 14:24 gezelter |
1008 |
|
1009 |
* samples/metals/EAM/Au_bulk_voter.md, |
1010 |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1011 |
samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, |
1012 |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, |
1013 |
src/UseTheForce/DarkSide/eam.F90, |
1014 |
src/UseTheForce/DarkSide/electrostatic.F90, |
1015 |
src/UseTheForce/DarkSide/suttonchen.F90, |
1016 |
src/UseTheForce/DarkSide/switcheroo.F90, |
1017 |
src/UseTheForce/DarkSide/switcheroo_interface.F90, |
1018 |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
1019 |
src/utils/interpolation.F90: Complete rewrite of spline code and |
1020 |
everything that uses it. |
1021 |
|
1022 |
2006-04-17 17:49 gezelter |
1023 |
|
1024 |
* configure, ac-tools/aclocal.m4, samples/argon/500.md, |
1025 |
samples/metals/EAM/Au_bulk_voter.md, |
1026 |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1027 |
samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, |
1028 |
src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, |
1029 |
src/UseTheForce/DarkSide/electrostatic.F90, |
1030 |
src/UseTheForce/DarkSide/interpolation.F90, |
1031 |
src/UseTheForce/DarkSide/sticky.F90, |
1032 |
src/UseTheForce/DarkSide/suttonchen.F90, |
1033 |
src/UseTheForce/DarkSide/switcheroo.F90, |
1034 |
src/applications/hydrodynamics/Hydro.ggo, |
1035 |
src/applications/hydrodynamics/HydroCmd.c, |
1036 |
src/applications/hydrodynamics/HydroCmd.h, |
1037 |
src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, |
1038 |
src/utils/interpolation.F90: Many performance improvements |
1039 |
|
1040 |
2006-04-15 22:51 chrisfen |
1041 |
|
1042 |
* configure, samples/argon/500.md, src/UseTheForce/doForces.F90, |
1043 |
src/UseTheForce/fSwitchingFunction.h, |
1044 |
src/UseTheForce/DarkSide/electrostatic.F90, |
1045 |
src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to |
1046 |
switcheroo |
1047 |
|
1048 |
2006-04-15 17:58 chrisfen |
1049 |
|
1050 |
* src/utils/Makefile.in: Since status.F90 is used by |
1051 |
interpolation.F90, the former needs to be listed above the later in |
1052 |
the Makefile. |
1053 |
|
1054 |
2006-04-14 17:59 gezelter |
1055 |
|
1056 |
* src/utils/interpolation.F90: changed the interface a bit |
1057 |
|
1058 |
2006-04-14 17:49 gezelter |
1059 |
|
1060 |
* src/utils/interpolation.F90: added some logical flags |
1061 |
|
1062 |
2006-04-14 17:06 chrisfen |
1063 |
|
1064 |
* src/utils/interpolation.F90: Wiped the spline with derivatives |
1065 |
and corrected a boundary comparision error by eliminating the |
1066 |
check. This algorithm REQUIRES known first derivatives at the |
1067 |
endpoints. |
1068 |
|
1069 |
2006-04-14 16:04 gezelter |
1070 |
|
1071 |
* src/utils/: Makefile.in, interpolation.F90: bug fixes for |
1072 |
interpolation module |
1073 |
|
1074 |
2006-04-14 15:57 gezelter |
1075 |
|
1076 |
* src/utils/interpolation.F90: Heavily modified interpolation |
1077 |
module, also moved to "utils" |
1078 |
|
1079 |
2006-04-12 17:15 chuckv |
1080 |
|
1081 |
* src/UseTheForce/DarkSide/interpolation.F90: Added interpolation |
1082 |
module. |
1083 |
|
1084 |
2006-04-11 11:33 gezelter |
1085 |
|
1086 |
* src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, |
1087 |
StaticPropsCmd.h: [no log message] |
1088 |
|
1089 |
2006-04-03 11:37 chuckv |
1090 |
|
1091 |
* configure, ac-tools/aclocal.m4, make/Makefile.in, |
1092 |
src/UseTheForce/DarkSide/simParallel.F90: Added status module to |
1093 |
simParallel for error reporting. |
1094 |
|
1095 |
2006-03-31 13:09 tim |
1096 |
|
1097 |
* src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now |
1098 |
|
1099 |
2006-03-30 16:08 chuckv |
1100 |
|
1101 |
* src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug |
1102 |
where SCList capacity was not reset to zero on destruction. |
1103 |
|
1104 |
2006-03-30 14:37 chuckv |
1105 |
|
1106 |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
1107 |
More testing of nanoparticleBuilder. |
1108 |
|
1109 |
2006-03-29 17:24 chuckv |
1110 |
|
1111 |
* src/mdParser/SimplePreprocessor.hpp: Added check to make sure md |
1112 |
file exists. |
1113 |
|
1114 |
2006-03-29 14:17 chuckv |
1115 |
|
1116 |
* src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, |
1117 |
lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed |
1118 |
latticeOrt in shapedlatice and latticebuilder. |
1119 |
|
1120 |
2006-03-29 13:11 tim |
1121 |
|
1122 |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
1123 |
LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem |
1124 |
in calculating correlation functions |
1125 |
|
1126 |
2006-03-29 13:09 tim |
1127 |
|
1128 |
* src/applications/hydrodynamics/: ApproximationModel.cpp, |
1129 |
ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, |
1130 |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) |
1131 |
RoughShell Model is working; (20)Adding a new option into Hydro |
1132 |
which allows user to generate the beads only |
1133 |
|
1134 |
2006-03-27 11:21 chuckv |
1135 |
|
1136 |
* src/applications/nanoparticleBuilder/Makefile: Makefile for |
1137 |
nanoparticle builder. |
1138 |
|
1139 |
2006-03-27 11:03 chuckv |
1140 |
|
1141 |
* make/Makefile.in, src/lattice/shapedLattice.cpp, |
1142 |
src/lattice/shapedLattice.hpp: Added nanoparticle builder to |
1143 |
makefile |
1144 |
|
1145 |
2006-03-24 15:46 chuckv |
1146 |
|
1147 |
* src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: |
1148 |
Debugging changes to nanoparticle builder. |
1149 |
|
1150 |
2006-03-24 12:29 tim |
1151 |
|
1152 |
* src/applications/dynamicProps/: DynamicProps.cpp, |
1153 |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
1154 |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps |
1155 |
|
1156 |
2006-03-24 11:49 tim |
1157 |
|
1158 |
* src/applications/dynamicProps/: DynamicProps.cpp, |
1159 |
DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, |
1160 |
RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation |
1161 |
function. The command line option for DynamicProps is now changed. |
1162 |
--rcorr is for position correlation and --rmsd is for mean square |
1163 |
displacement. |
1164 |
|
1165 |
2006-03-23 10:03 tim |
1166 |
|
1167 |
* src/applications/hydrodynamics/: AnalyticalModel.cpp, |
1168 |
AnalyticalModel.hpp, ApproximationModel.cpp, |
1169 |
ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads |
1170 |
method |
1171 |
|
1172 |
2006-03-23 10:02 tim |
1173 |
|
1174 |
* src/io/Globals.hpp: remove a unknown method |
1175 |
|
1176 |
2006-03-23 10:00 tim |
1177 |
|
1178 |
* src/math/CholeskyDecomposition.hpp: The off diagnal is not set |
1179 |
|
1180 |
2006-03-23 09:59 tim |
1181 |
|
1182 |
* src/mdParser/SimplePreprocessor.hpp: Throw exception if the file |
1183 |
can not be opened for preprocessing |
1184 |
|
1185 |
2006-03-22 15:57 chuckv |
1186 |
|
1187 |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
1188 |
shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added |
1189 |
shaped lattice. |
1190 |
|
1191 |
2006-03-21 10:33 tim |
1192 |
|
1193 |
* src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug |
1194 |
in calculating hydrodynamics tensor when the radius of beads are |
1195 |
not the same |
1196 |
|
1197 |
2006-03-20 19:26 tim |
1198 |
|
1199 |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1200 |
applications/hydrodynamics/BeadModel.cpp, |
1201 |
applications/hydrodynamics/ShapeBuilder.cpp, |
1202 |
integrators/LDForceManager.cpp: Fix a bug in friction calculation |
1203 |
for ellipsoid |
1204 |
|
1205 |
2006-03-20 14:12 tim |
1206 |
|
1207 |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1208 |
applications/hydrodynamics/Ellipsoid.cpp, |
1209 |
applications/hydrodynamics/Ellipsoid.hpp, |
1210 |
applications/hydrodynamics/ShapeBuilder.cpp, |
1211 |
integrators/LDForceManager.cpp: Verify the correctness of |
1212 |
Ellipsoid's hydrodynamics properties |
1213 |
|
1214 |
2006-03-17 18:51 tim |
1215 |
|
1216 |
* src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New |
1217 |
version of Hydro is working now. |
1218 |
|
1219 |
2006-03-17 18:20 tim |
1220 |
|
1221 |
* src/: applications/hydrodynamics/AnalyticalModel.cpp, |
1222 |
applications/hydrodynamics/AnalyticalModel.hpp, |
1223 |
applications/hydrodynamics/ApproximationModel.cpp, |
1224 |
applications/hydrodynamics/ApproximationModel.hpp, |
1225 |
applications/hydrodynamics/BeadModel.hpp, |
1226 |
applications/hydrodynamics/CompositeShape.cpp, |
1227 |
applications/hydrodynamics/CompositeShape.hpp, |
1228 |
applications/hydrodynamics/Ellipsoid.cpp, |
1229 |
applications/hydrodynamics/Ellipsoid.hpp, |
1230 |
applications/hydrodynamics/Hydro.cpp, |
1231 |
applications/hydrodynamics/Hydro.ggo, |
1232 |
applications/hydrodynamics/HydroCmd.c, |
1233 |
applications/hydrodynamics/HydroCmd.h, |
1234 |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
1235 |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1236 |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
1237 |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
1238 |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
1239 |
applications/hydrodynamics/Makefile, |
1240 |
applications/hydrodynamics/RoughShell.cpp, |
1241 |
applications/hydrodynamics/RoughShell.hpp, |
1242 |
applications/hydrodynamics/Shape.hpp, |
1243 |
applications/hydrodynamics/ShapeBuilder.cpp, |
1244 |
applications/hydrodynamics/ShapeBuilder.hpp, |
1245 |
applications/hydrodynamics/Spheric.cpp, |
1246 |
applications/hydrodynamics/Spheric.hpp, |
1247 |
applications/hydrodynamics/StuntDoubleShape.cpp, |
1248 |
applications/hydrodynamics/StuntDoubleShape.hpp, |
1249 |
integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, |
1250 |
io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, |
1251 |
utils/HydroProps.hpp: refactor Hydrodynamics module. |
1252 |
|
1253 |
2006-03-17 11:10 chuckv |
1254 |
|
1255 |
* src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: |
1256 |
Generic Shaped Lattice for oopse. Can overload to get spherical or |
1257 |
nanorod. |
1258 |
|
1259 |
2006-03-16 17:50 tim |
1260 |
|
1261 |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1262 |
integrators/LDForceManager.cpp, math/MersenneTwister.hpp: |
1263 |
LagevinDynamics is working? |
1264 |
|
1265 |
2006-03-16 16:52 gezelter |
1266 |
|
1267 |
* src/applications/hydrodynamics/RoughShell.hpp: fixed a const |
1268 |
problem |
1269 |
|
1270 |
2006-03-15 17:08 tim |
1271 |
|
1272 |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit |
1273 |
conversion for diffusion tensor is wrong |
1274 |
|
1275 |
2006-03-15 16:28 tim |
1276 |
|
1277 |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1278 |
utils/NumericConstant.hpp: change the epsilon of numeric_limit |
1279 |
|
1280 |
2006-03-15 15:58 tim |
1281 |
|
1282 |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting |
1283 |
the unit in HydrodynamicsModel |
1284 |
|
1285 |
2006-03-15 12:35 tim |
1286 |
|
1287 |
* src/primitives/RigidBody.cpp: using setFrc in |
1288 |
RigidBody::calcForcesAndTorques will discard if there are force and |
1289 |
torque applied in rigid body itself. use addFrc instead. |
1290 |
|
1291 |
2006-03-15 10:51 tim |
1292 |
|
1293 |
* src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, |
1294 |
RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel |
1295 |
|
1296 |
2006-03-15 10:50 tim |
1297 |
|
1298 |
* make/Makefile.in, src/applications/hydrodynamics/Makefile: adding |
1299 |
hydrodynamics module into build system |
1300 |
|
1301 |
2006-03-14 18:46 tim |
1302 |
|
1303 |
* src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition |
1304 |
|
1305 |
2006-03-13 17:42 tim |
1306 |
|
1307 |
* src/: applications/hydrodynamics/HydrodynamicsModel.cpp, |
1308 |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1309 |
applications/hydrodynamics/StuntDoubleShape.cpp, |
1310 |
applications/hydrodynamics/StuntDoubleShape.hpp, |
1311 |
brains/Register.cpp, integrators/LDForceManager.cpp, |
1312 |
integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, |
1313 |
integrators/LangevinDynamics.hpp, integrators/Makefile, |
1314 |
io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, |
1315 |
math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in |
1316 |
progress |
1317 |
|
1318 |
2006-03-07 11:43 gezelter |
1319 |
|
1320 |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a |
1321 |
double/int bug. Surprised no one ever noticed before... |
1322 |
|
1323 |
2006-02-24 16:17 tim |
1324 |
|
1325 |
* src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs |
1326 |
in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out |
1327 |
product of Rij |
1328 |
|
1329 |
2006-02-23 18:16 tim |
1330 |
|
1331 |
* src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, |
1332 |
HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, |
1333 |
HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, |
1334 |
HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, |
1335 |
MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, |
1336 |
StuntDoubleShape.hpp: Bead Model is working |
1337 |
|
1338 |
2006-02-22 15:35 tim |
1339 |
|
1340 |
* src/: applications/hydrodynamics/Hydro.cpp, |
1341 |
applications/hydrodynamics/Hydro.ggo, |
1342 |
applications/hydrodynamics/HydroCmd.c, |
1343 |
applications/hydrodynamics/HydroCmd.h, |
1344 |
applications/hydrodynamics/HydrodynamicsModel.cpp, |
1345 |
applications/hydrodynamics/HydrodynamicsModel.hpp, |
1346 |
applications/hydrodynamics/HydrodynamicsModelCreator.hpp, |
1347 |
applications/hydrodynamics/HydrodynamicsModelFactory.cpp, |
1348 |
applications/hydrodynamics/HydrodynamicsModelFactory.hpp, |
1349 |
applications/hydrodynamics/MoleculeShape.cpp, |
1350 |
applications/hydrodynamics/MoleculeShape.hpp, |
1351 |
math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, |
1352 |
math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics |
1353 |
Module |
1354 |
|
1355 |
2006-02-16 17:05 gezelter |
1356 |
|
1357 |
* src/brains/Snapshot.cpp: fixed a spelling error |
1358 |
|
1359 |
2006-02-16 16:40 gezelter |
1360 |
|
1361 |
* src/: UseTheForce/doForces.F90, |
1362 |
UseTheForce/DarkSide/simulation.F90, math/Makefile, |
1363 |
math/linearAlgebra.F90: fixed a problem with cutoff radii being set |
1364 |
larger than 1/2 the length of the shortest box dimension. added a |
1365 |
few fortran utility routines |
1366 |
|
1367 |
2006-02-15 15:46 chuckv |
1368 |
|
1369 |
* src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, |
1370 |
sphericalNanoparticle.hpp: Changed Names of class files. |
1371 |
|
1372 |
2006-02-10 10:45 kdaily |
1373 |
|
1374 |
* src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log |
1375 |
message] |
1376 |
|
1377 |
2006-02-10 10:12 tim |
1378 |
|
1379 |
* src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in |
1380 |
converting integer to double |
1381 |
|
1382 |
2006-02-08 13:21 chrisfen |
1383 |
|
1384 |
* forceFields/DUFF2.frc: added DPD molecule type parameters |
1385 |
|
1386 |
2006-02-07 11:39 tim |
1387 |
|
1388 |
* src/applications/dynamicProps/: DipoleCorrFunc.cpp, |
1389 |
LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of |
1390 |
trajectory file during analysis |
1391 |
|
1392 |
2006-02-02 12:14 tim |
1393 |
|
1394 |
* src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, |
1395 |
types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug |
1396 |
in AtomStamp where orientation is not set correctly. |
1397 |
|
1398 |
2006-02-02 11:49 gezelter |
1399 |
|
1400 |
* src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that |
1401 |
contain directional atoms |
1402 |
|
1403 |
2006-02-02 10:49 xsun |
1404 |
|
1405 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1406 |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor |
1407 |
for GBlipid atom type |
1408 |
|
1409 |
2006-02-01 21:57 gezelter |
1410 |
|
1411 |
* make/Makefile.in: added CXXFLAGS to the LinkOptions to allow |
1412 |
compilation with icc9 (skipping the gcc-4 std c++ libraries). |
1413 |
|
1414 |
2006-02-01 16:06 chrisfen |
1415 |
|
1416 |
* src/brains/SimInfo.cpp: Missing brace caused the last commit not |
1417 |
to build |
1418 |
|
1419 |
2006-02-01 15:54 chrisfen |
1420 |
|
1421 |
* samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to |
1422 |
cutoff radius setting to a more logical procedure - still may |
1423 |
change... |
1424 |
|
1425 |
2006-02-01 12:26 gezelter |
1426 |
|
1427 |
* src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: |
1428 |
Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X |
1429 |
|
1430 |
2006-01-30 17:25 tim |
1431 |
|
1432 |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
1433 |
applications/dynamicProps/DynamicProps.cpp, |
1434 |
applications/dynamicProps/DynamicProps.ggo, |
1435 |
applications/dynamicProps/DynamicPropsCmd.c, |
1436 |
applications/dynamicProps/DynamicPropsCmd.h, |
1437 |
applications/dynamicProps/LegendreCorrFunc.cpp, |
1438 |
applications/dynamicProps/LegendreCorrFunc.hpp, |
1439 |
applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, |
1440 |
math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: |
1441 |
Adding :LegendrePolynomial |
1442 |
|
1443 |
2006-01-19 17:54 chuckv |
1444 |
|
1445 |
* src/applications/nanoparticleBuilder/: Makefile, |
1446 |
nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to |
1447 |
nanoparticle builder |
1448 |
|
1449 |
2006-01-18 16:08 chuckv |
1450 |
|
1451 |
* src/applications/nanoparticleBuilder/Makefile: Added Makefile for |
1452 |
nanoparticle builder. |
1453 |
|
1454 |
2006-01-17 11:16 gezelter |
1455 |
|
1456 |
* AUTHORS, README: Cleaning up for 3.0.1 release |
1457 |
|
1458 |
2006-01-17 10:50 gezelter |
1459 |
|
1460 |
* ChangeLog: Prepping 3.0.1 release |
1461 |
|
1462 |
2006-01-17 10:32 gezelter |
1463 |
|
1464 |
* src/config.h.in: new version number |
1465 |
|
1466 |
2006-01-17 10:32 gezelter |
1467 |
|
1468 |
* doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, |
1469 |
definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, |
1470 |
oopseManual.pdf: Updated Documentation |
1471 |
|
1472 |
2006-01-16 18:10 gezelter |
1473 |
|
1474 |
* ChangeLog, README: Getting ready for release! |
1475 |
|
1476 |
2006-01-16 10:26 gezelter |
1477 |
|
1478 |
* configure: Testing commit |
1479 |
|
1480 |
2006-01-13 16:57 chuckv |
1481 |
|
1482 |
* src/: UseTheForce/SC_FF.cpp, |
1483 |
applications/nanoparticleBuilder/sphericalNanoparticle.cpp, |
1484 |
io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. |
1485 |
Handled by forceField now. |
1486 |
|
1487 |
2006-01-13 14:17 chuckv |
1488 |
|
1489 |
* src/io/Globals.cpp: Added NPAT to Globals integrators. |
1490 |
|
1491 |
2006-01-13 11:33 gezelter |
1492 |
|
1493 |
* Makefile: [no log message] |
1494 |
|
1495 |
2006-01-13 11:26 gezelter |
1496 |
|
1497 |
* Makefile: testing to make sure GNU make is the make that was used |
1498 |
to build OOPSE |
1499 |
|
1500 |
2006-01-13 10:48 gezelter |
1501 |
|
1502 |
* configure, ac-tools/configure.in: changed compiler search order |
1503 |
|
1504 |
2006-01-12 19:09 chuckv |
1505 |
|
1506 |
* forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, |
1507 |
samples/metals/Sutton-Chen/Au_bulk.in, |
1508 |
samples/metals/Sutton-Chen/Au_bulk_QSC.md, |
1509 |
samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen |
1510 |
units |
1511 |
|
1512 |
2006-01-12 16:16 gezelter |
1513 |
|
1514 |
* LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some |
1515 |
version info and the copyright date |
1516 |
|
1517 |
2006-01-12 15:52 gezelter |
1518 |
|
1519 |
* src/config.h.in: added some missing checks for header files |
1520 |
(particularly zlib.h), used autoheader to help generate config.h.in |
1521 |
|
1522 |
2006-01-12 15:51 gezelter |
1523 |
|
1524 |
* configure, ac-tools/configure.in: added some missing checks for |
1525 |
header files (particularly zlib.h) |
1526 |
|
1527 |
2006-01-12 15:19 gezelter |
1528 |
|
1529 |
* make/Makefile.in: fixed a dependency problem for the Executable |
1530 |
builds |
1531 |
|
1532 |
2006-01-12 15:02 gezelter |
1533 |
|
1534 |
* samples/gbljtest/Makefile: Missing Makefile in this sample |
1535 |
directory |
1536 |
|
1537 |
2006-01-12 15:01 gezelter |
1538 |
|
1539 |
* make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: |
1540 |
Old makefile.in no longer required |
1541 |
|
1542 |
2006-01-12 15:01 gezelter |
1543 |
|
1544 |
* forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff |
1545 |
needs to be installed |
1546 |
|
1547 |
2006-01-12 14:56 chuckv |
1548 |
|
1549 |
* src/io/DumpWriter.cpp: Changed formating. |
1550 |
|
1551 |
2006-01-12 11:47 chrisfen |
1552 |
|
1553 |
* samples/water/tip4p/tp4.md, |
1554 |
src/UseTheForce/DarkSide/electrostatic.F90, |
1555 |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
1556 |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
1557 |
src/brains/SimInfo.cpp: unifying function name in electrostatics |
1558 |
|
1559 |
2006-01-12 11:04 tim |
1560 |
|
1561 |
* samples/metals/: EAM/nanoparticle/Makefile, |
1562 |
EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, |
1563 |
Sutton-Chen/Makefile: fix make install problem for metals samples |
1564 |
|
1565 |
2006-01-12 10:22 tim |
1566 |
|
1567 |
* make/Makefile.in: remove samples/metals from install list. |
1568 |
|
1569 |
2006-01-12 09:31 tim |
1570 |
|
1571 |
* src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not |
1572 |
handle multiple line macro, just convert multiple line macro into |
1573 |
single line macro. |
1574 |
|
1575 |
2006-01-11 23:13 chrisfen |
1576 |
|
1577 |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
1578 |
UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some |
1579 |
changes to electrostatics for shifted-potential and shifted-force |
1580 |
with mono and multipoles |
1581 |
|
1582 |
2006-01-11 18:04 gezelter |
1583 |
|
1584 |
* src/config.h.in, src/UseTheForce/doForces_interface.h, |
1585 |
src/UseTheForce/DarkSide/atype_interface.h, |
1586 |
src/UseTheForce/DarkSide/eam_interface.h, |
1587 |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
1588 |
src/UseTheForce/DarkSide/fForceOptions_interface.h, |
1589 |
src/UseTheForce/DarkSide/gb_interface.h, |
1590 |
src/UseTheForce/DarkSide/lj_interface.h, |
1591 |
src/UseTheForce/DarkSide/shapes_interface.h, |
1592 |
src/UseTheForce/DarkSide/simParallel_interface.h, |
1593 |
src/UseTheForce/DarkSide/simulation_interface.h, |
1594 |
src/UseTheForce/DarkSide/sticky_interface.h, |
1595 |
src/UseTheForce/DarkSide/suttonchen_interface.h, |
1596 |
src/UseTheForce/DarkSide/switcheroo_interface.h, |
1597 |
src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, |
1598 |
src/utils/fError.c, configure, make/Makefile.in: autoconf |
1599 |
modernization and cruft removal |
1600 |
|
1601 |
2006-01-11 18:04 gezelter |
1602 |
|
1603 |
* ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf |
1604 |
modernization and cruft-removal |
1605 |
|
1606 |
2006-01-11 17:50 tim |
1607 |
|
1608 |
* src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix |
1609 |
some error messages |
1610 |
|
1611 |
2006-01-11 14:01 tim |
1612 |
|
1613 |
* src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, |
1614 |
io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, |
1615 |
types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, |
1616 |
types/TorsionStamp.hpp, utils/OOPSEException.hpp, |
1617 |
utils/StringUtils.hpp: instead of printing to std::cout, throwing |
1618 |
an exception when error is found. |
1619 |
|
1620 |
2006-01-11 13:41 gezelter |
1621 |
|
1622 |
* src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling |
1623 |
error |
1624 |
|
1625 |
2006-01-10 17:55 chuckv |
1626 |
|
1627 |
* forceFields/SuttonChen.frc: Changed conversion factor. |
1628 |
|
1629 |
2006-01-10 16:14 chuckv |
1630 |
|
1631 |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1632 |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be |
1633 |
working now. |
1634 |
|
1635 |
2006-01-09 17:22 chuckv |
1636 |
|
1637 |
* src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC |
1638 |
|
1639 |
2006-01-09 17:14 tim |
1640 |
|
1641 |
* src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, |
1642 |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
1643 |
StaticPropsCmd.h: fixing RhoZ |
1644 |
|
1645 |
2006-01-09 14:26 chuckv |
1646 |
|
1647 |
* forceFields/SuttonChen.frc, |
1648 |
samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1649 |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
1650 |
src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to |
1651 |
section parsers. |
1652 |
|
1653 |
2006-01-09 14:11 tim |
1654 |
|
1655 |
* src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, |
1656 |
utils/StringUtils.hpp: replace isType<int> with isInteger |
1657 |
|
1658 |
2006-01-06 16:15 tim |
1659 |
|
1660 |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra |
1661 |
forceFieldOptions from SC_FF |
1662 |
|
1663 |
2006-01-06 15:27 chuckv |
1664 |
|
1665 |
* forceFields/SuttonChen.frc: Add force file. |
1666 |
|
1667 |
2005-12-31 17:42 chuckv |
1668 |
|
1669 |
* src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer |
1670 |
segfaults or produces 0 potential, but rather produces Inf for the |
1671 |
potential. Progress.... |
1672 |
|
1673 |
2005-12-30 18:15 chuckv |
1674 |
|
1675 |
* samples/metals/Sutton-Chen/Au_bulk_SC.md, |
1676 |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
1677 |
src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, |
1678 |
src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More |
1679 |
Sutton-Chen bug fixes. |
1680 |
|
1681 |
2005-12-30 16:25 tim |
1682 |
|
1683 |
* src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range |
1684 |
potential return from fortran is already accumulated, it should not |
1685 |
be accumulated again; nGroupTypesCol is not initialized; |
1686 |
GroupMaxCutoffCol is not allocated; |
1687 |
|
1688 |
2005-12-30 10:32 tim |
1689 |
|
1690 |
* make/Makefile.in, src/brains/SimCreator.cpp: In order to compile |
1691 |
MPI version, we need to cast const char* to void* for |
1692 |
stringstream.str(); Previous Makefile use bjects of single version |
1693 |
to make the MPI library; |
1694 |
|
1695 |
2005-12-29 19:18 chuckv |
1696 |
|
1697 |
* make/Makefile.in, samples/metals/Makefile, |
1698 |
src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, |
1699 |
src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. |
1700 |
Almost there... |
1701 |
|
1702 |
2005-12-29 15:19 chuckv |
1703 |
|
1704 |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in |
1705 |
forcefield. |
1706 |
|
1707 |
2005-12-29 15:07 chuckv |
1708 |
|
1709 |
* samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, |
1710 |
metals.md: added files for sutton-chen |
1711 |
|
1712 |
2005-12-29 11:37 chuckv |
1713 |
|
1714 |
* samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, |
1715 |
metals.md: More cvs changing. |
1716 |
|
1717 |
2005-12-29 11:34 chuckv |
1718 |
|
1719 |
* samples/metals/Au_nanoparticle.in: More moving... |
1720 |
|
1721 |
2005-12-29 11:33 chuckv |
1722 |
|
1723 |
* samples/metals/EAM/nanoparticle/: |
1724 |
Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, |
1725 |
Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More |
1726 |
changes to directory structure. |
1727 |
|
1728 |
2005-12-29 11:21 chuckv |
1729 |
|
1730 |
* samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, |
1731 |
Au_bulk_voter.md, Makefile, metals.md: More Directory changes... |
1732 |
|
1733 |
2005-12-29 11:17 chuckv |
1734 |
|
1735 |
* samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, |
1736 |
Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, |
1737 |
Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of |
1738 |
directory structure |
1739 |
|
1740 |
2005-12-29 11:03 chuckv |
1741 |
|
1742 |
* src/: UseTheForce/DarkSide/fForceOptions_interface.F90, |
1743 |
brains/SimCreator.cpp: Fixed issue with symbol naming and added |
1744 |
call to set force options in SimCreator. |
1745 |
|
1746 |
2005-12-28 16:44 chuckv |
1747 |
|
1748 |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More |
1749 |
changes to forcefield options. |
1750 |
|
1751 |
2005-12-28 16:42 chuckv |
1752 |
|
1753 |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options |
1754 |
passed to fortran. |
1755 |
|
1756 |
2005-12-23 18:04 chuckv |
1757 |
|
1758 |
* src/: UseTheForce/DarkSide/fForceOptions_interface.h, |
1759 |
io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option |
1760 |
changes. |
1761 |
|
1762 |
2005-12-16 16:52 tim |
1763 |
|
1764 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1765 |
src/config.h.in, src/UseTheForce/DarkSide/gb.F90, |
1766 |
src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, |
1767 |
src/openbabel/chains.cpp, src/openbabel/chiral.cpp, |
1768 |
src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, |
1769 |
src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, |
1770 |
src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, |
1771 |
src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, |
1772 |
src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, |
1773 |
src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, |
1774 |
src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, |
1775 |
src/openbabel/obutil.cpp, src/openbabel/patty.cpp, |
1776 |
src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, |
1777 |
src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, |
1778 |
src/openbabel/ring.cpp, src/openbabel/rotor.cpp, |
1779 |
src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, |
1780 |
src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed |
1781 |
__FUNCTION__ to __func__ to match C99 standard, and then added an |
1782 |
autoconf test to check for __func__ usability. Changed some |
1783 |
default compile flags for the Sun architecture |
1784 |
|
1785 |
2005-12-16 14:01 gezelter |
1786 |
|
1787 |
* ac-tools/AC_CXX_HAVE_STL.m4: added the STL check |
1788 |
|
1789 |
2005-12-16 13:55 tim |
1790 |
|
1791 |
* src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor |
1792 |
change to build oopse under solaris |
1793 |
|
1794 |
2005-12-16 13:26 tim |
1795 |
|
1796 |
* src/: brains/SimCreator.cpp, io/Globals.cpp, |
1797 |
types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library |
1798 |
came with SUN compiler does not have a conforming std::use_facet, |
1799 |
define a macro to handle it. Adding exception handling to |
1800 |
SimCreator. |
1801 |
|
1802 |
2005-12-16 10:53 gezelter |
1803 |
|
1804 |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
1805 |
GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom |
1806 |
which was living inside the GB particle. No alien-like ripping out |
1807 |
of the stomach was required. |
1808 |
|
1809 |
2005-12-15 21:57 tim |
1810 |
|
1811 |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
1812 |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
1813 |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: |
1814 |
replace grammar for numerical parsing |
1815 |
|
1816 |
2005-12-15 16:43 gezelter |
1817 |
|
1818 |
* src/UseTheForce/doForces.F90: fixed a cutoff bug |
1819 |
|
1820 |
2005-12-15 09:48 gezelter |
1821 |
|
1822 |
* src/antlr/: CharScanner.hpp, config.hpp: Removing compiler |
1823 |
dependencies and replacing them with real autoconf checks |
1824 |
|
1825 |
2005-12-15 09:47 gezelter |
1826 |
|
1827 |
* configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, |
1828 |
ac-tools/configure.in, src/config.h.in: Adding checks for various |
1829 |
features used by ANTLR |
1830 |
|
1831 |
2005-12-14 13:02 tim |
1832 |
|
1833 |
* src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, |
1834 |
MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, |
1835 |
MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a |
1836 |
nasty negative integer parsing problem by refining the grammar |
1837 |
|
1838 |
2005-12-12 14:32 gezelter |
1839 |
|
1840 |
* src/: UseTheForce/doForces_interface.F90, |
1841 |
UseTheForce/doForces_interface.h, |
1842 |
UseTheForce/DarkSide/electrostatic.F90, |
1843 |
UseTheForce/DarkSide/electrostatic_interface.F90, |
1844 |
UseTheForce/DarkSide/electrostatic_interface.h, |
1845 |
brains/MoleculeCreator.cpp, brains/SimInfo.cpp, |
1846 |
math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made |
1847 |
some minor changes to allow compilation with the portland group |
1848 |
compilers |
1849 |
|
1850 |
2005-12-10 11:54 tim |
1851 |
|
1852 |
* src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation |
1853 |
problem for icc7 |
1854 |
|
1855 |
2005-12-09 16:18 gezelter |
1856 |
|
1857 |
* src/utils/CaseConversion.hpp: added missing include |
1858 |
|
1859 |
2005-12-09 12:11 gezelter |
1860 |
|
1861 |
* configure, ac-tools/aclocal.m4: added some checks for pathscale |
1862 |
compiler |
1863 |
|
1864 |
2005-12-08 17:05 gezelter |
1865 |
|
1866 |
* src/io/ForceFieldOptions.cpp: added copyright |
1867 |
|
1868 |
2005-12-08 17:04 gezelter |
1869 |
|
1870 |
* src/UseTheForce/doForces.F90: added info printout |
1871 |
|
1872 |
2005-12-08 17:04 gezelter |
1873 |
|
1874 |
* configure, ac-tools/configure.in: added pathscale |
1875 |
|
1876 |
2005-12-08 10:38 chuckv |
1877 |
|
1878 |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, |
1879 |
UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, |
1880 |
UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, |
1881 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
1882 |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
1883 |
io/ChargeAtomTypesSectionParser.hpp, |
1884 |
io/DirectionalAtomTypesSectionParser.cpp, |
1885 |
io/DirectionalAtomTypesSectionParser.hpp, |
1886 |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
1887 |
io/GayBerneAtomTypesSectionParser.cpp, |
1888 |
io/GayBerneAtomTypesSectionParser.hpp, |
1889 |
io/MultipoleAtomTypesSectionParser.cpp, |
1890 |
io/MultipoleAtomTypesSectionParser.hpp, |
1891 |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
1892 |
io/ShapeAtomTypesSectionParser.cpp, |
1893 |
io/ShapeAtomTypesSectionParser.hpp, |
1894 |
io/StickyAtomTypesSectionParser.cpp, |
1895 |
io/StickyAtomTypesSectionParser.hpp, |
1896 |
io/StickyPowerAtomTypesSectionParser.cpp, |
1897 |
io/StickyPowerAtomTypesSectionParser.hpp, |
1898 |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: |
1899 |
Wow thats alot o' files. Now passing forceFieldOptions to all of |
1900 |
the parsers. |
1901 |
|
1902 |
2005-12-07 18:10 chuckv |
1903 |
|
1904 |
* src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, |
1905 |
SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... |
1906 |
Started adding support for ForceOptions to section parsers. |
1907 |
|
1908 |
2005-12-07 18:01 gezelter |
1909 |
|
1910 |
* src/UseTheForce/DarkSide/gb_interface.h: [no log message] |
1911 |
|
1912 |
2005-12-07 18:00 chuckv |
1913 |
|
1914 |
* src/io/: LennardJonesAtomTypesSectionParser.cpp, |
1915 |
LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to |
1916 |
section parser |
1917 |
|
1918 |
2005-12-07 14:58 chuckv |
1919 |
|
1920 |
* src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, |
1921 |
lj_interface.h, suttonchen.F90, suttonchen_interface.F90, |
1922 |
suttonchen_interface.h: Removed geometric distance mixing from |
1923 |
individual modules and now use force options to detemine what the |
1924 |
deal is. |
1925 |
|
1926 |
2005-12-07 14:46 chuckv |
1927 |
|
1928 |
* src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: |
1929 |
Further fixes for compiler issues. |
1930 |
|
1931 |
2005-12-07 14:44 chuckv |
1932 |
|
1933 |
* src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. |
1934 |
|
1935 |
2005-12-07 14:38 chuckv |
1936 |
|
1937 |
* src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, |
1938 |
fForceOptions_interface.F90, fForceOptions_interface.h: Added |
1939 |
support for fortran force options. |
1940 |
|
1941 |
2005-12-06 16:01 tim |
1942 |
|
1943 |
* src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion |
1944 |
|
1945 |
2005-12-06 14:26 chuckv |
1946 |
|
1947 |
* src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. |
1948 |
|
1949 |
2005-12-06 12:53 chuckv |
1950 |
|
1951 |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
1952 |
GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned |
1953 |
crystal |
1954 |
|
1955 |
2005-12-06 12:52 chuckv |
1956 |
|
1957 |
* src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for |
1958 |
dumpwriter. |
1959 |
|
1960 |
2005-12-06 11:49 tim |
1961 |
|
1962 |
* samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, |
1963 |
argon/ar864.md, argon/argonNVT.md, argon/lj.md, |
1964 |
dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, |
1965 |
dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, |
1966 |
gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, |
1967 |
gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, |
1968 |
lipid/5x5.md, lipid/lipid.md, lipid/water.md, |
1969 |
metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, |
1970 |
metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, |
1971 |
metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, |
1972 |
minimizer/water.md, shape/linear.md, |
1973 |
thermoIntegration/liquid/ssde.md, |
1974 |
thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, |
1975 |
thermoIntegration/solid/water.md, water/dimer/cl.md, |
1976 |
water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, |
1977 |
water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, |
1978 |
water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, |
1979 |
water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, |
1980 |
water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, |
1981 |
water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, |
1982 |
water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, |
1983 |
water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, |
1984 |
zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated |
1985 |
keywords from samples |
1986 |
|
1987 |
2005-12-05 18:37 tim |
1988 |
|
1989 |
* src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, |
1990 |
Globals.cpp, Makefile: Fix parsing error in OptionSectionParser |
1991 |
|
1992 |
2005-12-05 17:23 gezelter |
1993 |
|
1994 |
* src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, |
1995 |
UseTheForce/Makefile, brains/Register.cpp, |
1996 |
io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding |
1997 |
handler for CLAY force field |
1998 |
|
1999 |
2005-12-05 16:45 chuckv |
2000 |
|
2001 |
* src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug |
2002 |
in openbabel. |
2003 |
|
2004 |
2005-12-05 14:10 tim |
2005 |
|
2006 |
* src/types/MoleculeStamp.cpp: reformat error message |
2007 |
|
2008 |
2005-12-05 14:07 gezelter |
2009 |
|
2010 |
* forceFields/CLAYFF.frc: Adding .frc file for CLAYFF |
2011 |
|
2012 |
2005-12-05 13:23 tim |
2013 |
|
2014 |
* src/: types/AtomStamp.cpp, types/AtomStamp.hpp, |
2015 |
types/BendStamp.hpp, types/MoleculeStamp.cpp, |
2016 |
types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: |
2017 |
adding more checking for topology |
2018 |
|
2019 |
2005-12-02 17:37 gezelter |
2020 |
|
2021 |
* src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon |
2022 |
removal |
2023 |
|
2024 |
2005-12-02 17:37 gezelter |
2025 |
|
2026 |
* src/config.h.in: We've made big changes. This isn't 2.0 anymore. |
2027 |
|
2028 |
2005-12-02 17:37 gezelter |
2029 |
|
2030 |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
2031 |
GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, |
2032 |
traditional.md: removing deprecated nAtoms and nComponents lines |
2033 |
|
2034 |
2005-12-02 15:34 tim |
2035 |
|
2036 |
* src/selection/SelectionToken.cpp: adding SelectionToken.cpp |
2037 |
|
2038 |
2005-12-02 15:18 tim |
2039 |
|
2040 |
* src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding |
2041 |
FragmentStamp |
2042 |
|
2043 |
2005-12-02 15:11 gezelter |
2044 |
|
2045 |
* src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no |
2046 |
longer thrown with consts (fixes compilation bug on the Mac). |
2047 |
|
2048 |
2005-12-02 15:10 gezelter |
2049 |
|
2050 |
* src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious |
2051 |
printing out of timestep |
2052 |
|
2053 |
2005-12-02 15:10 gezelter |
2054 |
|
2055 |
* src/brains/ForceManager.cpp: Got rid of spurious printing out of |
2056 |
junk |
2057 |
|
2058 |
2005-12-02 15:10 gezelter |
2059 |
|
2060 |
* make/Makefile.in: Change build process for libOOPSE.a so that the |
2061 |
libraries aren't unpacked. libOOPSE.a is now made directly from |
2062 |
the object files |
2063 |
|
2064 |
2005-12-02 15:09 gezelter |
2065 |
|
2066 |
* configure, ac-tools/configure.in: added check for egrep (grep -E) |
2067 |
needed for new build of libOOPSE.a |
2068 |
|
2069 |
2005-12-02 13:43 tim |
2070 |
|
2071 |
* src/types/DataHolder.hpp: adding DataHolder |
2072 |
|
2073 |
2005-12-02 12:01 gezelter |
2074 |
|
2075 |
* samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, |
2076 |
GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test |
2077 |
case for the cutoff policies |
2078 |
|
2079 |
2005-12-02 10:38 tim |
2080 |
|
2081 |
* make/Makefile.in: update Makefile |
2082 |
|
2083 |
2005-12-02 10:38 tim |
2084 |
|
2085 |
* src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, |
2086 |
antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, |
2087 |
antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, |
2088 |
antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, |
2089 |
antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, |
2090 |
antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, |
2091 |
antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, |
2092 |
antlr/CharScanner.cpp, antlr/CharScanner.hpp, |
2093 |
antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, |
2094 |
antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, |
2095 |
antlr/CommonASTWithHiddenTokens.cpp, |
2096 |
antlr/CommonASTWithHiddenTokens.hpp, |
2097 |
antlr/CommonHiddenStreamToken.cpp, |
2098 |
antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, |
2099 |
antlr/CommonToken.hpp, antlr/IOException.hpp, |
2100 |
antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, |
2101 |
antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, |
2102 |
antlr/Makefile, antlr/MismatchedCharException.cpp, |
2103 |
antlr/MismatchedCharException.hpp, |
2104 |
antlr/MismatchedTokenException.cpp, |
2105 |
antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, |
2106 |
antlr/NoViableAltException.hpp, |
2107 |
antlr/NoViableAltForCharException.cpp, |
2108 |
antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, |
2109 |
antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, |
2110 |
antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, |
2111 |
antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, |
2112 |
antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, |
2113 |
antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, |
2114 |
antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, |
2115 |
antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, |
2116 |
antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, |
2117 |
antlr/TokenStreamHiddenTokenFilter.cpp, |
2118 |
antlr/TokenStreamHiddenTokenFilter.hpp, |
2119 |
antlr/TokenStreamIOException.hpp, |
2120 |
antlr/TokenStreamRecognitionException.hpp, |
2121 |
antlr/TokenStreamRetryException.hpp, |
2122 |
antlr/TokenStreamRewriteEngine.cpp, |
2123 |
antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, |
2124 |
antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, |
2125 |
antlr/TreeParser.cpp, antlr/TreeParser.hpp, |
2126 |
antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, |
2127 |
applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
2128 |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
2129 |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2130 |
constraints/ZconstraintForceManager.cpp, |
2131 |
integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, |
2132 |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
2133 |
io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, |
2134 |
io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, |
2135 |
io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, |
2136 |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, |
2137 |
io/parse_interface.h, io/parse_me.h, io/parse_tree.c, |
2138 |
io/parse_tree.h, mdParser/FilenameObserver.cpp, |
2139 |
mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, |
2140 |
mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, |
2141 |
mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, |
2142 |
mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, |
2143 |
mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, |
2144 |
mdParser/Makefile, mdParser/SimplePreprocessor.hpp, |
2145 |
openbabel/obconversion.cpp, openbabel/oopseformat.cpp, |
2146 |
openbabel/xyzformat.cpp, primitives/RigidBody.cpp, |
2147 |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
2148 |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
2149 |
selection/Makefile, selection/NameFinder.cpp, |
2150 |
selection/NameFinder.hpp, selection/SelectionCompiler.hpp, |
2151 |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
2152 |
selection/SelectionManager.hpp, selection/SelectionToken.hpp, |
2153 |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, |
2154 |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, |
2155 |
types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, |
2156 |
types/Component.cpp, types/Component.hpp, |
2157 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
2158 |
types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, |
2159 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2160 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
2161 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
2162 |
types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, |
2163 |
types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, |
2164 |
utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, |
2165 |
utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, |
2166 |
utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the |
2167 |
Link --> List Return of the Oject-Oriented replace yacc/lex parser |
2168 |
with antlr parser |
2169 |
|
2170 |
2005-11-30 16:00 chuckv |
2171 |
|
2172 |
* src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to |
2173 |
calculate rho(Z) to calculate density profiles for water slabs. |
2174 |
|
2175 |
2005-11-29 17:54 chuckv |
2176 |
|
2177 |
* configure, ac-tools/configure.in: added checks for some functions |
2178 |
to configure script |
2179 |
|
2180 |
2005-11-22 20:05 chuckv |
2181 |
|
2182 |
* src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, |
2183 |
obbond.cpp: Changed file names that conflict w/ oopse file name |
2184 |
object files. |
2185 |
|
2186 |
2005-11-21 17:59 gezelter |
2187 |
|
2188 |
* src/utils/residentMem.c: compilation bug |
2189 |
|
2190 |
2005-11-21 17:59 gezelter |
2191 |
|
2192 |
* src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp |
2193 |
|
2194 |
2005-11-21 17:59 gezelter |
2195 |
|
2196 |
* src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes |
2197 |
|
2198 |
2005-11-21 17:59 gezelter |
2199 |
|
2200 |
* src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation |
2201 |
issue |
2202 |
|
2203 |
2005-11-21 17:58 gezelter |
2204 |
|
2205 |
* src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, |
2206 |
doForces_interface.F90, doForces_interface.h, fForceOptions.h, |
2207 |
notifyCutoffs.F90, notifyCutoffs_interface.F90, |
2208 |
notifyCutoffs_interface.h, DarkSide/LJ.F90, |
2209 |
DarkSide/electrostatic.F90, DarkSide/gb.F90, |
2210 |
DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. |
2211 |
|
2212 |
2005-11-21 11:22 tim |
2213 |
|
2214 |
* src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp |
2215 |
|
2216 |
2005-11-21 09:59 tim |
2217 |
|
2218 |
* forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, |
2219 |
atomtyp.txt, bondtyp.txt, element.txt, extable.txt, |
2220 |
isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, |
2221 |
resdata.txt, torlib.txt, types.txt: adding openbabel data files |
2222 |
|
2223 |
2005-11-18 15:17 tim |
2224 |
|
2225 |
* src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: |
2226 |
adding support for soft linking |
2227 |
|
2228 |
2005-11-18 15:17 tim |
2229 |
|
2230 |
* make/Makefile.in: Adding support for soft linking |
2231 |
|
2232 |
2005-11-18 12:50 gezelter |
2233 |
|
2234 |
* make/Makefile.in: Adding linking stuff |
2235 |
|
2236 |
2005-11-18 11:38 tim |
2237 |
|
2238 |
* make/Makefile.in, src/applications/atom2mdin/Makefile, |
2239 |
src/applications/atom2mdin/atom2mdin.cpp, |
2240 |
src/applications/mdinConverter/Makefile, |
2241 |
src/applications/mdinConverter/mdinConverter.cpp, |
2242 |
src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: |
2243 |
rename mdinConverter to atom2mdin |
2244 |
|
2245 |
2005-11-17 15:44 gezelter |
2246 |
|
2247 |
* src/openbabel/obconversion.cpp: fixed a bug |
2248 |
|
2249 |
2005-11-17 15:39 gezelter |
2250 |
|
2251 |
* configure: Adding some config checks for OpenBabel codes we are |
2252 |
using |
2253 |
|
2254 |
2005-11-17 15:39 gezelter |
2255 |
|
2256 |
* ac-tools/configure.in: Adding some checks for OpenBabel code |
2257 |
|
2258 |
2005-11-17 15:39 gezelter |
2259 |
|
2260 |
* src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel |
2261 |
|
2262 |
2005-11-17 15:38 gezelter |
2263 |
|
2264 |
* src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, |
2265 |
bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, |
2266 |
fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, |
2267 |
obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, |
2268 |
patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, |
2269 |
residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: |
2270 |
Unifying config.h stuff and making sure the OpenBabel codes can |
2271 |
find our default (and environment variable) Force Field |
2272 |
directories. |
2273 |
|
2274 |
2005-11-17 13:35 tim |
2275 |
|
2276 |
* src/io/ForceFieldOptions.hpp: adding ForceFieldOptions |
2277 |
|
2278 |
2005-11-16 18:10 tim |
2279 |
|
2280 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
2281 |
brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, |
2282 |
brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, |
2283 |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
2284 |
io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, |
2285 |
io/OptionSectionParser.hpp, io/ParamConstraint.hpp, |
2286 |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
2287 |
io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, |
2288 |
math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, |
2289 |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
2290 |
primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, |
2291 |
primitives/GhostTorsion.hpp, primitives/Torsion.cpp, |
2292 |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
2293 |
primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, |
2294 |
types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, |
2295 |
types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, |
2296 |
types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser |
2297 |
get compiled |
2298 |
|
2299 |
2005-11-16 16:37 chuckv |
2300 |
|
2301 |
* src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, |
2302 |
io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, |
2303 |
UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField |
2304 |
optional parameters.... |
2305 |
|
2306 |
2005-11-16 16:24 tim |
2307 |
|
2308 |
* src/applications/mdinConverter/: Makefile, mdinConverter.cpp: |
2309 |
adding mdinConverter |
2310 |
|
2311 |
2005-11-16 16:22 tim |
2312 |
|
2313 |
* src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, |
2314 |
fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, |
2315 |
gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, |
2316 |
oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, |
2317 |
povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, |
2318 |
tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: |
2319 |
adding more readers/writers |
2320 |
|
2321 |
2005-11-16 16:20 tim |
2322 |
|
2323 |
* make/Makefile.in: adding openbabel |
2324 |
|
2325 |
2005-11-16 16:20 tim |
2326 |
|
2327 |
* src/brains/: Register.cpp, Register.hpp: register openbabel |
2328 |
readers/writers |
2329 |
|
2330 |
2005-11-16 14:57 chrisfen |
2331 |
|
2332 |
* src/UseTheForce/DarkSide/electrostatic.F90: included shifted |
2333 |
potential self term |
2334 |
|
2335 |
2005-11-16 14:57 chrisfen |
2336 |
|
2337 |
* samples/water/spce/spce.md: just some parameters |
2338 |
|
2339 |
2005-11-16 14:42 tim |
2340 |
|
2341 |
* src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, |
2342 |
babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, |
2343 |
bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, |
2344 |
chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, |
2345 |
data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, |
2346 |
fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, |
2347 |
isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, |
2348 |
matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, |
2349 |
obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, |
2350 |
oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, |
2351 |
obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, |
2352 |
patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, |
2353 |
phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, |
2354 |
ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, |
2355 |
snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, |
2356 |
tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, |
2357 |
types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, |
2358 |
zipstreamimpl.hpp: adding openbabel |
2359 |
|
2360 |
2005-11-15 14:42 chrisfen |
2361 |
|
2362 |
* src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary |
2363 |
commented code |
2364 |
|
2365 |
2005-11-15 14:04 chrisfen |
2366 |
|
2367 |
* src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the |
2368 |
charge-charge interactions a bit... |
2369 |
|
2370 |
2005-11-15 14:03 chrisfen |
2371 |
|
2372 |
* samples/water/spce/: spce.md, water.md: just playing |
2373 |
|
2374 |
2005-11-15 11:38 chrisfen |
2375 |
|
2376 |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the |
2377 |
shifted_potential case |
2378 |
|
2379 |
2005-11-15 11:37 chrisfen |
2380 |
|
2381 |
* samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: |
2382 |
just playing around - we need to refresh all the samples sometime |
2383 |
soon... |
2384 |
|
2385 |
2005-11-15 11:18 chuckv |
2386 |
|
2387 |
* src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made |
2388 |
preforce calc public in suttonchen. |
2389 |
|
2390 |
2005-11-15 11:05 chuckv |
2391 |
|
2392 |
* src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to |
2393 |
SimInfo |
2394 |
|
2395 |
2005-11-15 11:01 chuckv |
2396 |
|
2397 |
* src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, |
2398 |
DarkSide/simulation.F90: Added Sutton-Chen to force loop... |
2399 |
|
2400 |
2005-11-15 10:34 chuckv |
2401 |
|
2402 |
* forceFields/Makefile: Added sutton-chen to makefile. |
2403 |
|
2404 |
2005-11-14 17:20 chuckv |
2405 |
|
2406 |
* src/UseTheForce/DarkSide/: suttonchen.F90, |
2407 |
suttonchen_interface.h: Build Fixes for sutton-chen. |
2408 |
|
2409 |
2005-11-14 17:03 chuckv |
2410 |
|
2411 |
* src/io/Makefile: Missed makefile for sutton-chen. |
2412 |
|
2413 |
2005-11-14 17:03 chuckv |
2414 |
|
2415 |
* src/UseTheForce/: Makefile, DarkSide/Makefile, |
2416 |
DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff |
2417 |
|
2418 |
2005-11-14 16:29 chuckv |
2419 |
|
2420 |
* src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, |
2421 |
io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, |
2422 |
UseTheForce/DarkSide/suttonchen.F90, |
2423 |
UseTheForce/DarkSide/suttonchen_interface.F90, |
2424 |
UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, |
2425 |
brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, |
2426 |
types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to |
2427 |
fix do_forces to use Sutton-Chen. |
2428 |
|
2429 |
2005-11-11 12:21 chrisfen |
2430 |
|
2431 |
* src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, |
2432 |
switcheroo_interface.F90, switcheroo_interface.h: Forgot to add |
2433 |
some files |
2434 |
|
2435 |
2005-11-11 10:22 chrisfen |
2436 |
|
2437 |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, |
2438 |
io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial |
2439 |
switching function option |
2440 |
|
2441 |
2005-11-11 10:21 chrisfen |
2442 |
|
2443 |
* src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a |
2444 |
5th order polynomial switching function |
2445 |
|
2446 |
2005-11-11 10:21 chrisfen |
2447 |
|
2448 |
* samples/water/ssd/ssd.md: playing with switching functions again |
2449 |
|
2450 |
2005-11-11 10:21 chrisfen |
2451 |
|
2452 |
* samples/argon/500.md: playing with switching functions |
2453 |
|
2454 |
2005-11-08 19:11 chuckv |
2455 |
|
2456 |
* forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force |
2457 |
files for Sutton-Chen and Quantum Sutton-Chen |
2458 |
|
2459 |
2005-11-08 08:32 chrisfen |
2460 |
|
2461 |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, |
2462 |
DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and |
2463 |
ability to output forces and torques |
2464 |
|
2465 |
2005-11-08 08:32 chrisfen |
2466 |
|
2467 |
* src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for |
2468 |
output of forces and torques |
2469 |
|
2470 |
2005-11-08 08:31 chrisfen |
2471 |
|
2472 |
* src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: |
2473 |
Working on shifted_force... |
2474 |
|
2475 |
2005-11-08 08:31 chrisfen |
2476 |
|
2477 |
* samples/water/: spce/spce.md, ssde/ssde.md: Just testing... |
2478 |
|
2479 |
2005-11-03 18:22 chrisfen |
2480 |
|
2481 |
* src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly |
2482 |
commented section |
2483 |
|
2484 |
2005-11-03 18:12 chrisfen |
2485 |
|
2486 |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
2487 |
UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, |
2488 |
UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, |
2489 |
io/Globals.cpp, io/Globals.hpp: improvements in shifted-force |
2490 |
|
2491 |
2005-11-03 18:11 chrisfen |
2492 |
|
2493 |
* samples/water/spce/spce.md: mmm... damped shifted force... |
2494 |
|
2495 |
2005-11-03 18:06 chuckv |
2496 |
|
2497 |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. |
2498 |
|
2499 |
2005-11-02 18:50 chuckv |
2500 |
|
2501 |
* src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. |
2502 |
|
2503 |
2005-11-02 16:01 chrisfen |
2504 |
|
2505 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
2506 |
removed some test code |
2507 |
|
2508 |
2005-11-02 15:45 chrisfen |
2509 |
|
2510 |
* src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the |
2511 |
screening method header |
2512 |
|
2513 |
2005-11-02 15:36 chrisfen |
2514 |
|
2515 |
* src/brains/SimInfo.cpp: again, changing how we deal with |
2516 |
summation and screening methods |
2517 |
|
2518 |
2005-11-02 15:36 chrisfen |
2519 |
|
2520 |
* src/: UseTheForce/DarkSide/electrostatic.F90, |
2521 |
UseTheForce/DarkSide/electrostatic_interface.F90, |
2522 |
UseTheForce/DarkSide/electrostatic_interface.h, |
2523 |
UseTheForce/DarkSide/fElectrostaticSummationMethod.h, |
2524 |
io/Globals.cpp, io/Globals.hpp: changing how we deal with summation |
2525 |
and screening methods |
2526 |
|
2527 |
2005-11-02 15:35 chrisfen |
2528 |
|
2529 |
* src/UseTheForce/doForces.F90: debug stuff for rf removed |
2530 |
|
2531 |
2005-11-01 18:32 chuckv |
2532 |
|
2533 |
* src/: UseTheForce/DarkSide/atype.F90, |
2534 |
UseTheForce/DarkSide/atype_interface.F90, |
2535 |
UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, |
2536 |
types/AtomTypeProperties.h: Added suppport to atypes for MEAM and |
2537 |
sutton-chen |
2538 |
|
2539 |
2005-11-01 14:24 chrisfen |
2540 |
|
2541 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
2542 |
removed some testing code... |
2543 |
|
2544 |
2005-11-01 14:14 chrisfen |
2545 |
|
2546 |
* src/: brains/Register.cpp, brains/SimInfo.cpp, |
2547 |
brains/fSimulation.h, integrators/IntegratorFactory.hpp, |
2548 |
io/Globals.cpp: fixed a capitalization problem with NPT integrator |
2549 |
initialization |
2550 |
|
2551 |
2005-11-01 14:13 chrisfen |
2552 |
|
2553 |
* src/applications/oopse/oopse.cpp: nothing |
2554 |
|
2555 |
2005-11-01 14:09 chrisfen |
2556 |
|
2557 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
2558 |
DarkSide/simulation.F90: still fixing up wolf... |
2559 |
|
2560 |
2005-11-01 13:29 chuckv |
2561 |
|
2562 |
* src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In |
2563 |
process of adding sutton-chen forcefield. |
2564 |
|
2565 |
2005-10-26 19:32 chrisfen |
2566 |
|
2567 |
* src/brains/SimInfo.cpp: changed the default switching radius to |
2568 |
85% of rcut |
2569 |
|
2570 |
2005-10-26 19:31 chrisfen |
2571 |
|
2572 |
* src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks |
2573 |
to be working now - for charges and dipoles alike |
2574 |
|
2575 |
2005-10-26 19:31 chrisfen |
2576 |
|
2577 |
* src/UseTheForce/doForces.F90: reaction field looks to be working |
2578 |
now |
2579 |
|
2580 |
2005-10-26 19:30 chrisfen |
2581 |
|
2582 |
* samples/water/ssdrf/water.md: added a test molecule |
2583 |
|
2584 |
2005-10-26 19:30 chrisfen |
2585 |
|
2586 |
* forceFields/DUFF2.frc: added a test atom type |
2587 |
|
2588 |
2005-10-24 10:06 chrisfen |
2589 |
|
2590 |
* src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole |
2591 |
reaction field - don't know if it works... |
2592 |
|
2593 |
2005-10-23 17:08 chrisfen |
2594 |
|
2595 |
* src/: UseTheForce/doForces.F90, |
2596 |
UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: |
2597 |
streamlined reaction field for dipoles (now a good bit faster) and |
2598 |
added reaction field for charges - still need to do charge-dipole |
2599 |
RF |
2600 |
|
2601 |
2005-10-23 17:07 chrisfen |
2602 |
|
2603 |
* samples/water/ssdrf/ssdrf.md: minor changes when testing reaction |
2604 |
field |
2605 |
|
2606 |
2005-10-23 17:06 chrisfen |
2607 |
|
2608 |
* samples/water/spce/spce.md: reaction field now works for charges |
2609 |
|
2610 |
2005-10-20 16:27 tim |
2611 |
|
2612 |
* src/primitives/Torsion.cpp: Fix the other branch of force |
2613 |
calculation in Torision.cpp |
2614 |
|
2615 |
2005-10-19 15:24 chrisfen |
2616 |
|
2617 |
* src/: UseTheForce/doForces.F90, |
2618 |
UseTheForce/DarkSide/electrostatic.F90, |
2619 |
UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, |
2620 |
brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals |
2621 |
toUpper problems - these changes should fix those... |
2622 |
|
2623 |
2005-10-19 15:23 chrisfen |
2624 |
|
2625 |
* samples/water/ssdrf/ssdrf.md: nothing |
2626 |
|
2627 |
2005-10-19 13:03 gezelter |
2628 |
|
2629 |
* src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in |
2630 |
GayBerne |
2631 |
|
2632 |
2005-10-19 12:49 tim |
2633 |
|
2634 |
* src/: UseTheForce/DarkSide/fInteractionMap.h, |
2635 |
brains/ForceManager.cpp: fix an index mismathcing between c and |
2636 |
fortran |
2637 |
|
2638 |
2005-10-18 19:03 gezelter |
2639 |
|
2640 |
* samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added |
2641 |
samples for the cutoff methods that Yang Zheng has been working on |
2642 |
|
2643 |
2005-10-18 17:13 gezelter |
2644 |
|
2645 |
* src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques |
2646 |
and a rotation matrix bug |
2647 |
|
2648 |
2005-10-18 17:13 gezelter |
2649 |
|
2650 |
* samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, |
2651 |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
2652 |
added a few GB test cases |
2653 |
|
2654 |
2005-10-18 17:13 gezelter |
2655 |
|
2656 |
* forceFields/DUFF2.frc: Fixing GB parameters |
2657 |
|
2658 |
2005-10-18 14:36 kdaily |
2659 |
|
2660 |
* forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne |
2661 |
type |
2662 |
|
2663 |
2005-10-18 11:01 chrisfen |
2664 |
|
2665 |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
2666 |
UseTheForce/DarkSide/Makefile, |
2667 |
UseTheForce/DarkSide/electrostatic.F90, |
2668 |
UseTheForce/DarkSide/electrostatic_interface.F90, |
2669 |
UseTheForce/DarkSide/electrostatic_interface.h, |
2670 |
UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged |
2671 |
reaction field with electrostatics.F90 |
2672 |
|
2673 |
2005-10-17 19:13 tim |
2674 |
|
2675 |
* src/: brains/ForceManager.cpp, brains/Stats.cpp, |
2676 |
brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, |
2677 |
io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, |
2678 |
io/StatWriter.hpp: Customized StatWriter is working |
2679 |
|
2680 |
2005-10-17 18:42 kdaily |
2681 |
|
2682 |
* src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver |
2683 |
paper |
2684 |
|
2685 |
2005-10-17 17:47 gezelter |
2686 |
|
2687 |
* src/UseTheForce/DarkSide/gb.F90: bugtracking gb |
2688 |
|
2689 |
2005-10-17 15:24 tim |
2690 |
|
2691 |
* src/io/ParamConstraint.hpp: Another bug fix |
2692 |
|
2693 |
2005-10-17 15:22 tim |
2694 |
|
2695 |
* src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace |
2696 |
issues in Globals |
2697 |
|
2698 |
2005-10-17 15:12 gezelter |
2699 |
|
2700 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, |
2701 |
UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, |
2702 |
UseTheForce/DarkSide/gb_interface.F90, |
2703 |
UseTheForce/DarkSide/gb_interface.h, |
2704 |
io/GayBerneAtomTypesSectionParser.cpp, |
2705 |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
2706 |
changing GB architecture |
2707 |
|
2708 |
2005-10-17 15:12 gezelter |
2709 |
|
2710 |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, |
2711 |
gbRotRoundZ.in: Adding samples for gb tests |
2712 |
|
2713 |
2005-10-16 23:06 tim |
2714 |
|
2715 |
* src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy |
2716 |
a string to event's err_msg, there are still tons of memory |
2717 |
leaking problem in Globals |
2718 |
|
2719 |
2005-10-16 20:51 tim |
2720 |
|
2721 |
* src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change |
2722 |
error message in Globals |
2723 |
|
2724 |
2005-10-14 17:43 tim |
2725 |
|
2726 |
* src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for |
2727 |
parameters are working now |
2728 |
|
2729 |
2005-10-14 12:43 gezelter |
2730 |
|
2731 |
* samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests |
2732 |
|
2733 |
2005-10-14 12:05 gezelter |
2734 |
|
2735 |
* samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, |
2736 |
gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: |
2737 |
Adding some Gay Berne tests |
2738 |
|
2739 |
2005-10-14 12:05 gezelter |
2740 |
|
2741 |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some |
2742 |
cutoff tests |
2743 |
|
2744 |
2005-10-14 11:44 kdaily |
2745 |
|
2746 |
* forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, |
2747 |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, |
2748 |
src/UseTheForce/DarkSide/gb_interface.F90, |
2749 |
src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne |
2750 |
LJ |
2751 |
|
2752 |
2005-10-14 10:48 tim |
2753 |
|
2754 |
* src/io/ParamConstraint.hpp: Adding Parameter Constraint class |
2755 |
|
2756 |
2005-10-14 10:18 chrisfen |
2757 |
|
2758 |
* samples/thermoIntegration/liquid/ssde.md, |
2759 |
samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, |
2760 |
src/restraints/Restraints.cpp: added default restraint spring |
2761 |
constants into Globals |
2762 |
|
2763 |
2005-10-13 18:26 tim |
2764 |
|
2765 |
* src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, |
2766 |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, |
2767 |
constraints/ZconstraintForceManager.cpp, |
2768 |
integrators/Integrator.cpp, integrators/NPT.cpp, |
2769 |
integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, |
2770 |
io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, |
2771 |
minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, |
2772 |
restraints/ThermoIntegrationForceManager.cpp, |
2773 |
visitors/ZconsVisitor.cpp: rewrite Globals |
2774 |
|
2775 |
2005-10-12 17:57 chuckv |
2776 |
|
2777 |
* src/brains/ForceManager.cpp: Fix to forceManager to pass |
2778 |
potential array to fortran. |
2779 |
|
2780 |
2005-10-12 17:00 gezelter |
2781 |
|
2782 |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't |
2783 |
remember what we did |
2784 |
|
2785 |
2005-10-12 17:00 gezelter |
2786 |
|
2787 |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
2788 |
DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, |
2789 |
DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, |
2790 |
DarkSide/sticky.F90: simplifying long range potential array |
2791 |
|
2792 |
2005-10-12 17:00 gezelter |
2793 |
|
2794 |
* samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new |
2795 |
cutoff methods |
2796 |
|
2797 |
2005-10-12 17:00 gezelter |
2798 |
|
2799 |
* forceFields/DUFF2.frc: Messing with 2-point water models |
2800 |
|
2801 |
2005-10-12 16:22 chuckv |
2802 |
|
2803 |
* src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran |
2804 |
interface now expects an array for pot. |
2805 |
|
2806 |
2005-10-12 16:18 chuckv |
2807 |
|
2808 |
* src/UseTheForce/: doForces.F90, DarkSide/gb.F90, |
2809 |
DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for |
2810 |
calculation of potential. |
2811 |
|
2812 |
2005-10-12 15:55 chuckv |
2813 |
|
2814 |
* src/UseTheForce/doForces.F90: More changes to MPI potential |
2815 |
calculations. |
2816 |
|
2817 |
2005-10-12 14:59 chuckv |
2818 |
|
2819 |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, |
2820 |
DarkSide/eam.F90, DarkSide/electrostatic.F90, |
2821 |
DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, |
2822 |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky |
2823 |
Breaky: Add Support for seperating potential contributions. |
2824 |
|
2825 |
2005-10-11 18:00 chuckv |
2826 |
|
2827 |
* src/UseTheForce/doForces.F90: Free some variables that weren't |
2828 |
freed before. |
2829 |
|
2830 |
2005-10-11 17:59 chuckv |
2831 |
|
2832 |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
2833 |
GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod |
2834 |
builder --twinned. |
2835 |
|
2836 |
2005-10-11 17:57 chuckv |
2837 |
|
2838 |
* src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, |
2839 |
nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, |
2840 |
nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, |
2841 |
sphericalNanoparticle.hpp: Added code for nanoparticle builder to |
2842 |
cvs. |
2843 |
|
2844 |
2005-10-10 17:34 chuckv |
2845 |
|
2846 |
* src/UseTheForce/doForces.F90: Bug fix, undeclared local variable |
2847 |
in MPI. |
2848 |
|
2849 |
2005-10-10 17:20 chuckv |
2850 |
|
2851 |
* src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column |
2852 |
indexing of groupToGtype. We now have two seperate maps |
2853 |
groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer |
2854 |
that is set to groupToGtypeRow in the single processor version. |
2855 |
|
2856 |
2005-10-06 14:44 chrisfen |
2857 |
|
2858 |
* samples/water/: dimer/water.md, spce/water.md, ssd/water.md, |
2859 |
ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, |
2860 |
tip3p_ice/water.md, tip4p/water.md: fixing up the samples |
2861 |
|
2862 |
2005-10-05 17:12 tim |
2863 |
|
2864 |
* src/primitives/RigidBody.cpp: There is still something wrong with |
2865 |
inertia tensor projection |
2866 |
|
2867 |
2005-10-05 15:35 tim |
2868 |
|
2869 |
* src/primitives/RigidBody.cpp: erase output of inertia tensor. |
2870 |
There is still something wrong with current implementation. |
2871 |
|
2872 |
2005-10-05 15:34 tim |
2873 |
|
2874 |
* src/brains/MoleculeCreator.cpp: fix a bug in creating |
2875 |
cutoffGroup. When cutoffGroup is turned off, there is a mismatch |
2876 |
between group and center of mass array |
2877 |
|
2878 |
2005-10-05 15:12 tim |
2879 |
|
2880 |
* src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. |
2881 |
When cutoffGroup is turned off, there is a mismatch between group |
2882 |
and center of mass array |
2883 |
|
2884 |
2005-10-04 15:34 chrisfen |
2885 |
|
2886 |
* src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying |
2887 |
mass ratio bug that results in simulation failure with massless |
2888 |
particles |
2889 |
|
2890 |
2005-10-04 15:33 chrisfen |
2891 |
|
2892 |
* src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on |
2893 |
wolf |
2894 |
|
2895 |
2005-10-04 15:32 chrisfen |
2896 |
|
2897 |
* samples/water/dimer/two.md, samples/water/dimer/water.md, |
2898 |
samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, |
2899 |
samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some |
2900 |
random changes when testing |
2901 |
|
2902 |
2005-10-03 11:54 tim |
2903 |
|
2904 |
* src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in |
2905 |
projecting the inertia tensor of directional atom in rigibody into |
2906 |
rigidbody's body frame (previous commit is wrong) |
2907 |
|
2908 |
2005-10-03 10:31 tim |
2909 |
|
2910 |
* src/primitives/RigidBody.cpp: fix a bug in projecting the inertia |
2911 |
tensor of directional atom in rigibody into rigidbody's body frame |
2912 |
|
2913 |
2005-09-28 14:47 chrisfen |
2914 |
|
2915 |
* src/UseTheForce/DarkSide/electrostatic.F90: working on wolf |
2916 |
|
2917 |
2005-09-28 14:46 chrisfen |
2918 |
|
2919 |
* samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, |
2920 |
dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, |
2921 |
ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, |
2922 |
tip4p/tp4.md: fixed some samples |
2923 |
|
2924 |
2005-09-28 14:46 chrisfen |
2925 |
|
2926 |
* ChangeLog: updated |
2927 |
|
2928 |
2005-09-28 12:55 tim |
2929 |
|
2930 |
* src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid |
2931 |
divergence in rotation matrix to quaternion transformation |
2932 |
|
2933 |
2005-09-28 12:32 gezelter |
2934 |
|
2935 |
* src/primitives/RigidBody.cpp: Rotation matrix multiplication |
2936 |
order error |
2937 |
|
2938 |
2005-09-28 12:32 gezelter |
2939 |
|
2940 |
* src/io/DumpReader.cpp: tracking down quaternion bug |
2941 |
|
2942 |
2005-09-28 12:32 gezelter |
2943 |
|
2944 |
* forceFields/DUFF2.frc: Added DIP atom types for 2-point water |
2945 |
model |
2946 |
|
2947 |
2005-09-27 16:02 tim |
2948 |
|
2949 |
* src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix |
2950 |
to quaternion |
2951 |
|
2952 |
2005-09-26 14:38 chuckv |
2953 |
|
2954 |
* src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc |
2955 |
7 so derfc is external. Other compilers should treat erfc as |
2956 |
intrinsic. |
2957 |
|
2958 |
2005-09-26 13:07 chuckv |
2959 |
|
2960 |
* src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc |
2961 |
and declared it to be external to fix issure with ifc7. Hopefully |
2962 |
this will not cause a problem with other compilers where derfc is |
2963 |
an intrinsic function. |
2964 |
|
2965 |
2005-09-26 12:42 chuckv |
2966 |
|
2967 |
* src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype |
2968 |
in simulation module. We needed a seperate receive buffer. |
2969 |
|
2970 |
2005-09-26 11:58 chuckv |
2971 |
|
2972 |
* src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added |
2973 |
support for skinThickness keyword to Globals. |
2974 |
|
2975 |
2005-09-26 11:56 tim |
2976 |
|
2977 |
* src/io/DumpReader.cpp: fix a typo in DumpReader |
2978 |
|
2979 |
2005-09-26 10:27 chrisfen |
2980 |
|
2981 |
* samples/: minimizer/tip4p_two.md, |
2982 |
thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, |
2983 |
water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, |
2984 |
water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, |
2985 |
water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, |
2986 |
water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, |
2987 |
water/tip4p/tp4.md: fixing up some samples |
2988 |
|
2989 |
2005-09-24 13:39 chrisfen |
2990 |
|
2991 |
* src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now |
2992 |
roughly the same speed as the old version when using dipoles |
2993 |
|
2994 |
energies are now exactly the same between the old version of OOPSE |
2995 |
and this version |
2996 |
|
2997 |
2005-09-24 13:38 chrisfen |
2998 |
|
2999 |
* samples/water/ssdrf/ssdrf.md: turned rf on |
3000 |
|
3001 |
2005-09-23 16:31 chuckv |
3002 |
|
3003 |
* src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the |
3004 |
skin thickness and hardcode listSkin to be 1.0. We now get listskin |
3005 |
from skin. This will get fixed to where we can manually set skin |
3006 |
thickness. |
3007 |
|
3008 |
2005-09-22 14:50 gezelter |
3009 |
|
3010 |
* src/math/derfc.F90: added error function |
3011 |
|
3012 |
2005-09-21 20:08 chuckv |
3013 |
|
3014 |
* src/integrators/Velocitizer.cpp: Removed print statement for |
3015 |
angular momentum and inertia tensor from velocitizer. |
3016 |
|
3017 |
2005-09-21 20:04 chuckv |
3018 |
|
3019 |
* src/integrators/Velocitizer.cpp: Removed print statements for |
3020 |
remove angular momentum. |
3021 |
|
3022 |
2005-09-21 19:45 chuckv |
3023 |
|
3024 |
* src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ |
3025 |
(say we are using EAM), we probably shouldn't rebuild the LJ mixing |
3026 |
map. |
3027 |
|
3028 |
2005-09-21 16:59 tim |
3029 |
|
3030 |
* src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: |
3031 |
DumpReader using pure c++ io |
3032 |
|
3033 |
2005-09-21 13:20 chrisfen |
3034 |
|
3035 |
* src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a |
3036 |
defaultCutoff bug (HEMES!) |
3037 |
|
3038 |
2005-09-20 18:13 gezelter |
3039 |
|
3040 |
* make/Makefile.in: libz additions |
3041 |
|
3042 |
2005-09-20 18:03 gezelter |
3043 |
|
3044 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
3045 |
src/config.h.in: added check for zlib in configure |
3046 |
|
3047 |
2005-09-20 17:22 tim |
3048 |
|
3049 |
* src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, |
3050 |
gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter |
3051 |
|
3052 |
2005-09-20 12:22 tim |
3053 |
|
3054 |
* test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding |
3055 |
testcase for zipstream |
3056 |
|
3057 |
2005-09-20 11:41 tim |
3058 |
|
3059 |
* src/io/zipstream.hpp: adding zipstream.hpp |
3060 |
|
3061 |
2005-09-20 11:34 chrisfen |
3062 |
|
3063 |
* samples/: dipole/splitInWater.md, dipole/split_SSD.md, |
3064 |
dipole/twoSplitDipole.md, minimizer/ssdEM.md, |
3065 |
minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, |
3066 |
zcons/zconsMoving.md: fixed up some sample md files |
3067 |
|
3068 |
2005-09-19 19:21 chrisfen |
3069 |
|
3070 |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
3071 |
src/UseTheForce/doForces.F90, |
3072 |
src/UseTheForce/DarkSide/electrostatic.F90, |
3073 |
src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, |
3074 |
src/brains/fSimulation.h: Fixed bugs in reaction field, now it |
3075 |
appears as though it really is working... |
3076 |
|
3077 |
2005-09-18 16:45 chrisfen |
3078 |
|
3079 |
* ChangeLog, samples/water/ssdrf/ssdrf.md, |
3080 |
src/UseTheForce/doForces.F90, |
3081 |
src/UseTheForce/doForces_interface.F90, |
3082 |
src/UseTheForce/doForces_interface.h, |
3083 |
src/UseTheForce/DarkSide/electrostatic.F90, |
3084 |
src/UseTheForce/DarkSide/electrostatic_interface.h, |
3085 |
src/brains/SimInfo.cpp: reaction field seems to work now, still |
3086 |
need to do some testing... |
3087 |
|
3088 |
2005-09-16 19:04 chuckv |
3089 |
|
3090 |
* src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed |
3091 |
dump files. |
3092 |
|
3093 |
2005-09-16 17:07 chrisfen |
3094 |
|
3095 |
* src/: UseTheForce/doForces_interface.F90, |
3096 |
UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a |
3097 |
bug that ifc missed... |
3098 |
|
3099 |
2005-09-16 16:36 chrisfen |
3100 |
|
3101 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: |
3102 |
fixing some summation method issues |
3103 |
|
3104 |
2005-09-16 15:35 chrisfen |
3105 |
|
3106 |
* src/brains/SimInfo.cpp: fixed a capitalization error |
3107 |
|
3108 |
2005-09-16 15:34 chrisfen |
3109 |
|
3110 |
* src/UseTheForce/: fElectrostaticSummationMethod.h, |
3111 |
DarkSide/fElectrostaticSummationMethod.h: moved a header file |
3112 |
around |
3113 |
|
3114 |
2005-09-16 15:00 chrisfen |
3115 |
|
3116 |
* src/: UseTheForce/DarkSide/electrostatic_interface.F90, |
3117 |
brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there |
3118 |
are known issues - particularly with reaction field... |
3119 |
|
3120 |
2005-09-16 12:07 chrisfen |
3121 |
|
3122 |
* src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, |
3123 |
io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking |
3124 |
(cutting out the old way to do reaction field) |
3125 |
|
3126 |
2005-09-15 18:05 gezelter |
3127 |
|
3128 |
* src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, |
3129 |
fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, |
3130 |
DarkSide/electrostatic_interface.F90, |
3131 |
DarkSide/electrostatic_interface.h: Working on adding WOLF |
3132 |
|
3133 |
2005-09-15 15:17 tim |
3134 |
|
3135 |
* src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame |
3136 |
is called without calling getNFrames |
3137 |
|
3138 |
2005-09-15 09:47 chrisfen |
3139 |
|
3140 |
* src/UseTheForce/fCoulombicCorrection.h: forgot to add a header |
3141 |
|
3142 |
2005-09-14 22:48 chuckv |
3143 |
|
3144 |
* src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was |
3145 |
not initialized after creation. When maxval(gtypeMaxCutoff) was |
3146 |
called, the largest random garbage value was returned from the |
3147 |
array. |
3148 |
|
3149 |
2005-09-14 20:14 chrisfen |
3150 |
|
3151 |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, |
3152 |
io/Globals.hpp: changes to include the coulombicCorrection selector |
3153 |
|
3154 |
2005-09-14 20:13 chrisfen |
3155 |
|
3156 |
* src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, |
3157 |
reactionField.F90: added in the undamped wolf, in the process of |
3158 |
doing the damped wolf |
3159 |
|
3160 |
2005-09-14 20:13 chrisfen |
3161 |
|
3162 |
* src/UseTheForce/: doForces.F90, doForces_interface.F90, |
3163 |
doForces_interface.h, notifyCutoffs.F90: some changes to activate |
3164 |
the coulombicCorrection selector |
3165 |
|
3166 |
2005-09-14 20:11 chrisfen |
3167 |
|
3168 |
* samples/water/dimer/: cl.in, cl.md, water.md: just some testing |
3169 |
|
3170 |
2005-09-14 20:11 chrisfen |
3171 |
|
3172 |
* samples/argon/: 500.in, 500.md: Equilibrated the sample |
3173 |
|
3174 |
2005-09-14 20:10 chrisfen |
3175 |
|
3176 |
* forceFields/DUFF2.frc: re-added Cl- and Na+ |
3177 |
|
3178 |
2005-09-14 16:31 chuckv |
3179 |
|
3180 |
* src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup |
3181 |
eamAtypes instead of assuming a 1-1 correspondence to atypes. |
3182 |
|
3183 |
2005-09-14 16:28 gezelter |
3184 |
|
3185 |
* src/UseTheForce/doForces.F90: fix to put back calculation of r in |
3186 |
do_prepair |
3187 |
|
3188 |
2005-09-14 15:02 gezelter |
3189 |
|
3190 |
* src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the |
3191 |
createMixingMap routine. It should now set doShift correctly |
3192 |
|
3193 |
2005-09-07 18:44 chuckv |
3194 |
|
3195 |
* src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. |
3196 |
|
3197 |
2005-09-07 18:23 chuckv |
3198 |
|
3199 |
* src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi |
3200 |
logical variables |
3201 |
|
3202 |
2005-09-07 18:08 gezelter |
3203 |
|
3204 |
* src/UseTheForce/doForces.F90: bugfix on the grouptype finding |
3205 |
algorithm |
3206 |
|
3207 |
2005-09-07 16:46 gezelter |
3208 |
|
3209 |
* src/: UseTheForce/doForces.F90, |
3210 |
UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, |
3211 |
UseTheForce/notifyCutoffs_interface.F90, |
3212 |
UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, |
3213 |
io/Globals.cpp, io/Globals.hpp: adding c-side interface to change |
3214 |
cutoff Policy |
3215 |
|
3216 |
2005-09-07 15:18 gezelter |
3217 |
|
3218 |
* src/UseTheForce/doForces.F90: Some bug hunting |
3219 |
|
3220 |
2005-09-07 15:18 gezelter |
3221 |
|
3222 |
* samples/argon/argonNVT.md: Just a longer test |
3223 |
|
3224 |
2005-09-06 13:32 chuckv |
3225 |
|
3226 |
* src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap |
3227 |
etc.. |
3228 |
|
3229 |
2005-09-01 18:56 gezelter |
3230 |
|
3231 |
* src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to |
3232 |
zero |
3233 |
|
3234 |
2005-09-01 16:17 gezelter |
3235 |
|
3236 |
* src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote |
3237 |
createGtypeCutoffMap |
3238 |
|
3239 |
2005-08-30 14:23 chrisfen |
3240 |
|
3241 |
* src/: UseTheForce/doForces.F90, |
3242 |
UseTheForce/doForces_interface.F90, |
3243 |
UseTheForce/doForces_interface.h, |
3244 |
UseTheForce/DarkSide/electrostatic.F90, |
3245 |
UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, |
3246 |
brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some |
3247 |
changes for implementing the wolf potential |
3248 |
|
3249 |
2005-08-26 18:39 chrisfen |
3250 |
|
3251 |
* src/UseTheForce/DarkSide/eam.F90: updated getEAMCut |
3252 |
|
3253 |
2005-08-26 17:30 chrisfen |
3254 |
|
3255 |
* src/UseTheForce/: doForces.F90, DarkSide/eam.F90, |
3256 |
DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added |
3257 |
some probably nonfunctional get*cut routines |
3258 |
|
3259 |
2005-08-26 16:34 chuckv |
3260 |
|
3261 |
* src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. |
3262 |
|
3263 |
2005-08-26 12:36 gezelter |
3264 |
|
3265 |
* src/UseTheForce/doForces.F90: fixing some of the problems in the |
3266 |
interactionHash and gtypeCutoff routines |
3267 |
|
3268 |
2005-08-17 11:26 gezelter |
3269 |
|
3270 |
* src/UseTheForce/: doForces.F90, fCutoffPolicy.h, |
3271 |
DarkSide/simulation.F90: added fCutoffPolicy.h |
3272 |
|
3273 |
2005-08-11 17:04 gezelter |
3274 |
|
3275 |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in |
3276 |
progress |
3277 |
|
3278 |
2005-08-10 15:17 gezelter |
3279 |
|
3280 |
* src/primitives/StuntDouble.hpp: putting spaceballs back where |
3281 |
they belong |
3282 |
|
3283 |
2005-08-09 18:33 gezelter |
3284 |
|
3285 |
* src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard |
3286 |
Jones module |
3287 |
|
3288 |
2005-08-09 18:33 gezelter |
3289 |
|
3290 |
* src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky |
3291 |
|
3292 |
2005-08-09 15:40 chuckv |
3293 |
|
3294 |
* src/UseTheForce/doForces.F90: In process of re-write for group |
3295 |
based cutoff.... |
3296 |
|
3297 |
2005-07-29 15:38 gezelter |
3298 |
|
3299 |
* src/UseTheForce/doForces.F90: fixes in progress |
3300 |
|
3301 |
2005-07-29 13:34 tim |
3302 |
|
3303 |
* src/UseTheForce/doForces.F90: fix a bug which does not update |
3304 |
me_i and me_j correctly |
3305 |
|
3306 |
2005-07-28 18:12 chuckv |
3307 |
|
3308 |
* src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed |
3309 |
cutoffs... Segfaults nicely now... |
3310 |
|
3311 |
2005-07-20 13:04 gezelter |
3312 |
|
3313 |
* configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text |
3314 |
error messages from pathscale compiler |
3315 |
|
3316 |
2005-07-13 12:48 tim |
3317 |
|
3318 |
* src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in |
3319 |
<functional> |
3320 |
|
3321 |
2005-07-13 11:54 tim |
3322 |
|
3323 |
* src/: UseTheForce/fSwitchingFunction.h, |
3324 |
UseTheForce/mpiComponentPlan.h, |
3325 |
UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, |
3326 |
io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, |
3327 |
io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, |
3328 |
io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, |
3329 |
io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, |
3330 |
utils/simError.c, utils/simError.h: replace c++ style comment in c |
3331 |
files |
3332 |
|
3333 |
2005-07-03 16:53 chuckv |
3334 |
|
3335 |
* src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, |
3336 |
UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added |
3337 |
subroutine to set cuttoff for Interaction map and function in |
3338 |
simulation.F90 to determine if a particular atype is present in a |
3339 |
simulation. |
3340 |
|
3341 |
2005-06-28 09:58 gezelter |
3342 |
|
3343 |
* src/UseTheForce/doForces.F90: [no log message] |
3344 |
|
3345 |
2005-06-27 18:21 chuckv |
3346 |
|
3347 |
* src/UseTheForce/doForces.F90: More breaking and destruction of |
3348 |
force code. Does not build at this point... |
3349 |
|
3350 |
2005-06-27 17:01 gezelter |
3351 |
|
3352 |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, |
3353 |
UseTheForce/DarkSide/fInteractionMap.h, |
3354 |
UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: |
3355 |
Breaky breaky! |
3356 |
|
3357 |
2005-06-20 12:03 gezelter |
3358 |
|
3359 |
* samples/water/ssd/ssd.md, |
3360 |
src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a |
3361 |
simulation |
3362 |
|
3363 |
2005-06-13 14:25 tim |
3364 |
|
3365 |
* src/: applications/staticProps/DensityPlot.cpp, |
3366 |
applications/staticProps/DensityPlot.hpp, |
3367 |
applications/staticProps/SCDOrderParameter.cpp, |
3368 |
applications/staticProps/StaticProps.cpp, |
3369 |
io/AtomTypesSectionParser.cpp: working version of DensityPlot |
3370 |
|
3371 |
2005-05-31 18:31 chuckv |
3372 |
|
3373 |
* src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to |
3374 |
remove angular momentum. |
3375 |
|
3376 |
2005-05-31 13:34 chuckv |
3377 |
|
3378 |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in |
3379 |
typo in nanorodBuilder. |
3380 |
|
3381 |
2005-05-30 10:01 chuckv |
3382 |
|
3383 |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
3384 |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, |
3385 |
brains/Stats.hpp, integrators/Velocitizer.cpp, |
3386 |
integrators/Velocitizer.hpp: Added method to remove system angular |
3387 |
momentum to velocitizer and added method to calculate system |
3388 |
angular momentum to siminfo. |
3389 |
|
3390 |
2005-05-29 17:16 chrisfen |
3391 |
|
3392 |
* src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed |
3393 |
balance from the Darkside (files) |
3394 |
|
3395 |
2005-05-29 17:15 chrisfen |
3396 |
|
3397 |
* src/UseTheForce/doForces.F90: Removed balance from doForces |
3398 |
|
3399 |
2005-05-29 17:15 chrisfen |
3400 |
|
3401 |
* samples/water/tap/: tap.in, tap.md: Updated tap sample |
3402 |
|
3403 |
2005-05-29 17:15 chrisfen |
3404 |
|
3405 |
* samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap |
3406 |
dimer for testing purposes |
3407 |
|
3408 |
2005-05-29 17:14 chrisfen |
3409 |
|
3410 |
* forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It |
3411 |
was apparently wiped earlier this month... |
3412 |
|
3413 |
2005-05-29 17:13 chrisfen |
3414 |
|
3415 |
* ChangeLog: ran make cvslog |
3416 |
|
3417 |
2005-05-28 20:16 tim |
3418 |
|
3419 |
* src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding |
3420 |
AtomNameVisitor |
3421 |
|
3422 |
2005-05-28 20:09 tim |
3423 |
|
3424 |
* src/integrators/Integrator.cpp: dding resetIntegrator |
3425 |
|
3426 |
2005-05-28 20:06 tim |
3427 |
|
3428 |
* src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, |
3429 |
NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, |
3430 |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding |
3431 |
resetIntegrator |
3432 |
|
3433 |
2005-05-27 17:11 tim |
3434 |
|
3435 |
* src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, |
3436 |
Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, |
3437 |
SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, |
3438 |
StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into |
3439 |
StaticProps |
3440 |
|
3441 |
2005-05-27 00:41 tim |
3442 |
|
3443 |
* src/: applications/staticProps/Makefile, |
3444 |
applications/staticProps/P2OrderParameter.cpp, |
3445 |
applications/staticProps/P2OrderParameter.hpp, |
3446 |
applications/staticProps/StaticProps.cpp, |
3447 |
applications/staticProps/StaticProps.ggo, |
3448 |
applications/staticProps/StaticPropsCmd.c, |
3449 |
applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, |
3450 |
utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps |
3451 |
|
3452 |
2005-05-26 18:45 tim |
3453 |
|
3454 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3455 |
applications/dump2Xyz/Dump2XYZCmd.c, |
3456 |
applications/dump2Xyz/Dump2XYZCmd.h, |
3457 |
applications/staticProps/Makefile, |
3458 |
applications/staticProps/P2OrderParameter.cpp, |
3459 |
applications/staticProps/P2OrderParameter.hpp, |
3460 |
applications/staticProps/RadialDistrFunc.cpp, |
3461 |
applications/staticProps/RadialDistrFunc.hpp, |
3462 |
applications/staticProps/StaticAnalyser.hpp, |
3463 |
applications/staticProps/StaticProps.cpp, |
3464 |
applications/staticProps/StaticProps.ggo, |
3465 |
applications/staticProps/StaticPropsCmd.c, |
3466 |
applications/staticProps/StaticPropsCmd.h, visitors/Makefile, |
3467 |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding |
3468 |
AtomNameVisitor to convert atom name to its base name; |
3469 |
wrappingvisitor now wrap back to the center of the mass; adding |
3470 |
P2OrderParameter into StaticProps |
3471 |
|
3472 |
2005-05-22 17:36 chuckv |
3473 |
|
3474 |
* src/: applications/nanoRodBuilder/Geometry.cpp, |
3475 |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
3476 |
applications/nanoRodBuilder/GeometryFactory.cpp, |
3477 |
applications/nanoRodBuilder/GeometryFactory.hpp, |
3478 |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
3479 |
integrators/VelocityVerletIntegrator.cpp: Fix to print pressure |
3480 |
tensor. |
3481 |
|
3482 |
2005-05-22 17:05 tim |
3483 |
|
3484 |
* src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
3485 |
integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, |
3486 |
io/Globals.hpp, io/SectionParserManager.cpp: adding keyword |
3487 |
printPressureTensor |
3488 |
|
3489 |
2005-05-20 15:27 tim |
3490 |
|
3491 |
* src/integrators/NPrT.cpp: NPrT in progress |
3492 |
|
3493 |
2005-05-20 12:01 tim |
3494 |
|
3495 |
* src/: integrators/NPrT.cpp, io/Globals.cpp, |
3496 |
utils/OOPSEConstant.hpp: NPrT in progress |
3497 |
|
3498 |
2005-05-19 17:31 tim |
3499 |
|
3500 |
* src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, |
3501 |
integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, |
3502 |
io/Globals.hpp: NPAT is working |
3503 |
|
3504 |
2005-05-19 11:49 tim |
3505 |
|
3506 |
* src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, |
3507 |
integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT |
3508 |
|
3509 |
2005-05-19 00:28 tim |
3510 |
|
3511 |
* src/: brains/Register.cpp, integrators/NPAT.cpp, |
3512 |
integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, |
3513 |
io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators |
3514 |
|
3515 |
2005-05-18 15:06 chrisfen |
3516 |
|
3517 |
* forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just |
3518 |
some tap changes |
3519 |
|
3520 |
2005-05-18 14:31 chrisfen |
3521 |
|
3522 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
3523 |
DarkSide/sticky.F90: Modifications to temper the dipolar strength |
3524 |
in the first solvation shell for tap |
3525 |
|
3526 |
2005-05-18 08:35 chrisfen |
3527 |
|
3528 |
* samples/water/tap/: tap.in, tap.md, water.md: added a tap example |
3529 |
for testing purposes |
3530 |
|
3531 |
2005-05-17 18:35 chrisfen |
3532 |
|
3533 |
* ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, |
3534 |
samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, |
3535 |
src/UseTheForce/doForces.F90, |
3536 |
src/UseTheForce/DarkSide/electrostatic.F90, |
3537 |
src/UseTheForce/DarkSide/electrostatic_interface.F90, |
3538 |
src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also |
3539 |
correcting changes to the previous merge that were not caught |
3540 |
|
3541 |
2005-05-17 00:20 chuckv |
3542 |
|
3543 |
* src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: |
3544 |
Fixed merge issues between Kyle and Chris so OOPSE will actually |
3545 |
build. |
3546 |
|
3547 |
2005-05-16 23:46 kdaily |
3548 |
|
3549 |
* src/io/: GayBerneAtomTypesSectionParser.cpp, |
3550 |
GayBerneAtomTypesSectionParser.hpp, Makefile: help |
3551 |
|
3552 |
2005-05-16 22:08 kdaily |
3553 |
|
3554 |
* forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, |
3555 |
src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, |
3556 |
src/types/DirectionalAtomType.cpp, |
3557 |
src/types/DirectionalAtomType.hpp: added gb |
3558 |
|
3559 |
2005-05-13 16:36 chrisfen |
3560 |
|
3561 |
* forceFields/DUFF2.frc: Better tap |
3562 |
|
3563 |
2005-05-12 15:43 chrisfen |
3564 |
|
3565 |
* forceFields/DUFF2.frc, samples/water/dimer/ssd.in, |
3566 |
samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, |
3567 |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
3568 |
src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. |
3569 |
Need to parametrize. |
3570 |
|
3571 |
2005-05-11 19:15 chuckv |
3572 |
|
3573 |
* src/: io/ShapeAtomTypesSectionParser.cpp, |
3574 |
math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed |
3575 |
build issues under ifc7. |
3576 |
|
3577 |
2005-05-09 18:07 chuckv |
3578 |
|
3579 |
* src/applications/nanoRodBuilder/Geometry.hpp: More geometry |
3580 |
builder changes. |
3581 |
|
3582 |
2005-05-05 11:06 chrisfen |
3583 |
|
3584 |
* forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED |
3585 |
to TAP |
3586 |
|
3587 |
2005-05-05 10:47 chrisfen |
3588 |
|
3589 |
* forceFields/DUFF2.frc, samples/water/ssde/ssde.md, |
3590 |
samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, |
3591 |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, |
3592 |
src/UseTheForce/DarkSide/atype.F90, |
3593 |
src/UseTheForce/DarkSide/atype_interface.F90, |
3594 |
src/UseTheForce/DarkSide/simulation.F90, |
3595 |
src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, |
3596 |
src/brains/fSimulation.h, src/io/Makefile, |
3597 |
src/io/StickyAtomTypesSectionParser.cpp, |
3598 |
src/io/StickyPowerAtomTypesSectionParser.cpp, |
3599 |
src/io/StickyPowerAtomTypesSectionParser.hpp, |
3600 |
src/types/AtomType.cpp, src/types/AtomType.hpp, |
3601 |
src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, |
3602 |
src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's |
3603 |
not parametrized, but OOPSE will now let me run it... |
3604 |
|
3605 |
2005-05-03 18:55 chuckv |
3606 |
|
3607 |
* src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, |
3608 |
GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: |
3609 |
Adding support for generic geometry to nanorodbuilder. |
3610 |
|
3611 |
2005-05-03 13:55 chuckv |
3612 |
|
3613 |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
3614 |
nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, |
3615 |
nanorodBuilderCmd.h: More changes to nanoRodBuilder.... |
3616 |
|
3617 |
2005-04-29 15:16 gezelter |
3618 |
|
3619 |
* make/Makefile.in: [no log message] |
3620 |
|
3621 |
2005-04-29 12:26 chrisfen |
3622 |
|
3623 |
* forceFields/DUFF2.frc, samples/water/spce/water.md, |
3624 |
samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, |
3625 |
samples/water/ssd-ion/water.md, samples/water/ssde/water.md, |
3626 |
samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, |
3627 |
samples/water/tip4p/water.md: Added TIP4P-Ew |
3628 |
|
3629 |
2005-04-27 20:24 chuckv |
3630 |
|
3631 |
* src/applications/nanoRodBuilder/: GeometryBuilder.cpp, |
3632 |
GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, |
3633 |
nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with |
3634 |
nanoRodBuilder.... |
3635 |
|
3636 |
2005-04-27 16:13 chrisfen |
3637 |
|
3638 |
* samples/shape/Shapes.frc, samples/shape/linear.shape, |
3639 |
src/UseTheForce/DarkSide/atype.F90, |
3640 |
src/UseTheForce/DarkSide/shapes.F90, |
3641 |
src/UseTheForce/DarkSide/shapes_interface.F90, |
3642 |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of |
3643 |
write statements and am closer to a working shapes |
3644 |
|
3645 |
2005-04-22 17:57 chuckv |
3646 |
|
3647 |
* src/utils/Predicate.hpp: Fixed gcc4 bug... |
3648 |
|
3649 |
2005-04-22 17:52 tim |
3650 |
|
3651 |
* src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, |
3652 |
Trim.hpp: adding CharClassificationFunctor to fix the locale |
3653 |
problem of c++ |
3654 |
|
3655 |
2005-04-21 10:12 chrisfen |
3656 |
|
3657 |
* samples/shape/Shapes.frc, samples/shape/linear.in, |
3658 |
samples/shape/linear.md, src/UseTheForce/ForceField.hpp, |
3659 |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, |
3660 |
src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, |
3661 |
src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, |
3662 |
src/UseTheForce/DarkSide/shapes.F90, |
3663 |
src/UseTheForce/DarkSide/shapes_interface.F90, |
3664 |
src/UseTheForce/DarkSide/shapes_interface.h, |
3665 |
src/brains/Register.cpp, src/brains/SimCreator.cpp, |
3666 |
src/io/Makefile, src/io/SectionParser.cpp, |
3667 |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
3668 |
src/io/ShapeAtomTypesSectionParser.cpp, |
3669 |
src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, |
3670 |
src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, |
3671 |
src/types/ShapeAtomType.hpp: Shapes is limping along with a array |
3672 |
bounds overwrite (I think...). At least the parser loads the |
3673 |
forcefield fine... |
3674 |
|
3675 |
2005-04-18 11:44 chrisfen |
3676 |
|
3677 |
* src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on |
3678 |
Mac (capitalization confusion of filenames) |
3679 |
|
3680 |
2005-04-17 23:50 chrisfen |
3681 |
|
3682 |
* src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, |
3683 |
UseTheForce/Shapes_FF.cpp, |
3684 |
io/DirectionalAtomTypesSectionParser.cpp, |
3685 |
io/ShapeAtomTypesSectionParser.cpp, |
3686 |
io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... |
3687 |
|
3688 |
2005-04-15 18:43 gezelter |
3689 |
|
3690 |
* README: gmake in case people forget |
3691 |
|
3692 |
2005-04-15 18:40 gezelter |
3693 |
|
3694 |
* src/applications/oopse/oopse.cpp: fixed the spacing on the |
3695 |
banner. Vanity. |
3696 |
|
3697 |
2005-04-15 18:22 gezelter |
3698 |
|
3699 |
* src/: config.h.in, applications/oopse/oopse.cpp: Version string |
3700 |
in banner (and version numbers in config.h) |
3701 |
|
3702 |
2005-04-15 18:22 gezelter |
3703 |
|
3704 |
* ChangeLog, LICENSE, README: Documentation changes |
3705 |
|
3706 |
2005-04-15 18:03 gezelter |
3707 |
|
3708 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3709 |
UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, |
3710 |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3711 |
UseTheForce/ForceFieldCreator.hpp, |
3712 |
UseTheForce/ForceFieldFactory.cpp, |
3713 |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
3714 |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, |
3715 |
UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, |
3716 |
UseTheForce/notifyCutoffs.F90, |
3717 |
UseTheForce/notifyCutoffs_interface.F90, |
3718 |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
3719 |
UseTheForce/DarkSide/atype.F90, |
3720 |
UseTheForce/DarkSide/atype_interface.F90, |
3721 |
UseTheForce/DarkSide/eam.F90, |
3722 |
UseTheForce/DarkSide/eam_interface.F90, |
3723 |
UseTheForce/DarkSide/eam_interface.h, |
3724 |
UseTheForce/DarkSide/electrostatic.F90, |
3725 |
UseTheForce/DarkSide/electrostatic_interface.F90, |
3726 |
UseTheForce/DarkSide/electrostatic_interface.h, |
3727 |
UseTheForce/DarkSide/force_globals.F90, |
3728 |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
3729 |
UseTheForce/DarkSide/lj_interface.F90, |
3730 |
UseTheForce/DarkSide/lj_interface.h, |
3731 |
UseTheForce/DarkSide/neighborLists.F90, |
3732 |
UseTheForce/DarkSide/reactionField.F90, |
3733 |
UseTheForce/DarkSide/shapes.F90, |
3734 |
UseTheForce/DarkSide/shapes_interface.F90, |
3735 |
UseTheForce/DarkSide/shapes_interface.h, |
3736 |
UseTheForce/DarkSide/simParallel.F90, |
3737 |
UseTheForce/DarkSide/simParallel_interface.F90, |
3738 |
UseTheForce/DarkSide/simParallel_interface.h, |
3739 |
UseTheForce/DarkSide/simulation.F90, |
3740 |
UseTheForce/DarkSide/simulation_interface.F90, |
3741 |
UseTheForce/DarkSide/simulation_interface.h, |
3742 |
UseTheForce/DarkSide/sticky.F90, |
3743 |
UseTheForce/DarkSide/sticky_interface.F90, |
3744 |
UseTheForce/DarkSide/sticky_interface.h, |
3745 |
UseTheForce/DarkSide/switcheroo.F90, |
3746 |
applications/dump2Xyz/Dump2XYZ.cpp, |
3747 |
applications/dump2Xyz/Dump2XYZCmd.c, |
3748 |
applications/dump2Xyz/Dump2XYZCmd.h, |
3749 |
applications/dynamicProps/CrossTimeCorrFunc.cpp, |
3750 |
applications/dynamicProps/CrossTimeCorrFunc.hpp, |
3751 |
applications/dynamicProps/DipoleCorrFunc.cpp, |
3752 |
applications/dynamicProps/DipoleCorrFunc.hpp, |
3753 |
applications/dynamicProps/DynamicProps.cpp, |
3754 |
applications/dynamicProps/DynamicPropsCmd.c, |
3755 |
applications/dynamicProps/DynamicPropsCmd.h, |
3756 |
applications/dynamicProps/FrameTimeCorrFunc.hpp, |
3757 |
applications/dynamicProps/ParticleTimeCorrFunc.cpp, |
3758 |
applications/dynamicProps/ParticleTimeCorrFunc.hpp, |
3759 |
applications/dynamicProps/RCorrFunc.cpp, |
3760 |
applications/dynamicProps/RCorrFunc.hpp, |
3761 |
applications/dynamicProps/TimeCorrFunc.cpp, |
3762 |
applications/dynamicProps/TimeCorrFunc.hpp, |
3763 |
applications/dynamicProps/VCorrFunc.cpp, |
3764 |
applications/dynamicProps/VCorrFunc.hpp, |
3765 |
applications/nanoRodBuilder/GeometryBuilder.cpp, |
3766 |
applications/nanoRodBuilder/GeometryBuilder.hpp, |
3767 |
applications/nanoRodBuilder/nanorodBuilder.cpp, |
3768 |
applications/nanoRodBuilder/nanorodBuilderCmd.c, |
3769 |
applications/nanoRodBuilder/nanorodBuilderCmd.h, |
3770 |
applications/oopse/oopse.cpp, |
3771 |
applications/simpleBuilder/simpleBuilder.cpp, |
3772 |
applications/simpleBuilder/simpleBuilderCmd.c, |
3773 |
applications/simpleBuilder/simpleBuilderCmd.h, |
3774 |
applications/staticProps/GofAngle2.cpp, |
3775 |
applications/staticProps/GofAngle2.hpp, |
3776 |
applications/staticProps/GofR.cpp, |
3777 |
applications/staticProps/GofR.hpp, |
3778 |
applications/staticProps/GofRAngle.cpp, |
3779 |
applications/staticProps/GofRAngle.hpp, |
3780 |
applications/staticProps/GofXyz.cpp, |
3781 |
applications/staticProps/GofXyz.hpp, |
3782 |
applications/staticProps/RadialDistrFunc.cpp, |
3783 |
applications/staticProps/RadialDistrFunc.hpp, |
3784 |
applications/staticProps/StaticProps.cpp, |
3785 |
applications/staticProps/StaticPropsCmd.c, |
3786 |
applications/staticProps/StaticPropsCmd.h, |
3787 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
3788 |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
3789 |
brains/Exclude.hpp, brains/ForceManager.cpp, |
3790 |
brains/ForceManager.hpp, brains/MoleculeCreator.cpp, |
3791 |
brains/MoleculeCreator.hpp, brains/Register.cpp, |
3792 |
brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3793 |
brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
3794 |
brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, |
3795 |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, |
3796 |
brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, |
3797 |
brains/fSimulation.h, constraints/ConstraintElem.hpp, |
3798 |
constraints/ConstraintPair.hpp, constraints/Rattle.cpp, |
3799 |
constraints/Rattle.hpp, constraints/ZconsStruct.hpp, |
3800 |
constraints/ZconstraintForceManager.cpp, |
3801 |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
3802 |
integrators/DLM.hpp, integrators/Integrator.cpp, |
3803 |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
3804 |
integrators/IntegratorFactory.cpp, |
3805 |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
3806 |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
3807 |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
3808 |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
3809 |
integrators/NVT.cpp, integrators/NVT.hpp, |
3810 |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
3811 |
integrators/Velocitizer.hpp, |
3812 |
integrators/VelocityVerletIntegrator.cpp, |
3813 |
integrators/VelocityVerletIntegrator.hpp, |
3814 |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
3815 |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
3816 |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
3817 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
3818 |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
3819 |
io/ChargeAtomTypesSectionParser.hpp, |
3820 |
io/DirectionalAtomTypesSectionParser.cpp, |
3821 |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
3822 |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
3823 |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
3824 |
io/Globals.cpp, io/Globals.hpp, |
3825 |
io/LennardJonesAtomTypesSectionParser.cpp, |
3826 |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
3827 |
io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, |
3828 |
io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, |
3829 |
io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, |
3830 |
io/SectionParser.cpp, io/SectionParser.hpp, |
3831 |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
3832 |
io/StatWriter.cpp, io/StatWriter.hpp, |
3833 |
io/StickyAtomTypesSectionParser.cpp, |
3834 |
io/StickyAtomTypesSectionParser.hpp, |
3835 |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
3836 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
3837 |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, |
3838 |
io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, |
3839 |
io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, |
3840 |
io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, |
3841 |
lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, |
3842 |
lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
3843 |
lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, |
3844 |
lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, |
3845 |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
3846 |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
3847 |
math/ParallelRandNumGen.hpp, math/Polynomial.hpp, |
3848 |
math/Quaternion.hpp, math/RandNumGen.hpp, |
3849 |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
3850 |
math/RectMatrix.hpp, math/SeqRandNumGen.cpp, |
3851 |
math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, |
3852 |
math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, |
3853 |
minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, |
3854 |
minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, |
3855 |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
3856 |
minimizers/MinimizerFactory.hpp, |
3857 |
minimizers/MinimizerParameterSet.cpp, |
3858 |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
3859 |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
3860 |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
3861 |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
3862 |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
3863 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
3864 |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
3865 |
primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, |
3866 |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
3867 |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
3868 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
3869 |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
3870 |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
3871 |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
3872 |
profiling/timing.F90, restraints/Restraints.cpp, |
3873 |
restraints/Restraints.hpp, |
3874 |
restraints/ThermoIntegrationForceManager.cpp, |
3875 |
restraints/ThermoIntegrationForceManager.hpp, |
3876 |
selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, |
3877 |
selection/IndexFinder.cpp, selection/IndexFinder.hpp, |
3878 |
selection/NameFinder.cpp, selection/NameFinder.hpp, |
3879 |
selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, |
3880 |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
3881 |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
3882 |
selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, |
3883 |
selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, |
3884 |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
3885 |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
3886 |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
3887 |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
3888 |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
3889 |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
3890 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
3891 |
types/DirectionalAtomType.hpp, types/FixedBondType.hpp, |
3892 |
types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, |
3893 |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
3894 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
3895 |
types/MorseBondType.hpp, types/OplsTorsionType.hpp, |
3896 |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
3897 |
types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, |
3898 |
types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, |
3899 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
3900 |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
3901 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
3902 |
types/TorsionType.hpp, types/UreyBradleyBendType.hpp, |
3903 |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, |
3904 |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
3905 |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
3906 |
utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, |
3907 |
utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, |
3908 |
utils/PropertyMap.cpp, utils/PropertyMap.hpp, |
3909 |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
3910 |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
3911 |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
3912 |
utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, |
3913 |
utils/any.hpp, utils/definitions.F90, utils/fError.c, |
3914 |
utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, |
3915 |
utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, |
3916 |
utils/residentMem.h, utils/simError.c, utils/simError.h, |
3917 |
utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, |
3918 |
visitors/AtomData.hpp, visitors/AtomVisitor.cpp, |
3919 |
visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, |
3920 |
visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, |
3921 |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
3922 |
visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, |
3923 |
visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, |
3924 |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has |
3925 |
been drafted to perform our indentation services |
3926 |
|
3927 |
2005-04-15 18:03 gezelter |
3928 |
|
3929 |
* configure, ac-tools/configure.in: Jedi mind-trick warning |
3930 |
messages have been added to make users ignore CGAL. |
3931 |
|
3932 |
2005-04-15 14:41 tim |
3933 |
|
3934 |
* make/Makefile.in: fix make install |
3935 |
|
3936 |
2005-04-15 14:41 tim |
3937 |
|
3938 |
* samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: |
3939 |
add Makefile of samples |
3940 |
|
3941 |
2005-04-15 14:33 tim |
3942 |
|
3943 |
* samples/: lipid/Makefile, water/dimer/Makefile, |
3944 |
water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not |
3945 |
installed correctly |
3946 |
|
3947 |
2005-04-14 17:41 gezelter |
3948 |
|
3949 |
* ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
3950 |
make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, |
3951 |
scripts/filepp, scripts/filepp.in: configure now searches for perl |
3952 |
to use with filepp |
3953 |
|
3954 |
2005-04-14 17:20 gezelter |
3955 |
|
3956 |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
3957 |
MoLocator |
3958 |
|
3959 |
2005-04-14 15:12 gezelter |
3960 |
|
3961 |
* LICENSE: [no log message] |
3962 |
|
3963 |
2005-04-14 12:10 chuckv |
3964 |
|
3965 |
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
3966 |
nanorodbuilder now exit's when libCGAL is not present. |
3967 |
|
3968 |
2005-04-14 11:20 tim |
3969 |
|
3970 |
* src/io/make_nodes.h: fix one more warning message in make_nodes |
3971 |
|
3972 |
2005-04-13 19:36 chuckv |
3973 |
|
3974 |
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
3975 |
interface name for SGI Compiler |
3976 |
|
3977 |
2005-04-13 19:29 chrisfen |
3978 |
|
3979 |
* samples/water/ssde/ssde.md: oops... bad sample |
3980 |
|
3981 |
2005-04-13 19:00 chuckv |
3982 |
|
3983 |
* src/config.h.in: Change typo in CGAL. |
3984 |
|
3985 |
2005-04-13 18:43 tim |
3986 |
|
3987 |
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
3988 |
selection/SelectionCompiler.hpp: fix some warning messages |
3989 |
|
3990 |
2005-04-13 18:30 gezelter |
3991 |
|
3992 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
3993 |
make/Makefile.in, src/config.h.in, |
3994 |
src/applications/nanoRodBuilder/Makefile, |
3995 |
src/applications/nanoRodBuilder/Makefile.in, |
3996 |
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
3997 |
checks |
3998 |
|
3999 |
2005-04-13 16:36 chuckv |
4000 |
|
4001 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
4002 |
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
4003 |
DarkSide/electrostatic_interface.F90, |
4004 |
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
4005 |
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
4006 |
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
4007 |
destroy methods for Fortran modules. |
4008 |
|
4009 |
2005-04-13 16:17 chuckv |
4010 |
|
4011 |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
4012 |
shapes_interface.h: Added destroy method to clean up memory |
4013 |
|
4014 |
2005-04-13 14:41 tim |
4015 |
|
4016 |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4017 |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
4018 |
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
4019 |
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
4020 |
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
4021 |
fixed |
4022 |
|
4023 |
2005-04-12 18:44 chuckv |
4024 |
|
4025 |
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
4026 |
for nanoRodBuilder. |
4027 |
|
4028 |
2005-04-12 18:42 tim |
4029 |
|
4030 |
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
4031 |
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
4032 |
and simpleBuilder(forget to delete lattice) |
4033 |
|
4034 |
2005-04-12 18:33 tim |
4035 |
|
4036 |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4037 |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
4038 |
refactory lattice |
4039 |
|
4040 |
2005-04-12 18:07 tim |
4041 |
|
4042 |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
4043 |
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
4044 |
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
4045 |
LatticeFactory and LatticeCreator |
4046 |
|
4047 |
2005-04-12 17:58 tim |
4048 |
|
4049 |
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
4050 |
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
4051 |
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
4052 |
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
4053 |
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
4054 |
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
4055 |
|
4056 |
2005-04-12 17:28 gezelter |
4057 |
|
4058 |
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
4059 |
vector_class.F90: cleaned up vector_class memory leak fix by |
4060 |
deallocating in reverse order of how we allocated. Also migrated |
4061 |
MoLocator into utils directory |
4062 |
|
4063 |
2005-04-12 17:27 gezelter |
4064 |
|
4065 |
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
4066 |
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
4067 |
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
4068 |
directory |
4069 |
|
4070 |
2005-04-12 17:27 gezelter |
4071 |
|
4072 |
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
4073 |
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
4074 |
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
4075 |
nanoRodBuilder/LatticeCreator.hpp, |
4076 |
nanoRodBuilder/LatticeFactory.cpp, |
4077 |
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
4078 |
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
4079 |
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
4080 |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
4081 |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
4082 |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
4083 |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
4084 |
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
4085 |
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
4086 |
these files are now redundant |
4087 |
|
4088 |
2005-04-12 17:27 gezelter |
4089 |
|
4090 |
* src/UseTheForce/DarkSide/: atype_interface.F90, |
4091 |
atype_interface.h: cleaned up memory leak fix |
4092 |
|
4093 |
2005-04-12 17:26 gezelter |
4094 |
|
4095 |
* make/Makefile.in: added lattice subdirectory |
4096 |
|
4097 |
2005-04-12 16:57 chrisfen |
4098 |
|
4099 |
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
4100 |
a space by accident |
4101 |
|
4102 |
2005-04-12 16:56 chrisfen |
4103 |
|
4104 |
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
4105 |
quadrupole sample |
4106 |
|
4107 |
2005-04-12 16:56 chrisfen |
4108 |
|
4109 |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
4110 |
samples |
4111 |
|
4112 |
2005-04-12 14:30 tim |
4113 |
|
4114 |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
4115 |
type in fortran side |
4116 |
|
4117 |
2005-04-12 13:45 chuckv |
4118 |
|
4119 |
* src/utils/vector_class.F90: Further changes to vector_class |
4120 |
destroy function. |
4121 |
|
4122 |
2005-04-12 13:39 chuckv |
4123 |
|
4124 |
* src/utils/vector_class.F90: Fixed pointer memory leak in |
4125 |
vector_class. |
4126 |
|
4127 |
2005-04-12 13:12 chuckv |
4128 |
|
4129 |
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
4130 |
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
4131 |
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
4132 |
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
4133 |
|
4134 |
2005-04-12 10:24 chrisfen |
4135 |
|
4136 |
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
4137 |
output |
4138 |
|
4139 |
2005-04-11 20:29 chuckv |
4140 |
|
4141 |
* src/: UseTheForce/DarkSide/atype.F90, |
4142 |
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
4143 |
|
4144 |
2005-04-11 20:28 chuckv |
4145 |
|
4146 |
* src/utils/vector_class.F90: Added code to delete vector. |
4147 |
|
4148 |
2005-04-11 17:58 tim |
4149 |
|
4150 |
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
4151 |
basic_ifstrstream |
4152 |
|
4153 |
2005-04-11 17:37 chuckv |
4154 |
|
4155 |
* make/Makefile.in, |
4156 |
src/applications/nanoRodBuilder/BaseLattice.cpp, |
4157 |
src/applications/nanoRodBuilder/BaseLattice.hpp, |
4158 |
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
4159 |
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
4160 |
src/applications/nanoRodBuilder/Lattice.cpp, |
4161 |
src/applications/nanoRodBuilder/Lattice.hpp, |
4162 |
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
4163 |
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
4164 |
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
4165 |
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
4166 |
src/applications/nanoRodBuilder/Makefile, |
4167 |
src/applications/nanoRodBuilder/MoLocator.cpp, |
4168 |
src/applications/nanoRodBuilder/MoLocator.hpp, |
4169 |
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
4170 |
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
4171 |
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
4172 |
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
4173 |
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
4174 |
nanoRodBuilder application (may not work yet). ((Doesn't work |
4175 |
yet.)) (((May never work....))) |
4176 |
|
4177 |
2005-04-11 16:54 tim |
4178 |
|
4179 |
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
4180 |
prepareVisitor in Dump2XYZ |
4181 |
|
4182 |
2005-04-11 16:19 chrisfen |
4183 |
|
4184 |
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
4185 |
quadrupoles. look! it's divide by 3 like stone says! |
4186 |
|
4187 |
2005-04-11 16:18 chrisfen |
4188 |
|
4189 |
* forceFields/DUFF2.frc: fixing of the quadrupoles |
4190 |
|
4191 |
2005-04-11 16:16 tim |
4192 |
|
4193 |
* src/selection/Token.hpp: change the parameter name in |
4194 |
constructors |
4195 |
|
4196 |
2005-04-11 15:49 gezelter |
4197 |
|
4198 |
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
4199 |
|
4200 |
2005-04-11 15:06 gezelter |
4201 |
|
4202 |
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
4203 |
versions < 3.80 |
4204 |
|
4205 |
2005-04-11 12:13 gezelter |
4206 |
|
4207 |
* make/Makefile.in, src/UseTheForce/Makefile, |
4208 |
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
4209 |
some stuff to clean out module files during "make clean" |
4210 |
|
4211 |
2005-04-08 18:13 chrisfen |
4212 |
|
4213 |
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
4214 |
interactions should be working with a remaining question of |
4215 |
interaction magnitude |
4216 |
|
4217 |
2005-04-08 18:12 chrisfen |
4218 |
|
4219 |
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
4220 |
samples |
4221 |
|
4222 |
2005-04-08 14:48 chrisfen |
4223 |
|
4224 |
* samples/water/ssd/ssd.md: oops... messed up a sample |
4225 |
|
4226 |
2005-04-08 10:43 chrisfen |
4227 |
|
4228 |
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
4229 |
charge-dipole interactions |
4230 |
|
4231 |
2005-04-08 10:42 chrisfen |
4232 |
|
4233 |
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
4234 |
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
4235 |
|
4236 |
2005-04-08 10:41 chrisfen |
4237 |
|
4238 |
* forceFields/DUFF2.frc: added Cl- and Na+ |
4239 |
|
4240 |
2005-04-06 19:59 tim |
4241 |
|
4242 |
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
4243 |
|
4244 |
2005-04-05 19:09 tim |
4245 |
|
4246 |
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
4247 |
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
4248 |
in atom type name;clean the code a little bit |
4249 |
|
4250 |
2005-03-29 16:00 tim |
4251 |
|
4252 |
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
4253 |
in converting rotation matrix to quaternion |
4254 |
|
4255 |
2005-03-28 17:41 tim |
4256 |
|
4257 |
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
4258 |
|
4259 |
2005-03-28 17:30 tim |
4260 |
|
4261 |
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
4262 |
the wrapping |
4263 |
|
4264 |
2005-03-28 10:54 tim |
4265 |
|
4266 |
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
4267 |
dimension of histogram |
4268 |
|
4269 |
2005-03-22 11:38 tim |
4270 |
|
4271 |
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
4272 |
src/applications/dynamicProps/Makefile, |
4273 |
src/applications/oopse/Makefile, |
4274 |
src/applications/simpleBuilder/Makefile, |
4275 |
src/applications/staticProps/Makefile: avoid building parallel |
4276 |
executable for dump2XYZ, simpleBuilder, staticProps and |
4277 |
dynamicProps |
4278 |
|
4279 |
2005-03-21 17:34 chrisfen |
4280 |
|
4281 |
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
4282 |
forcefield files |
4283 |
|
4284 |
2005-03-21 15:51 chrisfen |
4285 |
|
4286 |
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
4287 |
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
4288 |
data for reaction_field |
4289 |
|
4290 |
2005-03-21 15:50 chrisfen |
4291 |
|
4292 |
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
4293 |
WILL CHANGE THIS BACK, RIGHT? |
4294 |
|
4295 |
2005-03-21 14:23 gezelter |
4296 |
|
4297 |
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
4298 |
correct value |
4299 |
|
4300 |
2005-03-21 14:22 gezelter |
4301 |
|
4302 |
* make/Makefile.in: fixed an install-related bug. |
4303 |
$(InstallCommand) had been set to $(InstallData) |
4304 |
|
4305 |
2005-03-15 09:21 gezelter |
4306 |
|
4307 |
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
4308 |
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
4309 |
|
4310 |
2005-03-15 09:20 gezelter |
4311 |
|
4312 |
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
4313 |
|
4314 |
2005-03-13 02:39 gezelter |
4315 |
|
4316 |
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
4317 |
charge-quadrupole interactions |
4318 |
|
4319 |
2005-03-12 14:12 chrisfen |
4320 |
|
4321 |
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
4322 |
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
4323 |
|
4324 |
2005-03-12 14:05 chrisfen |
4325 |
|
4326 |
* samples/thermoIntegration/liquid/ssde.in, |
4327 |
samples/thermoIntegration/liquid/ssde.md, |
4328 |
samples/thermoIntegration/liquid/water.md, |
4329 |
samples/thermoIntegration/solid/idealCrystal.in, |
4330 |
samples/thermoIntegration/solid/ssde.in, |
4331 |
samples/thermoIntegration/solid/ssde.md, |
4332 |
samples/thermoIntegration/solid/ssde.zang0, |
4333 |
samples/thermoIntegration/solid/water.md, |
4334 |
samples/water/tip3p_ice/tp3.md, |
4335 |
src/UseTheForce/DarkSide/sticky.F90, |
4336 |
src/restraints/ThermoIntegrationForceManager.cpp: added some |
4337 |
samples |
4338 |
|
4339 |
2005-03-11 12:50 tim |
4340 |
|
4341 |
* src/: brains/SimCreator.cpp, |
4342 |
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
4343 |
MultipoleAtomTypesSectionParser |
4344 |
|
4345 |
2005-03-11 10:55 tim |
4346 |
|
4347 |
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
4348 |
excluded |
4349 |
|
4350 |
2005-03-11 10:53 gezelter |
4351 |
|
4352 |
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
4353 |
quadrupoles |
4354 |
|
4355 |
2005-03-11 10:52 gezelter |
4356 |
|
4357 |
* forceFields/DUFF2.frc: quadrupoles for SSD models |
4358 |
|
4359 |
2005-03-11 10:00 tim |
4360 |
|
4361 |
* ChangeLog, doc/SelectionExpression.html, |
4362 |
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
4363 |
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
4364 |
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
4365 |
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
4366 |
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
4367 |
SelectionExpression.html |
4368 |
|
4369 |
2005-03-10 19:43 chrisfen |
4370 |
|
4371 |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
4372 |
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
4373 |
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
4374 |
MPI restraints |
4375 |
|
4376 |
2005-03-10 18:56 tim |
4377 |
|
4378 |
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
4379 |
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
4380 |
and cutoff group |
4381 |
|
4382 |
2005-03-10 17:06 gezelter |
4383 |
|
4384 |
* src/types/MorseBondType.hpp: fixed a doxygen problem |
4385 |
|
4386 |
2005-03-10 16:51 gezelter |
4387 |
|
4388 |
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
4389 |
the split dipole test cases |
4390 |
|
4391 |
2005-03-10 16:51 gezelter |
4392 |
|
4393 |
* doc/SelectionExpression.html: updated some documentation |
4394 |
|
4395 |
2005-03-10 15:40 gezelter |
4396 |
|
4397 |
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
4398 |
Makefile: LinkedList removal project starts now |
4399 |
|
4400 |
2005-03-10 15:28 tim |
4401 |
|
4402 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4403 |
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
4404 |
using map to replace link list |
4405 |
|
4406 |
2005-03-10 14:11 tim |
4407 |
|
4408 |
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
4409 |
case of split dipole |
4410 |
|
4411 |
2005-03-10 14:10 chrisfen |
4412 |
|
4413 |
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
4414 |
src/io/RestWriter.cpp, |
4415 |
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
4416 |
builds... |
4417 |
|
4418 |
2005-03-10 13:44 tim |
4419 |
|
4420 |
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
4421 |
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
4422 |
adding test case for split dipole |
4423 |
|
4424 |
2005-03-10 12:54 gezelter |
4425 |
|
4426 |
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
4427 |
support for split dipoles |
4428 |
|
4429 |
2005-03-10 11:27 chrisfen |
4430 |
|
4431 |
* samples/water/tip3p_ice/tp3.md, |
4432 |
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
4433 |
restraints |
4434 |
|
4435 |
2005-03-10 11:15 chrisfen |
4436 |
|
4437 |
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
4438 |
src/UseTheForce/ForceFields.hpp, |
4439 |
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
4440 |
|
4441 |
2005-03-10 11:14 tim |
4442 |
|
4443 |
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
4444 |
src/io/MultipoleAtomTypesSectionParser.cpp, |
4445 |
src/selection/SelectionEvaluator.cpp: minor change |
4446 |
|
4447 |
2005-03-10 10:10 chrisfen |
4448 |
|
4449 |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
4450 |
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
4451 |
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
4452 |
src/integrators/VelocityVerletIntegrator.cpp, |
4453 |
src/integrators/VelocityVerletIntegrator.hpp, |
4454 |
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
4455 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
4456 |
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
4457 |
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
4458 |
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
4459 |
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
4460 |
src/restraints/ThermoIntegrationForceManager.cpp, |
4461 |
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
4462 |
the new restraints code |
4463 |
|
4464 |
2005-03-09 13:48 tim |
4465 |
|
4466 |
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
4467 |
IndexFinder |
4468 |
|
4469 |
2005-03-09 13:46 tim |
4470 |
|
4471 |
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
4472 |
applications/dump2Xyz/Dump2XYZCmd.c, |
4473 |
applications/dump2Xyz/Dump2XYZCmd.h, |
4474 |
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
4475 |
fix compilation issue |
4476 |
|
4477 |
2005-03-09 12:58 tim |
4478 |
|
4479 |
* forceFields/DUFF2.frc, scripts/filepp, |
4480 |
src/UseTheForce/EAM_FF.cpp, |
4481 |
src/io/MultipoleAtomTypesSectionParser.cpp, |
4482 |
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
4483 |
in SectionParser (lineNo is not updated) |
4484 |
|
4485 |
2005-03-09 12:30 tim |
4486 |
|
4487 |
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
4488 |
applications/dump2Xyz/Dump2XYZ.ggo, |
4489 |
applications/dump2Xyz/Dump2XYZCmd.c, |
4490 |
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
4491 |
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
4492 |
io/ChargeAtomTypesSectionParser.hpp, |
4493 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
4494 |
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
4495 |
io/MultipoleAtomTypesSectionParser.cpp, |
4496 |
io/MultipoleAtomTypesSectionParser.hpp, |
4497 |
io/SectionParserManager.cpp, selection/Makefile, |
4498 |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
4499 |
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
4500 |
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
4501 |
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
4502 |
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
4503 |
into ChargeAtomTypesSectionParser and |
4504 |
MultipoleAtomTypesSectionParser;remove print dipole option from |
4505 |
Dump2XYZ; |
4506 |
|
4507 |
2005-03-09 12:28 tim |
4508 |
|
4509 |
* forceFields/DUFF2.frc: change the format of DUFF2 |
4510 |
|
4511 |
2005-03-09 10:44 gezelter |
4512 |
|
4513 |
* src/UseTheForce/DarkSide/: electrostatic.F90, |
4514 |
electrostatic_interface.F90, electrostatic_interface.h: new |
4515 |
electrostatic module |
4516 |
|
4517 |
2005-03-09 09:26 gezelter |
4518 |
|
4519 |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
4520 |
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
4521 |
and fixed quadrupole stuff |
4522 |
|
4523 |
2005-03-09 09:25 gezelter |
4524 |
|
4525 |
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
4526 |
for outdated charge and dipole interfaces |
4527 |
|
4528 |
2005-03-08 16:08 gezelter |
4529 |
|
4530 |
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
4531 |
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
4532 |
charge-dipole test cases |
4533 |
|
4534 |
2005-03-08 16:07 gezelter |
4535 |
|
4536 |
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
4537 |
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
4538 |
strange icc8 bug (we think). |
4539 |
|
4540 |
2005-03-08 16:07 gezelter |
4541 |
|
4542 |
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
4543 |
|
4544 |
2005-03-08 16:07 gezelter |
4545 |
|
4546 |
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
4547 |
Unification Project |
4548 |
|
4549 |
2005-03-08 16:07 gezelter |
4550 |
|
4551 |
* src/io/Globals.cpp: Dunno |
4552 |
|
4553 |
2005-03-08 16:06 gezelter |
4554 |
|
4555 |
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
4556 |
OOPSE_itoa and checking a NULL left over from the LinkedList days |
4557 |
|
4558 |
2005-03-08 16:06 gezelter |
4559 |
|
4560 |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
4561 |
atype_interface.F90, atype_interface.h, charge.F90, |
4562 |
charge_interface.F90, charge_interface.h, dipole.F90, |
4563 |
dipole_interface.F90, dipole_interface.h: electrostatic unification |
4564 |
project fixed an uninitialized variable in Lennard Jones mixing map |
4565 |
|
4566 |
2005-03-08 16:05 gezelter |
4567 |
|
4568 |
* src/UseTheForce/doForces.F90: electrostatic unification project |
4569 |
|
4570 |
2005-03-08 16:05 gezelter |
4571 |
|
4572 |
* samples/water/dimer/: two.md, water.md: making some cool test |
4573 |
cases |
4574 |
|
4575 |
2005-03-08 16:05 gezelter |
4576 |
|
4577 |
* forceFields/DUFF2.frc: Added a charge for Chlorine |
4578 |
|
4579 |
2005-03-07 17:39 tim |
4580 |
|
4581 |
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
4582 |
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
4583 |
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
4584 |
Fixing a bug in BitSet.cpp |
4585 |
|
4586 |
2005-03-04 10:28 gezelter |
4587 |
|
4588 |
* src/config.h.in: Cleaning up config.h.in by adding comments |
4589 |
|
4590 |
2005-03-04 10:28 gezelter |
4591 |
|
4592 |
* configure, ac-tools/configure.in, make/Makefile.in, |
4593 |
src/brains/SimCreator.cpp: SPRNG eradication project |
4594 |
|
4595 |
2005-03-03 09:40 tim |
4596 |
|
4597 |
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
4598 |
missing atom type problem) |
4599 |
|
4600 |
2005-03-02 11:29 tim |
4601 |
|
4602 |
* src/math/RandNumGen.hpp: adding base class of Random Number |
4603 |
generator |
4604 |
|
4605 |
2005-03-02 11:28 tim |
4606 |
|
4607 |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
4608 |
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
4609 |
Velocitizer is not initialized which causes a seg fault |
4610 |
|
4611 |
2005-03-02 10:36 tim |
4612 |
|
4613 |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
4614 |
integrators/Velocitizer.hpp, math/Makefile, |
4615 |
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
4616 |
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
4617 |
math/SeqRandNumGen.hpp: remove default parameter from |
4618 |
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
4619 |
random number generator |
4620 |
|
4621 |
2005-03-02 02:32 tim |
4622 |
|
4623 |
* test/math/testRandNumGen.cpp: Adding unit test for random number |
4624 |
generator |
4625 |
|
4626 |
2005-03-01 18:17 tim |
4627 |
|
4628 |
* src/brains/Thermo.hpp: fixed a file inclusion problem |
4629 |
|
4630 |
2005-03-01 18:17 tim |
4631 |
|
4632 |
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
4633 |
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
4634 |
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
4635 |
RandNumGenTestCase.hpp: fixed compilation problem |
4636 |
|
4637 |
2005-03-01 18:02 tim |
4638 |
|
4639 |
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
4640 |
integrators/Velocitizer.hpp, math/Makefile, |
4641 |
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
4642 |
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
4643 |
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
4644 |
|
4645 |
2005-03-01 18:00 tim |
4646 |
|
4647 |
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
4648 |
ParallelandNumGenTestCase.hpp: Change the name of test case |
4649 |
|
4650 |
2005-03-01 16:00 tim |
4651 |
|
4652 |
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
4653 |
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
4654 |
generator |
4655 |
|
4656 |
2005-03-01 15:10 tim |
4657 |
|
4658 |
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
4659 |
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
4660 |
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
4661 |
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
4662 |
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
4663 |
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
4664 |
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
4665 |
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
4666 |
|
4667 |
2005-03-01 14:11 tim |
4668 |
|
4669 |
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
4670 |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
4671 |
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
4672 |
OOPSERandNumGen |
4673 |
|
4674 |
2005-03-01 10:44 gezelter |
4675 |
|
4676 |
* make/Makefile.in: Fixed the damned build problem with the |
4677 |
libraries not being removed in make clean and make distclean (at |
4678 |
least we think it is fixed). |
4679 |
|
4680 |
2005-03-01 10:26 gezelter |
4681 |
|
4682 |
* src/math/MersenneTwister.hpp: Making small modifications to allow |
4683 |
for use on MPI machines |
4684 |
|
4685 |
2005-03-01 09:45 tim |
4686 |
|
4687 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
4688 |
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
4689 |
math/MersenneTwister.hpp: adding MersenneTwister random number |
4690 |
generator |
4691 |
|
4692 |
2005-02-28 22:55 tim |
4693 |
|
4694 |
* src/math/MersenneTwister.hpp: Adding a modified version of |
4695 |
MersenneTwister.hpp |
4696 |
|
4697 |
2005-02-28 12:24 tim |
4698 |
|
4699 |
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
4700 |
definition.jpg: selection expression |
4701 |
|
4702 |
2005-02-25 16:22 tim |
4703 |
|
4704 |
* src/: UseTheForce/DarkSide/LJ.F90, |
4705 |
UseTheForce/DarkSide/lj_interface.F90, |
4706 |
UseTheForce/DarkSide/lj_interface.h, |
4707 |
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
4708 |
types/AtomType.hpp: adding soft potential to LJ Module |
4709 |
|
4710 |
2005-02-25 11:38 tim |
4711 |
|
4712 |
* doc/SelectionExpression.html: adding documentation for selection |
4713 |
expression |
4714 |
|
4715 |
2005-02-24 15:55 tim |
4716 |
|
4717 |
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
4718 |
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
4719 |
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
4720 |
adding basic_teebuf which can operate on multiple stream |
4721 |
simutaneously. |
4722 |
|
4723 |
2005-02-22 14:26 chrisfen |
4724 |
|
4725 |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
4726 |
sample |
4727 |
|
4728 |
2005-02-22 13:56 tim |
4729 |
|
4730 |
* src/: UseTheForce/DarkSide/reactionField.F90, |
4731 |
primitives/RigidBody.cpp: reactionfield get fixed |
4732 |
|
4733 |
2005-02-21 11:57 tim |
4734 |
|
4735 |
* src/: applications/staticProps/GofRAngle.cpp, |
4736 |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
4737 |
a bug in GofRAngle |
4738 |
|
4739 |
2005-02-21 10:28 tim |
4740 |
|
4741 |
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
4742 |
|
4743 |
2005-02-21 10:22 tim |
4744 |
|
4745 |
* src/utils/next_combination.hpp: fix for compilation on the Sun |
4746 |
|
4747 |
2005-02-21 10:21 tim |
4748 |
|
4749 |
* src/utils/GenericData.hpp: fix problem in sun |
4750 |
|
4751 |
2005-02-18 18:07 tim |
4752 |
|
4753 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
4754 |
applications/dump2Xyz/Dump2XYZ.ggo, |
4755 |
applications/dump2Xyz/Dump2XYZCmd.c, |
4756 |
applications/dump2Xyz/Dump2XYZCmd.h, |
4757 |
applications/dynamicProps/RCorrFunc.cpp, |
4758 |
applications/staticProps/GofXyz.cpp, |
4759 |
applications/staticProps/GofXyz.hpp, |
4760 |
applications/staticProps/StaticProps.cpp, |
4761 |
applications/staticProps/StaticProps.ggo, |
4762 |
applications/staticProps/StaticPropsCmd.c, |
4763 |
applications/staticProps/StaticPropsCmd.h, |
4764 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
4765 |
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
4766 |
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
4767 |
|
4768 |
2005-02-18 10:58 gezelter |
4769 |
|
4770 |
* src/brains/Register.cpp: Corrected filename collision for EAM on |
4771 |
Mac OS X |
4772 |
|
4773 |
2005-02-18 10:58 gezelter |
4774 |
|
4775 |
* src/applications/oopse/oopse.cpp: Updated copyright information |
4776 |
|
4777 |
2005-02-18 10:58 gezelter |
4778 |
|
4779 |
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
4780 |
Makefile: corrected filename collision for EAM on operating systems |
4781 |
which are not case sensitive (aka Mac OS X) |
4782 |
|
4783 |
2005-02-17 15:15 tim |
4784 |
|
4785 |
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
4786 |
|
4787 |
2005-02-17 14:50 tim |
4788 |
|
4789 |
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
4790 |
in GofXyz |
4791 |
|
4792 |
2005-02-17 14:09 tim |
4793 |
|
4794 |
* src/applications/staticProps/RadialDistrFunc.hpp: make |
4795 |
processHistogram non-abstrct function |
4796 |
|
4797 |
2005-02-17 13:41 tim |
4798 |
|
4799 |
* src/applications/staticProps/GofXyz.cpp: [no log message] |
4800 |
|
4801 |
2005-02-17 13:30 tim |
4802 |
|
4803 |
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
4804 |
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
4805 |
finish GofXyz |
4806 |
|
4807 |
2005-02-17 11:21 tim |
4808 |
|
4809 |
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
4810 |
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
4811 |
distribution function |
4812 |
|
4813 |
2005-02-17 10:23 tim |
4814 |
|
4815 |
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
4816 |
|
4817 |
2005-02-17 10:18 tim |
4818 |
|
4819 |
* src/: brains/BlockSnapshotManager.cpp, |
4820 |
selection/DistanceFinder.cpp: The change of interface of BitSet |
4821 |
cause a bug in SelectionEvaluation |
4822 |
|
4823 |
2005-02-16 16:13 tim |
4824 |
|
4825 |
* src/utils/residentMem.c: return residentMem in byte |
4826 |
|
4827 |
2005-02-16 16:00 tim |
4828 |
|
4829 |
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
4830 |
a bug in writing out the value of cosang |
4831 |
|
4832 |
2005-02-16 15:43 tim |
4833 |
|
4834 |
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
4835 |
estimate avaliable memory |
4836 |
|
4837 |
2005-02-16 15:30 tim |
4838 |
|
4839 |
* src/: applications/staticProps/GofAngle2.cpp, |
4840 |
applications/staticProps/GofAngle2.hpp, |
4841 |
applications/staticProps/GofR.cpp, |
4842 |
applications/staticProps/GofR.hpp, |
4843 |
applications/staticProps/GofRAngle.cpp, |
4844 |
applications/staticProps/GofRAngle.hpp, |
4845 |
applications/staticProps/GofXyz.cpp, |
4846 |
applications/staticProps/GofXyz.hpp, |
4847 |
applications/staticProps/StaticProps.cpp, |
4848 |
applications/staticProps/StaticProps.ggo, |
4849 |
applications/staticProps/StaticPropsCmd.c, |
4850 |
applications/staticProps/StaticPropsCmd.h, |
4851 |
brains/BlockSnapshotManager.cpp: change the default bin number |
4852 |
|
4853 |
2005-02-16 14:36 tim |
4854 |
|
4855 |
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
4856 |
applications/dynamicProps/RCorrFunc.cpp, |
4857 |
applications/dynamicProps/TimeCorrFunc.cpp, |
4858 |
applications/dynamicProps/VCorrFunc.cpp, |
4859 |
applications/staticProps/GofAngle2.cpp, |
4860 |
applications/staticProps/GofR.cpp, |
4861 |
applications/staticProps/GofR.hpp, |
4862 |
applications/staticProps/GofRAngle.cpp, |
4863 |
applications/staticProps/GofRAngle.hpp, |
4864 |
applications/staticProps/RadialDistrFunc.cpp, |
4865 |
applications/staticProps/RadialDistrFunc.hpp, |
4866 |
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
4867 |
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
4868 |
files;fix the problem of counting in staticProps |
4869 |
|
4870 |
2005-02-15 14:39 tim |
4871 |
|
4872 |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
4873 |
BlockSnapshotManager |
4874 |
|
4875 |
2005-02-15 14:36 tim |
4876 |
|
4877 |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
4878 |
applications/staticProps/RadialDistrFunc.cpp, |
4879 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
4880 |
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
4881 |
reference counting now |
4882 |
|
4883 |
2005-02-15 12:49 tim |
4884 |
|
4885 |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
4886 |
replace std::make_pair by VariablesType::value_type to make Sun |
4887 |
Compiler happy |
4888 |
|
4889 |
2005-02-15 12:35 tim |
4890 |
|
4891 |
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
4892 |
TokenMap, using TokenMapType::value_type instead of std::make_pair |
4893 |
to make Sun compiler happy |
4894 |
|
4895 |
2005-02-15 12:24 tim |
4896 |
|
4897 |
* src/applications/staticProps/: GofRAngle.cpp, |
4898 |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
4899 |
|
4900 |
2005-02-15 12:11 tim |
4901 |
|
4902 |
* src/: applications/staticProps/GofR.cpp, |
4903 |
applications/staticProps/RadialDistrFunc.cpp, |
4904 |
applications/staticProps/RadialDistrFunc.hpp, |
4905 |
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
4906 |
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
4907 |
calculation problem when two selections intersect with each other |
4908 |
|
4909 |
2005-02-15 10:24 gezelter |
4910 |
|
4911 |
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
4912 |
xlc++ |
4913 |
|
4914 |
2005-02-15 10:17 gezelter |
4915 |
|
4916 |
* configure, ac-tools/configure.in, src/config.h.in, |
4917 |
src/utils/residentMem.c: [no log message] |
4918 |
|
4919 |
2005-02-15 01:17 gezelter |
4920 |
|
4921 |
* src/utils/residentMem.c: bug fix for null termination |
4922 |
|
4923 |
2005-02-15 01:11 gezelter |
4924 |
|
4925 |
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
4926 |
bugfixing residentMem |
4927 |
|
4928 |
2005-02-15 00:59 gezelter |
4929 |
|
4930 |
* configure, ac-tools/configure.in, src/config.h.in, |
4931 |
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
4932 |
|
4933 |
2005-02-15 00:08 gezelter |
4934 |
|
4935 |
* src/utils/Makefile.in: added residentMem |
4936 |
|
4937 |
2005-02-15 00:05 gezelter |
4938 |
|
4939 |
* configure, ac-tools/configure.in, make/Makefile.in, |
4940 |
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
4941 |
src/utils/residentMem.h: modifications to estimate memory in use by |
4942 |
other processes autoconf fixes ps syntax checking config.h file |
4943 |
cleaning |
4944 |
|
4945 |
2005-02-14 18:26 gezelter |
4946 |
|
4947 |
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
4948 |
|
4949 |
2005-02-14 18:16 gezelter |
4950 |
|
4951 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
4952 |
strangeness |
4953 |
|
4954 |
2005-02-14 14:42 tim |
4955 |
|
4956 |
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
4957 |
BlockSnapshotManager.hpp |
4958 |
|
4959 |
2005-02-14 13:51 tim |
4960 |
|
4961 |
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
4962 |
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
4963 |
length of first frame |
4964 |
|
4965 |
2005-02-14 13:12 tim |
4966 |
|
4967 |
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
4968 |
VelocityVerletIntegrator : last frame is written twice |
4969 |
|
4970 |
2005-02-14 12:57 tim |
4971 |
|
4972 |
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
4973 |
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
4974 |
primitives/StuntDouble.hpp: begin bug fix |
4975 |
|
4976 |
2005-02-14 12:35 tim |
4977 |
|
4978 |
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
4979 |
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
4980 |
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
4981 |
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
4982 |
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
4983 |
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
4984 |
VCorrFunc.hpp: refactory CorrelationFunction |
4985 |
|
4986 |
2005-02-14 10:18 gezelter |
4987 |
|
4988 |
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
4989 |
and start of switch for type of correlation function |
4990 |
|
4991 |
2005-02-13 16:18 tim |
4992 |
|
4993 |
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
4994 |
calculating bytes per stuntdouble |
4995 |
|
4996 |
2005-02-13 16:03 tim |
4997 |
|
4998 |
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
4999 |
|
5000 |
2005-02-13 15:57 tim |
5001 |
|
5002 |
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
5003 |
bug in CorrelationFunction |
5004 |
|
5005 |
2005-02-13 15:36 tim |
5006 |
|
5007 |
* src/: applications/staticProps/GofR.cpp, |
5008 |
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
5009 |
bug in SimInfo::getCutoff() |
5010 |
|
5011 |
2005-02-13 15:08 tim |
5012 |
|
5013 |
* make/Makefile.in: adding staticProps and dynamicProps into |
5014 |
Makefile.in |
5015 |
|
5016 |
2005-02-13 15:05 tim |
5017 |
|
5018 |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5019 |
applications/dynamicProps/CorrelationFunction.hpp, |
5020 |
applications/staticProps/StaticProps.cpp, |
5021 |
applications/staticProps/StaticProps.ggo, |
5022 |
applications/staticProps/StaticPropsCmd.c, |
5023 |
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
5024 |
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
5025 |
defaults to the cutoff radius |
5026 |
|
5027 |
2005-02-13 14:14 tim |
5028 |
|
5029 |
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
5030 |
|
5031 |
2005-02-13 14:10 tim |
5032 |
|
5033 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5034 |
applications/dynamicProps/CorrelationFunction.cpp, |
5035 |
applications/dynamicProps/CorrelationFunction.hpp, |
5036 |
applications/dynamicProps/DynamicProps.cpp, |
5037 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5038 |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
5039 |
integrators/VelocityVerletIntegrator.cpp, |
5040 |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
5041 |
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
5042 |
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
5043 |
visitors/OtherVisitor.cpp: dynamicProps get built |
5044 |
|
5045 |
2005-02-13 10:56 tim |
5046 |
|
5047 |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5048 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5049 |
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
5050 |
progress |
5051 |
|
5052 |
2005-02-13 03:04 tim |
5053 |
|
5054 |
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
5055 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5056 |
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
5057 |
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
5058 |
work in dynamicProps |
5059 |
|
5060 |
2005-02-13 02:25 tim |
5061 |
|
5062 |
* src/applications/dynamicProps/DynamicProps.cpp: adding |
5063 |
dynamicProps |
5064 |
|
5065 |
2005-02-13 02:14 tim |
5066 |
|
5067 |
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
5068 |
DynamicPropsCmd.h: adding command line option to DynamicProps |
5069 |
|
5070 |
2005-02-13 02:13 tim |
5071 |
|
5072 |
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
5073 |
adding command line option for DynamicProps |
5074 |
|
5075 |
2005-02-13 01:57 tim |
5076 |
|
5077 |
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
5078 |
applications/dynamicProps/CorrelationFunction.hpp, |
5079 |
applications/dynamicProps/DipoleCorrFunc.cpp, |
5080 |
applications/dynamicProps/DipoleCorrFunc.hpp, |
5081 |
applications/dynamicProps/RCorrFunc.cpp, |
5082 |
applications/dynamicProps/RCorrFunc.hpp, |
5083 |
applications/dynamicProps/VCorrFunc.cpp, |
5084 |
applications/dynamicProps/VCorrFunc.hpp, |
5085 |
applications/staticProps/RadialDistrFunc.cpp, |
5086 |
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
5087 |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
5088 |
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
5089 |
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
5090 |
dynamicProps |
5091 |
|
5092 |
2005-02-12 15:09 tim |
5093 |
|
5094 |
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
5095 |
|
5096 |
2005-02-11 17:41 tim |
5097 |
|
5098 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
5099 |
more constructor to Snapshot to create customized DataStorage |
5100 |
|
5101 |
2005-02-11 17:39 tim |
5102 |
|
5103 |
* src/selection/: DistanceFinder.hpp, Makefile, |
5104 |
SelectionManager.hpp: adding beginSelected, nextSelected method to |
5105 |
SelectionManager |
5106 |
|
5107 |
2005-02-11 17:36 tim |
5108 |
|
5109 |
* src/config.h.in, configure: adding support for physmem |
5110 |
|
5111 |
2005-02-11 17:35 tim |
5112 |
|
5113 |
* ac-tools/configure.in: adding supprot for physmem |
5114 |
|
5115 |
2005-02-11 17:35 tim |
5116 |
|
5117 |
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
5118 |
physmem |
5119 |
|
5120 |
2005-02-10 17:37 tim |
5121 |
|
5122 |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
5123 |
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
5124 |
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
5125 |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
5126 |
StaticPropsCmd.h: more work in StaticProps |
5127 |
|
5128 |
2005-02-10 13:14 tim |
5129 |
|
5130 |
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
5131 |
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
5132 |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
5133 |
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
5134 |
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
5135 |
StaticPropsCmd.h: change the filenames |
5136 |
|
5137 |
2005-02-10 09:15 tim |
5138 |
|
5139 |
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
5140 |
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
5141 |
RadialDistrFunc.hpp: adding GofRAngle |
5142 |
|
5143 |
2005-02-09 13:21 tim |
5144 |
|
5145 |
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
5146 |
useless files |
5147 |
|
5148 |
2005-02-09 13:12 tim |
5149 |
|
5150 |
* src/applications/staticProps/: GofR.cpp, Makefile, |
5151 |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
5152 |
|
5153 |
2005-02-09 12:08 tim |
5154 |
|
5155 |
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
5156 |
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
5157 |
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
5158 |
|
5159 |
2005-02-07 17:39 tim |
5160 |
|
5161 |
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
5162 |
Molecule class |
5163 |
|
5164 |
2005-02-07 17:38 tim |
5165 |
|
5166 |
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
5167 |
|
5168 |
2005-02-07 17:36 tim |
5169 |
|
5170 |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5171 |
SelectionCompiler.cpp: support select internal index selection, for |
5172 |
example, select DMPC.3 |
5173 |
|
5174 |
2005-02-07 16:11 tim |
5175 |
|
5176 |
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
5177 |
help info for Dump2XYZ |
5178 |
|
5179 |
2005-02-07 15:39 chrisfen |
5180 |
|
5181 |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
5182 |
selection librarys added |
5183 |
|
5184 |
2005-02-07 15:31 tim |
5185 |
|
5186 |
* src/selection/Makefile, make/Makefile.in: adding Makefile |
5187 |
|
5188 |
2005-02-07 15:20 chrisfen |
5189 |
|
5190 |
* src/utils/wildcards.hpp: issue commented out in wildcards |
5191 |
|
5192 |
2005-02-07 15:06 tim |
5193 |
|
5194 |
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
5195 |
which cause reevaluate return NULL |
5196 |
|
5197 |
2005-02-07 14:14 tim |
5198 |
|
5199 |
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
5200 |
SimSnapshotManager.hpp: fix a bug in determing the global index for |
5201 |
rigidbodies |
5202 |
|
5203 |
2005-02-07 14:13 tim |
5204 |
|
5205 |
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
5206 |
in Bitset |
5207 |
|
5208 |
2005-02-07 14:13 tim |
5209 |
|
5210 |
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
5211 |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5212 |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
5213 |
TokenMap.cpp: selection library is working |
5214 |
|
5215 |
2005-02-04 17:46 tim |
5216 |
|
5217 |
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
5218 |
|
5219 |
2005-02-04 17:45 tim |
5220 |
|
5221 |
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
5222 |
and XYZVisitor now use selection library |
5223 |
|
5224 |
2005-02-04 17:44 tim |
5225 |
|
5226 |
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
5227 |
adding SelectionManager into SimInfo |
5228 |
|
5229 |
2005-02-04 17:43 tim |
5230 |
|
5231 |
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
5232 |
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
5233 |
selection library |
5234 |
|
5235 |
2005-02-04 17:42 tim |
5236 |
|
5237 |
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
5238 |
in BitSet |
5239 |
|
5240 |
2005-02-04 17:41 tim |
5241 |
|
5242 |
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
5243 |
implementation |
5244 |
|
5245 |
2005-02-04 17:39 tim |
5246 |
|
5247 |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5248 |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5249 |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
5250 |
SelectionManager.hpp, Token.hpp: half of the selection utility is |
5251 |
working need to debug within keyword and atomproperty keyword |
5252 |
|
5253 |
2005-02-04 00:42 tim |
5254 |
|
5255 |
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
5256 |
get built |
5257 |
|
5258 |
2005-02-04 00:42 tim |
5259 |
|
5260 |
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
5261 |
|
5262 |
2005-02-04 00:26 tim |
5263 |
|
5264 |
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
5265 |
remove some useless files |
5266 |
|
5267 |
2005-02-03 23:57 tim |
5268 |
|
5269 |
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
5270 |
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
5271 |
adding wildcard class; NameFinder is finished |
5272 |
|
5273 |
2005-02-03 18:14 tim |
5274 |
|
5275 |
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
5276 |
SelectionCompiler.cpp, SelectionCompiler.hpp, |
5277 |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
5278 |
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
5279 |
selection library |
5280 |
|
5281 |
2005-02-03 09:04 tim |
5282 |
|
5283 |
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
5284 |
selection in progress |
5285 |
|
5286 |
2005-02-02 18:13 tim |
5287 |
|
5288 |
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
5289 |
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
5290 |
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
5291 |
progress, except SelectionEvaluator, other files are compiled |
5292 |
|
5293 |
2005-02-02 18:12 tim |
5294 |
|
5295 |
* src/utils/: Makefile.in, any.hpp: adding boost::any |
5296 |
|
5297 |
2005-02-02 07:51 tim |
5298 |
|
5299 |
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
5300 |
|
5301 |
2005-02-01 17:49 tim |
5302 |
|
5303 |
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
5304 |
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
5305 |
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
5306 |
selection/Token.hpp: Selection in progress |
5307 |
|
5308 |
2005-02-01 01:55 tim |
5309 |
|
5310 |
* src/: selection/SelectionCompiler.hpp, |
5311 |
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
5312 |
selection/SelectionManager.hpp, selection/Token.hpp, |
5313 |
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
5314 |
|
5315 |
2005-01-26 10:26 tim |
5316 |
|
5317 |
* src/integrators/: Integrator.cpp, Integrator.hpp, |
5318 |
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
5319 |
to add eorWriter |
5320 |
|
5321 |
2005-01-26 10:15 tim |
5322 |
|
5323 |
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
5324 |
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
5325 |
wrong column of electroframe |
5326 |
|
5327 |
2005-01-25 16:59 tim |
5328 |
|
5329 |
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
5330 |
SimInfo, use number of cutoff stamp as counter to loop over |
5331 |
rigidbody stamp |
5332 |
|
5333 |
2005-01-25 12:45 tim |
5334 |
|
5335 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
5336 |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
5337 |
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
5338 |
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
5339 |
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
5340 |
io/EAMAtomTypesSectionParser.cpp, |
5341 |
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
5342 |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
5343 |
io/StickyAtomTypesSectionParser.cpp, |
5344 |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
5345 |
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
5346 |
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
5347 |
primitives/GhostTorsion.hpp, primitives/Makefile, |
5348 |
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
5349 |
section parser's error message (2) add GhostTorsion (3) accumulate |
5350 |
inertial tensor from the directional atoms before calculate |
5351 |
rigidbody's inertial tensor |
5352 |
|
5353 |
2005-01-17 17:17 tim |
5354 |
|
5355 |
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
5356 |
|
5357 |
2005-01-17 11:58 tim |
5358 |
|
5359 |
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
5360 |
system parameters |
5361 |
|
5362 |
2005-01-17 11:05 tim |
5363 |
|
5364 |
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
5365 |
|
5366 |
2005-01-14 17:02 tim |
5367 |
|
5368 |
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
5369 |
|
5370 |
2005-01-14 16:37 tim |
5371 |
|
5372 |
* forceFields/Makefile: sync Makefile |
5373 |
|
5374 |
2005-01-14 16:13 gezelter |
5375 |
|
5376 |
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
5377 |
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
5378 |
src/applications/dump2Xyz/Makefile, |
5379 |
src/applications/oopse/Makefile, |
5380 |
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
5381 |
src/constraints/Makefile, src/integrators/Makefile, |
5382 |
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
5383 |
src/primitives/Makefile, src/profiling/Makefile, |
5384 |
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
5385 |
src/visitors/Makefile: moved Package variable into subdirectory |
5386 |
makefiles to speed up the building process |
5387 |
|
5388 |
2005-01-14 15:48 gezelter |
5389 |
|
5390 |
* src/applications/oopse/oopse.cpp: Fixed publication details in |
5391 |
banner |
5392 |
|
5393 |
2005-01-14 15:48 gezelter |
5394 |
|
5395 |
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
5396 |
simParallel_interface.h: added dummy subroutine to avoid empty |
5397 |
unit, synchronized this dummy routine between C and fortran |
5398 |
|
5399 |
2005-01-14 15:31 gezelter |
5400 |
|
5401 |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
5402 |
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
5403 |
DarkSide/Makefile, DarkSide/atype.F90, |
5404 |
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
5405 |
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
5406 |
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
5407 |
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
5408 |
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
5409 |
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
5410 |
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
5411 |
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
5412 |
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
5413 |
modules and C/Fortran interface subroutines |
5414 |
|
5415 |
2005-01-14 15:15 gezelter |
5416 |
|
5417 |
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
5418 |
|
5419 |
2005-01-14 15:09 gezelter |
5420 |
|
5421 |
* configure, ac-tools/configure.in, src/config.h.in, |
5422 |
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
5423 |
|
5424 |
2005-01-14 11:49 tim |
5425 |
|
5426 |
* src/: io/EAMAtomTypesSectionParser.cpp, |
5427 |
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
5428 |
utils/StringUtils.hpp: using c library to do conversion instead of |
5429 |
using iostream due to a bug in libstdc++(GCC 3.2) |
5430 |
|
5431 |
2005-01-13 21:40 tim |
5432 |
|
5433 |
* src/brains/SimSetup.cpp: no message |
5434 |
|
5435 |
2005-01-13 20:56 tim |
5436 |
|
5437 |
* src/primitives/Molecule.hpp: fix a bug in global index |
5438 |
|
5439 |
2005-01-13 20:04 tim |
5440 |
|
5441 |
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
5442 |
Integrator.hpp in Minimizer |
5443 |
|
5444 |
2005-01-13 17:14 gezelter |
5445 |
|
5446 |
* src/utils/Makefile: compile getopt and getopt1 if we need to |
5447 |
|
5448 |
2005-01-13 16:56 gezelter |
5449 |
|
5450 |
* make/Makefile.in: template flags |
5451 |
|
5452 |
2005-01-13 16:48 gezelter |
5453 |
|
5454 |
* src/applications/oopse/Makefile: formatting |
5455 |
|
5456 |
2005-01-13 16:48 gezelter |
5457 |
|
5458 |
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
5459 |
target |
5460 |
|
5461 |
2005-01-13 14:40 tim |
5462 |
|
5463 |
* src/: UseTheForce/fSwitchingFunction.h, |
5464 |
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
5465 |
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
5466 |
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
5467 |
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
5468 |
|
5469 |
2005-01-13 13:26 tim |
5470 |
|
5471 |
* make/Makefile.in: change the order of linking (object file comes |
5472 |
first and then follow by user built library) |
5473 |
|
5474 |
2005-01-12 18:24 tim |
5475 |
|
5476 |
* src/io/DumpWriter.cpp: remove useless debug info |
5477 |
|
5478 |
2005-01-12 18:21 tim |
5479 |
|
5480 |
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
5481 |
|
5482 |
2005-01-12 18:17 tim |
5483 |
|
5484 |
* make/: Makefile.in, Makefile.in: missing tab |
5485 |
|
5486 |
2005-01-12 18:15 tim |
5487 |
|
5488 |
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
5489 |
get fixed |
5490 |
|
5491 |
2005-01-12 17:40 gezelter |
5492 |
|
5493 |
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
5494 |
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
5495 |
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
5496 |
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
5497 |
src/UseTheForce/ForceFieldCreator.hpp, |
5498 |
src/UseTheForce/ForceFieldFactory.cpp, |
5499 |
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
5500 |
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
5501 |
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
5502 |
src/UseTheForce/fSwitchingFunction.h, |
5503 |
src/UseTheForce/mpiComponentPlan.h, |
5504 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
5505 |
src/UseTheForce/notifyCutoffs.F90, |
5506 |
src/UseTheForce/notifyCutoffs_interface.h, |
5507 |
src/UseTheForce/DarkSide/LJ.F90, |
5508 |
src/UseTheForce/DarkSide/atype.F90, |
5509 |
src/UseTheForce/DarkSide/atype_interface.h, |
5510 |
src/UseTheForce/DarkSide/charge.F90, |
5511 |
src/UseTheForce/DarkSide/charge_interface.h, |
5512 |
src/UseTheForce/DarkSide/dipole.F90, |
5513 |
src/UseTheForce/DarkSide/dipole_interface.h, |
5514 |
src/UseTheForce/DarkSide/eam.F90, |
5515 |
src/UseTheForce/DarkSide/eam_interface.h, |
5516 |
src/UseTheForce/DarkSide/force_globals.F90, |
5517 |
src/UseTheForce/DarkSide/gb.F90, |
5518 |
src/UseTheForce/DarkSide/gb_interface.h, |
5519 |
src/UseTheForce/DarkSide/lj_interface.h, |
5520 |
src/UseTheForce/DarkSide/neighborLists.F90, |
5521 |
src/UseTheForce/DarkSide/reactionField.F90, |
5522 |
src/UseTheForce/DarkSide/shapes.F90, |
5523 |
src/UseTheForce/DarkSide/shapes_interface.h, |
5524 |
src/UseTheForce/DarkSide/simParallel.F90, |
5525 |
src/UseTheForce/DarkSide/simParallel_interface.h, |
5526 |
src/UseTheForce/DarkSide/simulation.F90, |
5527 |
src/UseTheForce/DarkSide/simulation_interface.h, |
5528 |
src/UseTheForce/DarkSide/sticky.F90, |
5529 |
src/UseTheForce/DarkSide/sticky_interface.h, |
5530 |
src/UseTheForce/DarkSide/switcheroo.F90, |
5531 |
src/applications/Makedepend, src/applications/quickLate.c, |
5532 |
src/applications/dump2Xyz/Dump2XYZ.cpp, |
5533 |
src/applications/oopse/oopse.cpp, |
5534 |
src/applications/simpleBuilder/BaseLattice.cpp, |
5535 |
src/applications/simpleBuilder/BaseLattice.hpp, |
5536 |
src/applications/simpleBuilder/Lattice.cpp, |
5537 |
src/applications/simpleBuilder/Lattice.hpp, |
5538 |
src/applications/simpleBuilder/LatticeCreator.cpp, |
5539 |
src/applications/simpleBuilder/LatticeCreator.hpp, |
5540 |
src/applications/simpleBuilder/LatticeFactory.cpp, |
5541 |
src/applications/simpleBuilder/LatticeFactory.hpp, |
5542 |
src/applications/simpleBuilder/MoLocator.cpp, |
5543 |
src/applications/simpleBuilder/MoLocator.hpp, |
5544 |
src/applications/simpleBuilder/simpleBuilder.cpp, |
5545 |
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
5546 |
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
5547 |
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
5548 |
src/brains/Makefile, src/brains/Migrator.hpp, |
5549 |
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
5550 |
src/brains/Register.cpp, src/brains/Register.hpp, |
5551 |
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
5552 |
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
5553 |
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
5554 |
src/brains/SimSnapshotManager.cpp, |
5555 |
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
5556 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
5557 |
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
5558 |
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
5559 |
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
5560 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
5561 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
5562 |
src/constraints/AbstractClasses.hpp, |
5563 |
src/constraints/ConstraintElem.hpp, |
5564 |
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
5565 |
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
5566 |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
5567 |
src/constraints/ZconsStruct.hpp, |
5568 |
src/constraints/ZconstraintForceManager.cpp, |
5569 |
src/constraints/ZconstraintForceManager.hpp, |
5570 |
src/integrators/AbstractClasses.hpp, |
5571 |
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
5572 |
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
5573 |
src/integrators/Integrator.hpp, |
5574 |
src/integrators/IntegratorCreator.hpp, |
5575 |
src/integrators/IntegratorFactory.cpp, |
5576 |
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
5577 |
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
5578 |
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
5579 |
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
5580 |
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
5581 |
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
5582 |
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
5583 |
src/integrators/RotationAlgorithm.hpp, |
5584 |
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
5585 |
src/integrators/VelocityVerletIntegrator.cpp, |
5586 |
src/integrators/VelocityVerletIntegrator.hpp, |
5587 |
src/io/AtomTypesSectionParser.cpp, |
5588 |
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
5589 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
5590 |
src/io/BendTypesSectionParser.cpp, |
5591 |
src/io/BendTypesSectionParser.hpp, |
5592 |
src/io/BondTypesSectionParser.cpp, |
5593 |
src/io/BondTypesSectionParser.hpp, |
5594 |
src/io/DirectionalAtomTypesSectionParser.cpp, |
5595 |
src/io/DirectionalAtomTypesSectionParser.hpp, |
5596 |
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
5597 |
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
5598 |
src/io/EAMAtomTypesSectionParser.cpp, |
5599 |
src/io/EAMAtomTypesSectionParser.hpp, |
5600 |
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
5601 |
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
5602 |
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
5603 |
src/io/LennardJonesAtomTypesSectionParser.cpp, |
5604 |
src/io/LennardJonesAtomTypesSectionParser.hpp, |
5605 |
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
5606 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
5607 |
src/io/Makefile, src/io/SectionParser.cpp, |
5608 |
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
5609 |
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
5610 |
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
5611 |
src/io/StickyAtomTypesSectionParser.hpp, |
5612 |
src/io/TorsionTypesSectionParser.cpp, |
5613 |
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
5614 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
5615 |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
5616 |
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
5617 |
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
5618 |
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
5619 |
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
5620 |
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
5621 |
src/math/MatVec3.h, src/math/Polynomial.hpp, |
5622 |
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
5623 |
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
5624 |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
5625 |
src/math/Vector.hpp, src/math/Vector3.hpp, |
5626 |
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
5627 |
src/minimizers/CGFamilyMinimizer.cpp, |
5628 |
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
5629 |
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
5630 |
src/minimizers/MinimizerCreator.hpp, |
5631 |
src/minimizers/MinimizerFactory.cpp, |
5632 |
src/minimizers/MinimizerFactory.hpp, |
5633 |
src/minimizers/MinimizerParameterSet.cpp, |
5634 |
src/minimizers/MinimizerParameterSet.hpp, |
5635 |
src/minimizers/OOPSEMinimizer.cpp, |
5636 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
5637 |
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
5638 |
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
5639 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
5640 |
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
5641 |
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
5642 |
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
5643 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
5644 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
5645 |
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
5646 |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
5647 |
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
5648 |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
5649 |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
5650 |
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
5651 |
src/primitives/UreyBradleyBend.cpp, |
5652 |
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
5653 |
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
5654 |
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
5655 |
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
5656 |
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
5657 |
src/types/BendType.hpp, src/types/BondStamp.cpp, |
5658 |
src/types/BondStamp.hpp, src/types/BondType.hpp, |
5659 |
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
5660 |
src/types/Component.cpp, src/types/Component.hpp, |
5661 |
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
5662 |
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
5663 |
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
5664 |
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
5665 |
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
5666 |
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
5667 |
src/types/Makefile, src/types/MoleculeStamp.cpp, |
5668 |
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
5669 |
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
5670 |
src/types/PolynomialBondType.hpp, |
5671 |
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
5672 |
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
5673 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
5674 |
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
5675 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
5676 |
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
5677 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
5678 |
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
5679 |
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
5680 |
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
5681 |
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
5682 |
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
5683 |
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
5684 |
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
5685 |
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
5686 |
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
5687 |
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
5688 |
src/utils/Utility.cpp, src/utils/Utility.hpp, |
5689 |
src/utils/definitions.F90, src/utils/fError.c, |
5690 |
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
5691 |
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
5692 |
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
5693 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
5694 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
5695 |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
5696 |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
5697 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
5698 |
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
5699 |
OOPSE-2.0 |
5700 |
|
5701 |
2005-01-12 13:13 tim |
5702 |
|
5703 |
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
5704 |
utils/TypeContainer.hpp: forget to include <algorithm> |
5705 |
|
5706 |
2005-01-12 12:25 tim |
5707 |
|
5708 |
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
5709 |
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
5710 |
fields |
5711 |
|
5712 |
2005-01-12 12:14 tim |
5713 |
|
5714 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
5715 |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
5716 |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
5717 |
UseTheForce/ForceFieldCreator.hpp, |
5718 |
UseTheForce/ForceFieldFactory.cpp, |
5719 |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
5720 |
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
5721 |
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
5722 |
UseTheForce/notifyCutoffs.F90, |
5723 |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
5724 |
UseTheForce/DarkSide/atype.F90, |
5725 |
UseTheForce/DarkSide/atype_interface.h, |
5726 |
UseTheForce/DarkSide/charge.F90, |
5727 |
UseTheForce/DarkSide/charge_interface.h, |
5728 |
UseTheForce/DarkSide/dipole.F90, |
5729 |
UseTheForce/DarkSide/dipole_interface.h, |
5730 |
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
5731 |
UseTheForce/DarkSide/force_globals.F90, |
5732 |
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
5733 |
UseTheForce/DarkSide/lj_interface.h, |
5734 |
UseTheForce/DarkSide/neighborLists.F90, |
5735 |
UseTheForce/DarkSide/reactionField.F90, |
5736 |
UseTheForce/DarkSide/shapes.F90, |
5737 |
UseTheForce/DarkSide/shapes_interface.h, |
5738 |
UseTheForce/DarkSide/simParallel.F90, |
5739 |
UseTheForce/DarkSide/simParallel_interface.h, |
5740 |
UseTheForce/DarkSide/simulation.F90, |
5741 |
UseTheForce/DarkSide/simulation_interface.h, |
5742 |
UseTheForce/DarkSide/sticky.F90, |
5743 |
UseTheForce/DarkSide/sticky_interface.h, |
5744 |
UseTheForce/DarkSide/switcheroo.F90, |
5745 |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
5746 |
applications/simpleBuilder/BaseLattice.cpp, |
5747 |
applications/simpleBuilder/BaseLattice.hpp, |
5748 |
applications/simpleBuilder/Lattice.cpp, |
5749 |
applications/simpleBuilder/Lattice.hpp, |
5750 |
applications/simpleBuilder/LatticeCreator.cpp, |
5751 |
applications/simpleBuilder/LatticeCreator.hpp, |
5752 |
applications/simpleBuilder/LatticeFactory.cpp, |
5753 |
applications/simpleBuilder/LatticeFactory.hpp, |
5754 |
applications/simpleBuilder/MoLocator.cpp, |
5755 |
applications/simpleBuilder/MoLocator.hpp, |
5756 |
applications/simpleBuilder/simpleBuilder.cpp, |
5757 |
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
5758 |
brains/Exclude.hpp, brains/ForceManager.cpp, |
5759 |
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
5760 |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
5761 |
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
5762 |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
5763 |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
5764 |
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
5765 |
brains/Snapshot.cpp, brains/Snapshot.hpp, |
5766 |
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
5767 |
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
5768 |
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
5769 |
constraints/Rattle.cpp, constraints/Rattle.hpp, |
5770 |
constraints/ZconsStruct.hpp, |
5771 |
constraints/ZconstraintForceManager.cpp, |
5772 |
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
5773 |
integrators/DLM.hpp, integrators/Integrator.cpp, |
5774 |
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
5775 |
integrators/IntegratorFactory.cpp, |
5776 |
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
5777 |
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
5778 |
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
5779 |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
5780 |
integrators/NVT.cpp, integrators/NVT.hpp, |
5781 |
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
5782 |
integrators/Velocitizer.hpp, |
5783 |
integrators/VelocityVerletIntegrator.cpp, |
5784 |
integrators/VelocityVerletIntegrator.hpp, |
5785 |
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
5786 |
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
5787 |
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
5788 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
5789 |
io/BondTypesSectionParser.hpp, |
5790 |
io/DirectionalAtomTypesSectionParser.cpp, |
5791 |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
5792 |
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
5793 |
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
5794 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
5795 |
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
5796 |
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
5797 |
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
5798 |
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
5799 |
io/SectionParser.cpp, io/SectionParser.hpp, |
5800 |
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
5801 |
io/StatWriter.cpp, io/StatWriter.hpp, |
5802 |
io/StickyAtomTypesSectionParser.cpp, |
5803 |
io/StickyAtomTypesSectionParser.hpp, |
5804 |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
5805 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
5806 |
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
5807 |
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
5808 |
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
5809 |
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
5810 |
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
5811 |
math/Polynomial.hpp, math/Quaternion.hpp, |
5812 |
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
5813 |
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
5814 |
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
5815 |
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
5816 |
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
5817 |
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
5818 |
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
5819 |
minimizers/MinimizerParameterSet.cpp, |
5820 |
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
5821 |
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
5822 |
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
5823 |
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
5824 |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
5825 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
5826 |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
5827 |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
5828 |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
5829 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
5830 |
primitives/Torsion.cpp, primitives/Torsion.hpp, |
5831 |
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
5832 |
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
5833 |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
5834 |
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
5835 |
types/AtomType.hpp, types/AtomTypeProperties.h, |
5836 |
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
5837 |
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
5838 |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
5839 |
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
5840 |
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
5841 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
5842 |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
5843 |
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
5844 |
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
5845 |
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
5846 |
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
5847 |
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
5848 |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
5849 |
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
5850 |
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
5851 |
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
5852 |
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
5853 |
types/TorsionStamp.hpp, types/TorsionType.hpp, |
5854 |
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
5855 |
types/ZconStamp.hpp, utils/GenericData.hpp, |
5856 |
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
5857 |
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
5858 |
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
5859 |
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
5860 |
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
5861 |
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
5862 |
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
5863 |
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
5864 |
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
5865 |
utils/simError.c, utils/simError.h, utils/status.F90, |
5866 |
utils/vector_class.F90, visitors/AtomData.hpp, |
5867 |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
5868 |
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
5869 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
5870 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5871 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
5872 |
visitors/ZconsVisitor.hpp: change license |
5873 |
|
5874 |
2005-01-12 12:14 tim |
5875 |
|
5876 |
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
5877 |
branch new_design. |
5878 |
|
5879 |
2005-01-11 16:03 tim |
5880 |
|
5881 |
* src/: constraints/ZconstraintForceManager.cpp, |
5882 |
constraints/ZconstraintForceManager.hpp, |
5883 |
minimizers/MinimizerParameterSet.cpp, |
5884 |
minimizers/MinimizerParameterSet.hpp: change const static double |
5885 |
data member to const double |
5886 |
|
5887 |
2005-01-11 15:50 tim |
5888 |
|
5889 |
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
5890 |
|
5891 |
2005-01-11 15:39 tim |
5892 |
|
5893 |
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
5894 |
change data type from logical to integer in AtomTypeProperties.h |
5895 |
|
5896 |
2005-01-11 11:36 tim |
5897 |
|
5898 |
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
5899 |
new format of EAM force field |
5900 |
|
5901 |
2005-01-11 11:24 tim |
5902 |
|
5903 |
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
5904 |
to DUFF2.frc |
5905 |
|
5906 |
2005-01-11 11:23 tim |
5907 |
|
5908 |
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
5909 |
DUFF2.frc |
5910 |
|
5911 |
2005-01-11 11:09 tim |
5912 |
|
5913 |
* make/Makefile.in: adding constraints and minimizers into |
5914 |
Makefile.in |
5915 |
|
5916 |
2005-01-11 11:03 tim |
5917 |
|
5918 |
* src/io/: ChargeAtomTypesSectionParser.cpp, |
5919 |
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
5920 |
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
5921 |
files |
5922 |
|
5923 |
2005-01-11 10:59 tim |
5924 |
|
5925 |
* src/io/ZConsWriter.cpp: [no log message] |
5926 |
|
5927 |
2005-01-11 10:53 tim |
5928 |
|
5929 |
* src/UseTheForce/EAM.cpp: minor fix |
5930 |
|
5931 |
2005-01-11 10:52 tim |
5932 |
|
5933 |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
5934 |
on branch new_design. |
5935 |
|
5936 |
2005-01-11 10:52 tim |
5937 |
|
5938 |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
5939 |
on branch new_design. |
5940 |
|
5941 |
2005-01-11 10:52 tim |
5942 |
|
5943 |
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
5944 |
|
5945 |
2005-01-11 10:47 tim |
5946 |
|
5947 |
* make/Makefile.in: forget a '$' sign |
5948 |
|
5949 |
2005-01-11 10:46 tim |
5950 |
|
5951 |
* make/Makefile.in: missing tab in rules |
5952 |
|
5953 |
2005-01-10 17:04 tim |
5954 |
|
5955 |
* src/: UseTheForce/ForceFieldCreator.cpp, |
5956 |
UseTheForce/ForceFieldCreator.hpp, |
5957 |
UseTheForce/ForceFieldFactory.cpp, |
5958 |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
5959 |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
5960 |
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
5961 |
brains/Register.cpp, brains/Register.hpp, |
5962 |
integrators/IntegratorCreator.cpp, |
5963 |
integrators/IntegratorCreator.hpp, |
5964 |
integrators/IntegratorFactory.cpp, |
5965 |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
5966 |
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
5967 |
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
5968 |
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
5969 |
minimizers/MinimizerFactory.hpp: create a register module to |
5970 |
register force fields, integrators and minimizers |
5971 |
|
5972 |
2005-01-10 17:04 tim |
5973 |
|
5974 |
* src/brains/Register.cpp: file Register.cpp was initially added on |
5975 |
branch new_design. |
5976 |
|
5977 |
2005-01-10 17:04 tim |
5978 |
|
5979 |
* src/brains/Register.hpp: file Register.hpp was initially added on |
5980 |
branch new_design. |
5981 |
|
5982 |
2005-01-10 15:52 tim |
5983 |
|
5984 |
* src/: UseTheForce/ForceFieldFactory.cpp, |
5985 |
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
5986 |
constraints/ZconstraintForceManager.cpp, |
5987 |
constraints/ZconstraintForceManager.hpp, |
5988 |
integrators/IntegratorFactory.cpp, |
5989 |
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
5990 |
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
5991 |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
5992 |
method is working now |
5993 |
|
5994 |
2005-01-10 13:05 tim |
5995 |
|
5996 |
* src/: constraints/ConstraintElem.hpp, |
5997 |
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
5998 |
constraints/ZconstraintForceManager.cpp, |
5999 |
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
6000 |
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
6001 |
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
6002 |
zconstraint |
6003 |
|
6004 |
2005-01-10 13:05 tim |
6005 |
|
6006 |
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
6007 |
initially added on branch new_design. |
6008 |
|
6009 |
2005-01-07 16:50 tim |
6010 |
|
6011 |
* src/constraints/ZconstraintForceManager.cpp: file |
6012 |
ZconstraintForceManager.cpp was initially added on branch |
6013 |
new_design. |
6014 |
|
6015 |
2005-01-07 16:50 tim |
6016 |
|
6017 |
* src/constraints/ZconstraintForceManager.hpp: file |
6018 |
ZconstraintForceManager.hpp was initially added on branch |
6019 |
new_design. |
6020 |
|
6021 |
2005-01-07 16:50 tim |
6022 |
|
6023 |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
6024 |
applications/simpleBuilder/Lattice.hpp, |
6025 |
applications/simpleBuilder/LatticeCreator.hpp, |
6026 |
applications/simpleBuilder/LatticeFactory.hpp, |
6027 |
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
6028 |
constraints/ConstraintElem.hpp, constraints/Makefile, |
6029 |
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
6030 |
constraints/ZconstraintForceManager.cpp, |
6031 |
constraints/ZconstraintForceManager.hpp, |
6032 |
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
6033 |
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
6034 |
|
6035 |
2005-01-07 16:50 tim |
6036 |
|
6037 |
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
6038 |
initially added on branch new_design. |
6039 |
|
6040 |
2005-01-06 17:31 tim |
6041 |
|
6042 |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6043 |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6044 |
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
6045 |
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
6046 |
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
6047 |
constraint is almost working |
6048 |
|
6049 |
2005-01-05 19:36 tim |
6050 |
|
6051 |
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
6052 |
working |
6053 |
|
6054 |
2005-01-05 19:16 tim |
6055 |
|
6056 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
6057 |
applications/oopse/oopse.cpp, |
6058 |
applications/simpleBuilder/BaseLattice.cpp, |
6059 |
applications/simpleBuilder/Lattice.cpp, |
6060 |
applications/simpleBuilder/LatticeFactory.cpp, |
6061 |
applications/simpleBuilder/LatticeFactory.hpp, |
6062 |
applications/simpleBuilder/MoLocator.cpp, |
6063 |
applications/simpleBuilder/MoLocator.hpp, |
6064 |
applications/simpleBuilder/simpleBuilder.cpp, |
6065 |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
6066 |
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
6067 |
in progress |
6068 |
|
6069 |
2005-01-05 12:35 tim |
6070 |
|
6071 |
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
6072 |
was initially added on branch new_design. |
6073 |
|
6074 |
2005-01-05 12:35 tim |
6075 |
|
6076 |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
6077 |
added on branch new_design. |
6078 |
|
6079 |
2005-01-05 12:35 tim |
6080 |
|
6081 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
6082 |
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
6083 |
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
6084 |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
6085 |
SDMinimizer.hpp: minimizer in progress |
6086 |
|
6087 |
2005-01-05 12:35 tim |
6088 |
|
6089 |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
6090 |
was initially added on branch new_design. |
6091 |
|
6092 |
2005-01-05 12:35 tim |
6093 |
|
6094 |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
6095 |
was initially added on branch new_design. |
6096 |
|
6097 |
2005-01-05 12:35 tim |
6098 |
|
6099 |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
6100 |
was initially added on branch new_design. |
6101 |
|
6102 |
2005-01-05 12:35 tim |
6103 |
|
6104 |
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
6105 |
added on branch new_design. |
6106 |
|
6107 |
2005-01-04 17:18 tim |
6108 |
|
6109 |
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
6110 |
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
6111 |
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
6112 |
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
6113 |
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
6114 |
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
6115 |
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
6116 |
progress |
6117 |
|
6118 |
2005-01-04 17:18 tim |
6119 |
|
6120 |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
6121 |
initially added on branch new_design. |
6122 |
|
6123 |
2005-01-04 17:18 tim |
6124 |
|
6125 |
* src/minimizers/MinimizerParameterSet.cpp: file |
6126 |
MinimizerParameterSet.cpp was initially added on branch new_design. |
6127 |
|
6128 |
2005-01-04 17:18 tim |
6129 |
|
6130 |
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
6131 |
initially added on branch new_design. |
6132 |
|
6133 |
2005-01-04 17:18 tim |
6134 |
|
6135 |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
6136 |
was initially added on branch new_design. |
6137 |
|
6138 |
2005-01-04 17:18 tim |
6139 |
|
6140 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
6141 |
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
6142 |
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
6143 |
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
6144 |
|
6145 |
2005-01-04 17:18 tim |
6146 |
|
6147 |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
6148 |
branch new_design. |
6149 |
|
6150 |
2004-12-20 15:50 chuckv |
6151 |
|
6152 |
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
6153 |
other BSD's, replaced test -f *.mod with ls function since BSD test |
6154 |
apparently doesn't support wildcards. |
6155 |
|
6156 |
2004-12-20 15:36 tim |
6157 |
|
6158 |
* make/Makefile.in: fix a test command incompatiable problem |
6159 |
|
6160 |
2004-12-20 14:49 tim |
6161 |
|
6162 |
* src/integrators/NPTi.cpp: NPT is working now |
6163 |
|
6164 |
2004-12-16 14:20 tim |
6165 |
|
6166 |
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
6167 |
invalid stamp id |
6168 |
|
6169 |
2004-12-16 14:00 tim |
6170 |
|
6171 |
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
6172 |
newEAM.u6.frc: adding new EAM force field files |
6173 |
|
6174 |
2004-12-16 13:55 tim |
6175 |
|
6176 |
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
6177 |
in EAM parameter file is incorrect |
6178 |
|
6179 |
2004-12-16 12:27 tim |
6180 |
|
6181 |
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
6182 |
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
6183 |
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
6184 |
|
6185 |
2004-12-15 17:34 tim |
6186 |
|
6187 |
* src/: applications/simpleBuilder/BaseLattice.cpp, |
6188 |
applications/simpleBuilder/BaseLattice.hpp, |
6189 |
applications/simpleBuilder/Lattice.cpp, |
6190 |
applications/simpleBuilder/Lattice.hpp, |
6191 |
applications/simpleBuilder/LatticeCreator.cpp, |
6192 |
applications/simpleBuilder/LatticeCreator.hpp, |
6193 |
applications/simpleBuilder/LatticeFactory.cpp, |
6194 |
applications/simpleBuilder/LatticeFactory.hpp, |
6195 |
applications/simpleBuilder/simpleBuilder.cpp, |
6196 |
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
6197 |
|
6198 |
2004-12-15 16:07 tim |
6199 |
|
6200 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6201 |
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
6202 |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
6203 |
add EAM Force Field |
6204 |
|
6205 |
2004-12-15 14:40 tim |
6206 |
|
6207 |
* src/applications/oopse/oopse.cpp: add more force fields |
6208 |
|
6209 |
2004-12-15 11:44 tim |
6210 |
|
6211 |
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
6212 |
to call All_reduce in MPI version) |
6213 |
|
6214 |
2004-12-15 11:13 tim |
6215 |
|
6216 |
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
6217 |
io/DumpReader.cpp: MPI in NVE is working |
6218 |
|
6219 |
2004-12-14 16:57 tim |
6220 |
|
6221 |
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
6222 |
Master nodes does not brocast the total number of frames |
6223 |
|
6224 |
2004-12-14 14:08 tim |
6225 |
|
6226 |
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
6227 |
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
6228 |
minimizers/CGFamilyMinimizer.cpp, |
6229 |
minimizers/MinimizerParameterSet.hpp, |
6230 |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
6231 |
minimizers/SDMinimizer.cpp: more fix in MPI version |
6232 |
|
6233 |
2004-12-13 17:30 tim |
6234 |
|
6235 |
* src/: UseTheForce/DarkSide/simParallel.F90, |
6236 |
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
6237 |
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
6238 |
integrators/DLM.cpp, integrators/Integrator.cpp, |
6239 |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
6240 |
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
6241 |
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
6242 |
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
6243 |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
6244 |
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
6245 |
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
6246 |
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
6247 |
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
6248 |
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
6249 |
is built |
6250 |
|
6251 |
2004-12-10 13:41 tim |
6252 |
|
6253 |
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
6254 |
|
6255 |
2004-12-10 11:14 tim |
6256 |
|
6257 |
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
6258 |
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
6259 |
and Dipole is working now |
6260 |
|
6261 |
2004-12-09 18:15 tim |
6262 |
|
6263 |
* src/: UseTheForce/DarkSide/dipole.F90, |
6264 |
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
6265 |
fix an index problem in eFrame matrix |
6266 |
|
6267 |
2004-12-09 18:09 tim |
6268 |
|
6269 |
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
6270 |
initializing the new Charge AtomType |
6271 |
|
6272 |
2004-12-09 16:15 tim |
6273 |
|
6274 |
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
6275 |
types/DirectionalAtomType.cpp: sticky module get compiled |
6276 |
|
6277 |
2004-12-09 15:43 gezelter |
6278 |
|
6279 |
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
6280 |
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
6281 |
GB |
6282 |
|
6283 |
2004-12-09 15:42 gezelter |
6284 |
|
6285 |
* src/UseTheForce/doForces.F90: u_l -> eFrame |
6286 |
|
6287 |
2004-12-09 15:27 gezelter |
6288 |
|
6289 |
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
6290 |
module now has the option for multiple sticky types |
6291 |
|
6292 |
2004-12-09 15:27 gezelter |
6293 |
|
6294 |
* src/UseTheForce/doForces.F90: sticky |
6295 |
|
6296 |
2004-12-09 11:22 tim |
6297 |
|
6298 |
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
6299 |
inconsistency in lab2Bidy |
6300 |
|
6301 |
2004-12-09 10:45 tim |
6302 |
|
6303 |
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
6304 |
in calculating torque in rigid body |
6305 |
|
6306 |
2004-12-08 15:37 tim |
6307 |
|
6308 |
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
6309 |
brains/SnapShot.cpp, brains/Snapshot.hpp, |
6310 |
integrators/Integrator.cpp, |
6311 |
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
6312 |
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
6313 |
|
6314 |
2004-12-08 12:03 tim |
6315 |
|
6316 |
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
6317 |
in NVT is working |
6318 |
|
6319 |
2004-12-07 18:08 tim |
6320 |
|
6321 |
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
6322 |
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
6323 |
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
6324 |
io/DumpWriter.cpp: NPT in progress |
6325 |
|
6326 |
2004-12-07 09:43 tim |
6327 |
|
6328 |
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
6329 |
message] |
6330 |
|
6331 |
2004-12-07 00:12 tim |
6332 |
|
6333 |
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
6334 |
UseInitXSstate |
6335 |
|
6336 |
2004-12-07 00:00 tim |
6337 |
|
6338 |
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
6339 |
|
6340 |
2004-12-06 23:47 tim |
6341 |
|
6342 |
* src/types/DirectionalAtomType.cpp: [no log message] |
6343 |
|
6344 |
2004-12-06 21:18 tim |
6345 |
|
6346 |
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
6347 |
|
6348 |
2004-12-06 20:33 tim |
6349 |
|
6350 |
* forceFields/newDUFF.frc: change the force constant of bonds |
6351 |
|
6352 |
2004-12-06 18:29 tim |
6353 |
|
6354 |
* src/: UseTheForce/DarkSide/charge.F90, |
6355 |
UseTheForce/DarkSide/charge_interface.h, |
6356 |
UseTheForce/DarkSide/dipole.F90, |
6357 |
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
6358 |
fix atom type ident in Charge and Dipole Module |
6359 |
|
6360 |
2004-12-06 17:56 tim |
6361 |
|
6362 |
* src/primitives/Torsion.cpp: butane is working now |
6363 |
|
6364 |
2004-12-06 15:15 tim |
6365 |
|
6366 |
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
6367 |
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
6368 |
interaction for butane is correct.Still something wrong with long |
6369 |
range one |
6370 |
|
6371 |
2004-12-05 23:49 tim |
6372 |
|
6373 |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
6374 |
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6375 |
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
6376 |
primitives/Atom.hpp, utils/NumericConstant.hpp, |
6377 |
utils/TypeContainer.hpp: fix a bug in Exclude List |
6378 |
|
6379 |
2004-12-05 17:21 tim |
6380 |
|
6381 |
* forceFields/newDUFF.frc: minor fix in DUFF |
6382 |
|
6383 |
2004-12-05 17:02 tim |
6384 |
|
6385 |
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
6386 |
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
6387 |
fix a bug in filling MolMembership |
6388 |
|
6389 |
2004-12-05 12:12 tim |
6390 |
|
6391 |
* forceFields/newDUFF.frc: minor fix in force field file |
6392 |
|
6393 |
2004-12-05 12:09 tim |
6394 |
|
6395 |
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
6396 |
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
6397 |
|
6398 |
2004-12-04 15:09 tim |
6399 |
|
6400 |
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
6401 |
math/Vector3.hpp: NVE is working now, get the same result as |
6402 |
OOPSE-1.0 |
6403 |
|
6404 |
2004-12-04 14:29 tim |
6405 |
|
6406 |
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
6407 |
|
6408 |
2004-12-04 14:24 gezelter |
6409 |
|
6410 |
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
6411 |
|
6412 |
2004-12-04 14:24 gezelter |
6413 |
|
6414 |
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
6415 |
|
6416 |
2004-12-04 00:24 tim |
6417 |
|
6418 |
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
6419 |
integrators/Integrator.hpp, |
6420 |
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
6421 |
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
6422 |
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
6423 |
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
6424 |
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
6425 |
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
6426 |
|
6427 |
2004-12-03 19:01 tim |
6428 |
|
6429 |
* src/: UseTheForce/DarkSide/LJ.F90, |
6430 |
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
6431 |
integrators/VelocityVerletIntegrator.cpp, |
6432 |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
6433 |
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
6434 |
energy of NVE is not conserved |
6435 |
|
6436 |
2004-12-03 17:36 tim |
6437 |
|
6438 |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
6439 |
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
6440 |
|
6441 |
2004-12-03 16:30 tim |
6442 |
|
6443 |
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
6444 |
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
6445 |
integrators/NVE.cpp, primitives/Molecule.cpp, |
6446 |
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
6447 |
primitives/Torsion.hpp: more missing function get implemented |
6448 |
|
6449 |
2004-12-03 15:30 tim |
6450 |
|
6451 |
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
6452 |
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
6453 |
|
6454 |
2004-12-03 12:59 tim |
6455 |
|
6456 |
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
6457 |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6458 |
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
6459 |
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
6460 |
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
6461 |
utils/TypeContainer.hpp: begin to fix bugs |
6462 |
|
6463 |
2004-12-02 19:26 tim |
6464 |
|
6465 |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
6466 |
new_design. |
6467 |
|
6468 |
2004-12-02 19:26 tim |
6469 |
|
6470 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6471 |
UseTheForce/ForceFieldCreator.cpp, |
6472 |
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
6473 |
integrators/IntegratorCreator.cpp, |
6474 |
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
6475 |
io/SectionParserManager.hpp, utils/Makefile, |
6476 |
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
6477 |
bug in countTokens in StringTokenizer |
6478 |
|
6479 |
2004-12-02 19:06 tim |
6480 |
|
6481 |
* forceFields/newDUFF.frc: minor fix |
6482 |
|
6483 |
2004-12-02 18:15 tim |
6484 |
|
6485 |
* forceFields/newDUFF.frc: new ForceField format |
6486 |
|
6487 |
2004-12-02 17:15 tim |
6488 |
|
6489 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6490 |
UseTheForce/ForceFieldCreator.cpp, |
6491 |
UseTheForce/ForceFieldCreator.hpp, |
6492 |
UseTheForce/ForceFieldFactory.cpp, |
6493 |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
6494 |
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
6495 |
integrators/IntegratorCreator.hpp, |
6496 |
integrators/IntegratorFactory.cpp, |
6497 |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
6498 |
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
6499 |
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
6500 |
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
6501 |
integrators/NVT.cpp, integrators/NVT.hpp, |
6502 |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
6503 |
types/Makefile: refine factory pattern to make it initialized |
6504 |
correctly |
6505 |
|
6506 |
2004-12-02 17:15 tim |
6507 |
|
6508 |
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
6509 |
was initially added on branch new_design. |
6510 |
|
6511 |
2004-12-02 17:15 tim |
6512 |
|
6513 |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
6514 |
was initially added on branch new_design. |
6515 |
|
6516 |
2004-12-02 17:15 tim |
6517 |
|
6518 |
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
6519 |
was initially added on branch new_design. |
6520 |
|
6521 |
2004-12-02 17:15 tim |
6522 |
|
6523 |
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
6524 |
was initially added on branch new_design. |
6525 |
|
6526 |
2004-12-02 11:53 tim |
6527 |
|
6528 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
6529 |
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
6530 |
|
6531 |
2004-12-02 11:04 tim |
6532 |
|
6533 |
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
6534 |
applications/simpleBuilder/LatticeCreator.hpp, |
6535 |
applications/simpleBuilder/LatticeFactory.cpp, |
6536 |
applications/simpleBuilder/LatticeFactory.hpp, |
6537 |
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
6538 |
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
6539 |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
6540 |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
6541 |
brains/SnapshotManager.hpp, brains/Stats.cpp, |
6542 |
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
6543 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
6544 |
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
6545 |
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
6546 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
6547 |
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
6548 |
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
6549 |
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
6550 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
6551 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6552 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
6553 |
have two linking problem |
6554 |
|
6555 |
2004-12-02 00:17 tim |
6556 |
|
6557 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
6558 |
applications/simpleBuilder/Lattice.cpp, |
6559 |
applications/simpleBuilder/simpleBuilder.cpp, |
6560 |
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
6561 |
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
6562 |
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
6563 |
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
6564 |
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
6565 |
visitors/ZconsVisitor.cpp: change endl to std::endl |
6566 |
|
6567 |
2004-12-02 00:14 tim |
6568 |
|
6569 |
* src/: UseTheForce/Shapes_FF.cpp, |
6570 |
applications/dump2Xyz/Dump2XYZ.cpp, |
6571 |
applications/simpleBuilder/BaseLattice.hpp, |
6572 |
applications/simpleBuilder/Lattice.hpp, |
6573 |
applications/simpleBuilder/LatticeCreator.hpp, |
6574 |
applications/simpleBuilder/LatticeFactory.cpp, |
6575 |
applications/simpleBuilder/LatticeFactory.hpp, |
6576 |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
6577 |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
6578 |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
6579 |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
6580 |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6581 |
visitors/RigidBodyVisitor.hpp: minor fix |
6582 |
|
6583 |
2004-12-02 00:09 tim |
6584 |
|
6585 |
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
6586 |
remove StreamTokenizer |
6587 |
|
6588 |
2004-12-02 00:06 tim |
6589 |
|
6590 |
* src/: UseTheForce/Shapes_FF.cpp, |
6591 |
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
6592 |
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
6593 |
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
6594 |
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
6595 |
namespace std in .cpp file |
6596 |
|
6597 |
2004-12-02 00:04 tim |
6598 |
|
6599 |
* src/: UseTheForce/Shapes_FF.cpp, |
6600 |
applications/dump2Xyz/Dump2XYZ.cpp, |
6601 |
applications/simpleBuilder/BaseLattice.hpp, |
6602 |
applications/simpleBuilder/Lattice.cpp, |
6603 |
applications/simpleBuilder/Lattice.hpp, |
6604 |
applications/simpleBuilder/LatticeFactory.cpp, |
6605 |
applications/simpleBuilder/LatticeFactory.hpp, |
6606 |
applications/simpleBuilder/MoLocator.cpp, |
6607 |
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
6608 |
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
6609 |
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
6610 |
minimizers/MinimizerParameterSet.hpp, |
6611 |
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
6612 |
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
6613 |
restraints/Restraints.cpp, restraints/Restraints.hpp, |
6614 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
6615 |
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
6616 |
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
6617 |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6618 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
6619 |
qulified name prefix std |
6620 |
|
6621 |
2004-12-01 23:55 tim |
6622 |
|
6623 |
* src/: UseTheForce/Shapes_FF.cpp, |
6624 |
applications/dump2Xyz/Dump2XYZ.cpp, |
6625 |
applications/simpleBuilder/BaseLattice.hpp, |
6626 |
applications/simpleBuilder/Lattice.hpp, |
6627 |
applications/simpleBuilder/LatticeCreator.hpp, |
6628 |
applications/simpleBuilder/LatticeFactory.cpp, |
6629 |
applications/simpleBuilder/LatticeFactory.hpp, |
6630 |
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
6631 |
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
6632 |
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
6633 |
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
6634 |
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
6635 |
visitors/RigidBodyVisitor.hpp: replace string by std::string |
6636 |
|
6637 |
2004-12-01 22:12 tim |
6638 |
|
6639 |
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
6640 |
src/applications/simpleBuilder/BaseLattice.hpp, |
6641 |
src/applications/simpleBuilder/Lattice.hpp, |
6642 |
src/applications/simpleBuilder/LatticeCreator.hpp, |
6643 |
src/applications/simpleBuilder/LatticeFactory.hpp, |
6644 |
src/applications/simpleBuilder/MoLocator.hpp, |
6645 |
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
6646 |
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
6647 |
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
6648 |
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
6649 |
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
6650 |
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
6651 |
src/utils/Makefile, src/utils/StringUtils.cpp, |
6652 |
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
6653 |
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
6654 |
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
6655 |
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
6656 |
header files |
6657 |
|
6658 |
2004-12-01 21:23 tim |
6659 |
|
6660 |
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
6661 |
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
6662 |
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
6663 |
begin to fix linking problem |
6664 |
|
6665 |
2004-12-01 21:08 tim |
6666 |
|
6667 |
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
6668 |
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
6669 |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
6670 |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
6671 |
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
6672 |
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
6673 |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
6674 |
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
6675 |
still has some linking problem |
6676 |
|
6677 |
2004-12-01 19:26 tim |
6678 |
|
6679 |
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
6680 |
utils/OOPSEConstant.hpp: NVT get built |
6681 |
|
6682 |
2004-12-01 19:09 tim |
6683 |
|
6684 |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
6685 |
branch new_design. |
6686 |
|
6687 |
2004-12-01 19:09 tim |
6688 |
|
6689 |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
6690 |
branch new_design. |
6691 |
|
6692 |
2004-12-01 19:09 tim |
6693 |
|
6694 |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
6695 |
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
6696 |
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
6697 |
integrators/Integrator.hpp, integrators/Makefile, |
6698 |
integrators/NVE.cpp, integrators/NVE.hpp, |
6699 |
integrators/RotationAlgorithm.hpp, |
6700 |
integrators/VelocityVerletIntegrator.cpp, |
6701 |
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
6702 |
get built |
6703 |
|
6704 |
2004-12-01 19:09 tim |
6705 |
|
6706 |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
6707 |
was initially added on branch new_design. |
6708 |
|
6709 |
2004-12-01 17:45 tim |
6710 |
|
6711 |
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
6712 |
integrators/IntegratorFactory.cpp, |
6713 |
integrators/IntegratorFactory.hpp, integrators/Makefile, |
6714 |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
6715 |
integrators/VelocityVerletIntegrator.cpp, |
6716 |
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
6717 |
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
6718 |
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
6719 |
|
6720 |
2004-12-01 17:45 tim |
6721 |
|
6722 |
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
6723 |
branch new_design. |
6724 |
|
6725 |
2004-12-01 15:05 tim |
6726 |
|
6727 |
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
6728 |
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
6729 |
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
6730 |
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
6731 |
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
6732 |
visitors/ZconsVisitor.hpp: visitors get built |
6733 |
|
6734 |
2004-12-01 14:32 chrisfen |
6735 |
|
6736 |
* samples/water/tip3p_ice/tp3.md: fixed a sample |
6737 |
|
6738 |
2004-12-01 14:10 tim |
6739 |
|
6740 |
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
6741 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
6742 |
src/types/AtomType.hpp, src/utils/Utility.hpp, |
6743 |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
6744 |
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
6745 |
spell check |
6746 |
|
6747 |
2004-12-01 13:42 tim |
6748 |
|
6749 |
* src/: UseTheForce/DarkSide/atype.F90, |
6750 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
6751 |
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
6752 |
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
6753 |
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
6754 |
and constraint, other directories get built |
6755 |
|
6756 |
2004-12-01 12:38 tim |
6757 |
|
6758 |
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
6759 |
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
6760 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
6761 |
io/ElectrostaticAtomTypesSectionParser.hpp, |
6762 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
6763 |
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
6764 |
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
6765 |
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
6766 |
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
6767 |
refactory AtomType |
6768 |
|
6769 |
2004-11-30 22:11 tim |
6770 |
|
6771 |
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
6772 |
|
6773 |
2004-11-30 21:30 tim |
6774 |
|
6775 |
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
6776 |
NumericConstant |
6777 |
|
6778 |
2004-11-30 21:24 tim |
6779 |
|
6780 |
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
6781 |
primitives/RigidBody.cpp: minor fix |
6782 |
|
6783 |
2004-11-30 18:14 tim |
6784 |
|
6785 |
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
6786 |
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
6787 |
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
6788 |
get built, next is integrator |
6789 |
|
6790 |
2004-11-30 17:43 tim |
6791 |
|
6792 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
6793 |
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
6794 |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
6795 |
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
6796 |
utils/StringUtils.hpp: brains get built |
6797 |
|
6798 |
2004-11-30 15:50 tim |
6799 |
|
6800 |
* src/: brains/ForceManager.cpp, brains/Makefile, |
6801 |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
6802 |
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
6803 |
utils/StringUtils.hpp: brains get built, io is next |
6804 |
|
6805 |
2004-11-30 14:58 tim |
6806 |
|
6807 |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
6808 |
brains/ForceManager.cpp, brains/ForceManager.hpp, |
6809 |
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
6810 |
brains/SimInfo.cpp, brains/SimInfo.hpp, |
6811 |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
6812 |
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
6813 |
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
6814 |
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
6815 |
|
6816 |
2004-11-30 14:58 tim |
6817 |
|
6818 |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
6819 |
added on branch new_design. |
6820 |
|
6821 |
2004-11-30 12:54 tim |
6822 |
|
6823 |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
6824 |
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
6825 |
utils/LocalIndexManager.hpp: more get fixed |
6826 |
|
6827 |
2004-11-30 00:03 tim |
6828 |
|
6829 |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
6830 |
initially added on branch new_design. |
6831 |
|
6832 |
2004-11-30 00:03 tim |
6833 |
|
6834 |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
6835 |
LocalndexManager.hpp to LocalIndexManager.hpp |
6836 |
|
6837 |
2004-11-29 23:43 tim |
6838 |
|
6839 |
* src/: io/BendTypesSectionParser.cpp, |
6840 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
6841 |
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
6842 |
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
6843 |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
6844 |
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
6845 |
|
6846 |
2004-11-29 23:14 tim |
6847 |
|
6848 |
* src/: io/BendTypesSectionParser.cpp, |
6849 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
6850 |
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
6851 |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
6852 |
fixed |
6853 |
|
6854 |
2004-11-29 22:49 tim |
6855 |
|
6856 |
* src/: io/TorsionTypesSectionParser.cpp, |
6857 |
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
6858 |
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
6859 |
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
6860 |
types/QuarticTorsionType.hpp: minor fixed |
6861 |
|
6862 |
2004-11-29 22:32 tim |
6863 |
|
6864 |
* src/: io/TorsionTypesSectionParser.cpp, |
6865 |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
6866 |
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
6867 |
embedded |
6868 |
|
6869 |
2004-11-29 16:42 tim |
6870 |
|
6871 |
* test/math/: Makefile, PolynomialTestCase.cpp, |
6872 |
PolynomialTestCase.hpp: add PolynomialTestCase |
6873 |
|
6874 |
2004-11-29 16:42 tim |
6875 |
|
6876 |
* src/math/Polynomial.hpp: Polynomial passes unit test |
6877 |
|
6878 |
2004-11-29 15:03 tim |
6879 |
|
6880 |
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
6881 |
QuarticTorsion.hpp to QuarticTorsionType.hpp |
6882 |
|
6883 |
2004-11-29 15:03 tim |
6884 |
|
6885 |
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
6886 |
initially added on branch new_design. |
6887 |
|
6888 |
2004-11-29 14:56 tim |
6889 |
|
6890 |
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
6891 |
initially added on branch new_design. |
6892 |
|
6893 |
2004-11-29 14:56 tim |
6894 |
|
6895 |
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
6896 |
CubicTorsionType and QuarticTorsionType |
6897 |
|
6898 |
2004-11-29 14:56 tim |
6899 |
|
6900 |
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
6901 |
initially added on branch new_design. |
6902 |
|
6903 |
2004-11-29 13:00 tim |
6904 |
|
6905 |
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
6906 |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
6907 |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
6908 |
fixed |
6909 |
|
6910 |
2004-11-29 12:59 tim |
6911 |
|
6912 |
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
6913 |
new_design. |
6914 |
|
6915 |
2004-11-29 12:59 tim |
6916 |
|
6917 |
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
6918 |
Algorithm for std::string |
6919 |
|
6920 |
2004-11-29 10:52 tim |
6921 |
|
6922 |
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
6923 |
some useless files |
6924 |
|
6925 |
2004-11-29 10:50 tim |
6926 |
|
6927 |
* src/io/: BondTypesSectionParser.cpp, |
6928 |
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
6929 |
ElectrostaticAtomTypesSectionParser.cpp, |
6930 |
HarmonicBondTypesSectionParser.cpp, |
6931 |
HarmonicBondTypesSectionParser.hpp, |
6932 |
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
6933 |
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
6934 |
StickyAtomTypesSectionParser.hpp: more files get fixed |
6935 |
|
6936 |
2004-11-29 10:27 tim |
6937 |
|
6938 |
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
6939 |
DirectionalAtomTypesSectionParser.cpp, |
6940 |
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
6941 |
Makefile, SectionParser.cpp, SectionParser.hpp, |
6942 |
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
6943 |
built |
6944 |
|
6945 |
2004-11-29 09:49 tim |
6946 |
|
6947 |
* src/types/UreyBradleyBendType.hpp: types get built |
6948 |
|
6949 |
2004-11-29 09:40 tim |
6950 |
|
6951 |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
6952 |
types get built |
6953 |
|
6954 |
2004-11-25 21:13 tim |
6955 |
|
6956 |
* src/: UseTheForce/ForceField.hpp, |
6957 |
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
6958 |
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
6959 |
files |
6960 |
|
6961 |
2004-11-25 15:18 tim |
6962 |
|
6963 |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
6964 |
initially added on branch new_design. |
6965 |
|
6966 |
2004-11-25 15:18 tim |
6967 |
|
6968 |
* src/: io/AtomTypesSectionParser.cpp, |
6969 |
io/BondTypesSectionParser.cpp, |
6970 |
io/DirectionalAtomTypesSectionParser.cpp, |
6971 |
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
6972 |
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
6973 |
files |
6974 |
|
6975 |
2004-11-25 15:18 tim |
6976 |
|
6977 |
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
6978 |
initially added on branch new_design. |
6979 |
|
6980 |
2004-11-24 17:12 tim |
6981 |
|
6982 |
* src/: io/AtomTypesSectionParser.cpp, |
6983 |
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
6984 |
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
6985 |
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
6986 |
io/ChargeAtomTypesSectionParser.hpp, |
6987 |
io/DipoleAtomTypesSectionParser.cpp, |
6988 |
io/DipoleAtomTypesSectionParser.hpp, |
6989 |
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
6990 |
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
6991 |
io/EAMAtomTypesSectionParser.hpp, |
6992 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
6993 |
io/ElectrostaticAtomTypesSectionParser.hpp, |
6994 |
io/HarmonicBondTypesSectionParser.hpp, |
6995 |
io/LennardJonesAtomTypesSectionParser.cpp, |
6996 |
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
6997 |
io/SectionParser.hpp, io/SectionParserManager.hpp, |
6998 |
io/StickyAtomTypesSectionParser.cpp, |
6999 |
io/StickyAtomTypesSectionParser.hpp, |
7000 |
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
7001 |
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
7002 |
|
7003 |
2004-11-24 16:33 tim |
7004 |
|
7005 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
7006 |
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
7007 |
LJFF.cpp, Makefile: UseTheForce get built |
7008 |
|
7009 |
2004-11-24 15:55 tim |
7010 |
|
7011 |
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
7012 |
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
7013 |
primitives/Makefile, primitives/Molecule.cpp, |
7014 |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
7015 |
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
7016 |
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
7017 |
primitives/UreyBradleyBend.hpp: types and primitives get built |
7018 |
|
7019 |
2004-11-24 14:49 tim |
7020 |
|
7021 |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
7022 |
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
7023 |
StringTokenizerTestCase |
7024 |
|
7025 |
2004-11-24 14:49 tim |
7026 |
|
7027 |
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
7028 |
StringTokenizer.hpp: StringTokenizer passes unit test |
7029 |
|
7030 |
2004-11-24 13:20 tim |
7031 |
|
7032 |
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
7033 |
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
7034 |
change Makefile |
7035 |
|
7036 |
2004-11-24 13:06 chrisfen |
7037 |
|
7038 |
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
7039 |
fine |
7040 |
|
7041 |
2004-11-24 13:06 chrisfen |
7042 |
|
7043 |
* src/integrators/Integrator.cpp: improved restraints |
7044 |
|
7045 |
2004-11-24 13:05 chrisfen |
7046 |
|
7047 |
* samples/water/tip3p_ice/tp3.md: oops... |
7048 |
|
7049 |
2004-11-24 12:42 tim |
7050 |
|
7051 |
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
7052 |
brains/DataStorage.hpp, brains/SimCreator.cpp, |
7053 |
brains/SimCreator.hpp, integrators/Integrator.hpp, |
7054 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
7055 |
primitives/DirectionalAtom.cpp: add SetForceManager method to |
7056 |
integrator |
7057 |
|
7058 |
2004-11-23 18:12 tim |
7059 |
|
7060 |
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
7061 |
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
7062 |
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
7063 |
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
7064 |
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
7065 |
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
7066 |
integrators/VelocityVerletIntegrator.cpp, |
7067 |
integrators/VelocityVerletIntegrator.hpp, |
7068 |
types/UreyBradleyBendType.hpp: refactory NPT integrator |
7069 |
|
7070 |
2004-11-23 17:50 chrisfen |
7071 |
|
7072 |
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
7073 |
Restraints should work in parallel now |
7074 |
|
7075 |
2004-11-23 17:48 chrisfen |
7076 |
|
7077 |
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
7078 |
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
7079 |
integrators/Integrator.cpp, integrators/Integrator.hpp, |
7080 |
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
7081 |
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
7082 |
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
7083 |
to restraints |
7084 |
|
7085 |
2004-11-23 17:47 chrisfen |
7086 |
|
7087 |
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
7088 |
return to the original on next commit |
7089 |
|
7090 |
2004-11-23 12:53 tim |
7091 |
|
7092 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7093 |
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
7094 |
applications/simpleBuilder/simpleBuilder.cpp, |
7095 |
io/ChargeAtomTypesSectionParser.cpp, |
7096 |
io/DirectionalAtomTypesSectionParser.hpp, |
7097 |
io/EAMAtomTypesSectionParser.cpp, |
7098 |
io/ElectrostaticAtomTypesSectionParser.cpp, |
7099 |
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
7100 |
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
7101 |
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
7102 |
|
7103 |
2004-11-23 12:53 tim |
7104 |
|
7105 |
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
7106 |
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
7107 |
branch new_design. |
7108 |
|
7109 |
2004-11-23 12:53 tim |
7110 |
|
7111 |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
7112 |
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
7113 |
branch new_design. |
7114 |
|
7115 |
2004-11-23 01:03 tim |
7116 |
|
7117 |
* src/: io/EAMAtomTypesSectionParser.cpp, |
7118 |
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
7119 |
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
7120 |
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
7121 |
|
7122 |
2004-11-23 01:03 tim |
7123 |
|
7124 |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
7125 |
was initially added on branch new_design. |
7126 |
|
7127 |
2004-11-23 01:03 tim |
7128 |
|
7129 |
* src/io/EAMAtomTypesSectionParser.hpp: file |
7130 |
EAMAtomTypesSectionParser.hpp was initially added on branch |
7131 |
new_design. |
7132 |
|
7133 |
2004-11-23 01:03 tim |
7134 |
|
7135 |
* src/io/EAMAtomTypesSectionParser.cpp: file |
7136 |
EAMAtomTypesSectionParser.cpp was initially added on branch |
7137 |
new_design. |
7138 |
|
7139 |
2004-11-22 23:35 tim |
7140 |
|
7141 |
* src/io/TorsionTypesSectionParser.hpp: file |
7142 |
TorsionTypesSectionParser.hpp was initially added on branch |
7143 |
new_design. |
7144 |
|
7145 |
2004-11-22 23:35 tim |
7146 |
|
7147 |
* src/io/BendTypesSectionParser.hpp: file |
7148 |
BendTypesSectionParser.hpp was initially added on branch |
7149 |
new_design. |
7150 |
|
7151 |
2004-11-22 23:35 tim |
7152 |
|
7153 |
* src/io/BondTypesSectionParser.hpp: file |
7154 |
BondTypesSectionParser.hpp was initially added on branch |
7155 |
new_design. |
7156 |
|
7157 |
2004-11-22 23:35 tim |
7158 |
|
7159 |
* src/io/BondTypesSectionParser.cpp: file |
7160 |
BondTypesSectionParser.cpp was initially added on branch |
7161 |
new_design. |
7162 |
|
7163 |
2004-11-22 23:35 tim |
7164 |
|
7165 |
* src/io/TorsionTypesSectionParser.cpp: file |
7166 |
TorsionTypesSectionParser.cpp was initially added on branch |
7167 |
new_design. |
7168 |
|
7169 |
2004-11-22 23:35 tim |
7170 |
|
7171 |
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
7172 |
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
7173 |
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
7174 |
BondTypesSectionParser, BendTypesSectionParser and |
7175 |
TorsionTypeSectionParser |
7176 |
|
7177 |
2004-11-22 23:35 tim |
7178 |
|
7179 |
* src/io/BendTypesSectionParser.cpp: file |
7180 |
BendTypesSectionParser.cpp was initially added on branch |
7181 |
new_design. |
7182 |
|
7183 |
2004-11-22 18:04 tim |
7184 |
|
7185 |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
7186 |
DUFF and EAM |
7187 |
|
7188 |
2004-11-22 18:02 tim |
7189 |
|
7190 |
* src/io/: DirectionalAtomTypesParser.hpp, |
7191 |
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
7192 |
|
7193 |
2004-11-22 18:02 tim |
7194 |
|
7195 |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
7196 |
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
7197 |
new_design. |
7198 |
|
7199 |
2004-11-22 15:55 tim |
7200 |
|
7201 |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
7202 |
DipoleAtomTypesSectionParser.hpp was initially added on branch |
7203 |
new_design. |
7204 |
|
7205 |
2004-11-22 15:55 tim |
7206 |
|
7207 |
* src/io/AtomTypesSectionParser.hpp: file |
7208 |
AtomTypesSectionParser.hpp was initially added on branch |
7209 |
new_design. |
7210 |
|
7211 |
2004-11-22 15:55 tim |
7212 |
|
7213 |
* src/io/HarmonicBondTypesSectionParser.hpp: file |
7214 |
HarmonicBondTypesSectionParser.hpp was initially added on branch |
7215 |
new_design. |
7216 |
|
7217 |
2004-11-22 15:55 tim |
7218 |
|
7219 |
* src/io/StickyAtomTypesSectionParser.cpp: file |
7220 |
StickyAtomTypesSectionParser.cpp was initially added on branch |
7221 |
new_design. |
7222 |
|
7223 |
2004-11-22 15:55 tim |
7224 |
|
7225 |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
7226 |
LennardJonesAtomTypesSectionParser.hpp was initially added on |
7227 |
branch new_design. |
7228 |
|
7229 |
2004-11-22 15:55 tim |
7230 |
|
7231 |
* src/io/HarmonicBondTypesSectionParser.cpp: file |
7232 |
HarmonicBondTypesSectionParser.cpp was initially added on branch |
7233 |
new_design. |
7234 |
|
7235 |
2004-11-22 15:55 tim |
7236 |
|
7237 |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
7238 |
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
7239 |
new_design. |
7240 |
|
7241 |
2004-11-22 15:55 tim |
7242 |
|
7243 |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
7244 |
was initially added on branch new_design. |
7245 |
|
7246 |
2004-11-22 15:55 tim |
7247 |
|
7248 |
* src/io/AtomTypesSectionParser.cpp: file |
7249 |
AtomTypesSectionParser.cpp was initially added on branch |
7250 |
new_design. |
7251 |
|
7252 |
2004-11-22 15:55 tim |
7253 |
|
7254 |
* src/io/ChargeAtomTypesSectionParser.cpp: file |
7255 |
ChargeAtomTypesSectionParser.cpp was initially added on branch |
7256 |
new_design. |
7257 |
|
7258 |
2004-11-22 15:55 tim |
7259 |
|
7260 |
* src/io/DipoleAtomTypesSectionParser.cpp: file |
7261 |
DipoleAtomTypesSectionParser.cpp was initially added on branch |
7262 |
new_design. |
7263 |
|
7264 |
2004-11-22 15:55 tim |
7265 |
|
7266 |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
7267 |
LennardJonesAtomTypesSectionParser.cpp was initially added on |
7268 |
branch new_design. |
7269 |
|
7270 |
2004-11-22 15:55 tim |
7271 |
|
7272 |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
7273 |
ChargeAtomTypesSectionParser.hpp was initially added on branch |
7274 |
new_design. |
7275 |
|
7276 |
2004-11-22 15:55 tim |
7277 |
|
7278 |
* src/io/StickyAtomTypesSectionParser.hpp: file |
7279 |
StickyAtomTypesSectionParser.hpp was initially added on branch |
7280 |
new_design. |
7281 |
|
7282 |
2004-11-22 15:55 tim |
7283 |
|
7284 |
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
7285 |
added on branch new_design. |
7286 |
|
7287 |
2004-11-22 15:55 tim |
7288 |
|
7289 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
7290 |
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
7291 |
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
7292 |
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
7293 |
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
7294 |
io/ChargeAtomTypesSectionParser.hpp, |
7295 |
io/DipoleAtomTypesSectionParser.cpp, |
7296 |
io/DipoleAtomTypesSectionParser.hpp, |
7297 |
io/DirectionalAtomTypesParser.hpp, |
7298 |
io/DirectionalAtomTypesSectionParser.cpp, |
7299 |
io/HarmonicBondTypesSectionParser.cpp, |
7300 |
io/HarmonicBondTypesSectionParser.hpp, |
7301 |
io/LennardJonesAtomTypesSectionParser.cpp, |
7302 |
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
7303 |
io/SectionParser.hpp, io/SectionParserManager.cpp, |
7304 |
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
7305 |
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
7306 |
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
7307 |
utils/GenericData.hpp: adding section parsers |
7308 |
|
7309 |
2004-11-22 15:55 tim |
7310 |
|
7311 |
* src/io/DirectionalAtomTypesParser.hpp: file |
7312 |
DirectionalAtomTypesParser.hpp was initially added on branch |
7313 |
new_design. |
7314 |
|
7315 |
2004-11-22 15:55 tim |
7316 |
|
7317 |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
7318 |
was initially added on branch new_design. |
7319 |
|
7320 |
2004-11-22 15:55 tim |
7321 |
|
7322 |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
7323 |
added on branch new_design. |
7324 |
|
7325 |
2004-11-19 17:12 tim |
7326 |
|
7327 |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
7328 |
added on branch new_design. |
7329 |
|
7330 |
2004-11-19 17:12 tim |
7331 |
|
7332 |
* src/: brains/SimState.cpp, brains/SimState.hpp, |
7333 |
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
7334 |
types/FixedBondType.hpp: remove more useless files |
7335 |
|
7336 |
2004-11-19 16:47 tim |
7337 |
|
7338 |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
7339 |
integrators/Integrator.cpp, applications/Makedepend: remove more |
7340 |
useless files |
7341 |
|
7342 |
2004-11-19 16:38 tim |
7343 |
|
7344 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7345 |
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
7346 |
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
7347 |
integrators/NVT.hpp: refactory integrator |
7348 |
|
7349 |
2004-11-19 16:38 tim |
7350 |
|
7351 |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
7352 |
branch new_design. |
7353 |
|
7354 |
2004-11-19 16:38 tim |
7355 |
|
7356 |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
7357 |
branch new_design. |
7358 |
|
7359 |
2004-11-19 16:38 tim |
7360 |
|
7361 |
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
7362 |
branch new_design. |
7363 |
|
7364 |
2004-11-19 16:38 tim |
7365 |
|
7366 |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
7367 |
on branch new_design. |
7368 |
|
7369 |
2004-11-19 16:38 tim |
7370 |
|
7371 |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
7372 |
branch new_design. |
7373 |
|
7374 |
2004-11-19 15:37 tim |
7375 |
|
7376 |
* forceFields/newDUFF.frc: new DUFF forcefield |
7377 |
|
7378 |
2004-11-19 15:23 tim |
7379 |
|
7380 |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
7381 |
branch new_design. |
7382 |
|
7383 |
2004-11-19 15:23 tim |
7384 |
|
7385 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
7386 |
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
7387 |
utils/TypeContainer.hpp: add EAM |
7388 |
|
7389 |
2004-11-19 15:23 tim |
7390 |
|
7391 |
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
7392 |
branch new_design. |
7393 |
|
7394 |
2004-11-19 13:02 tim |
7395 |
|
7396 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
7397 |
error checking |
7398 |
|
7399 |
2004-11-19 12:56 tim |
7400 |
|
7401 |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
7402 |
was initially added on branch new_design. |
7403 |
|
7404 |
2004-11-19 12:56 tim |
7405 |
|
7406 |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
7407 |
was initially added on branch new_design. |
7408 |
|
7409 |
2004-11-19 12:56 tim |
7410 |
|
7411 |
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
7412 |
added on branch new_design. |
7413 |
|
7414 |
2004-11-19 12:56 tim |
7415 |
|
7416 |
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
7417 |
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
7418 |
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
7419 |
integrators/IntegratorFactory.cpp, |
7420 |
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
7421 |
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
7422 |
utils/StringTokenizer.cpp: DUFF is almost done except error |
7423 |
checking |
7424 |
|
7425 |
2004-11-18 19:11 tim |
7426 |
|
7427 |
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
7428 |
|
7429 |
2004-11-18 18:26 tim |
7430 |
|
7431 |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
7432 |
initially added on branch new_design. |
7433 |
|
7434 |
2004-11-18 18:26 tim |
7435 |
|
7436 |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
7437 |
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
7438 |
integrators/VelocityVerletIntegrator.cpp, |
7439 |
integrators/VelocityVerletIntegrator.hpp, |
7440 |
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
7441 |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
7442 |
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
7443 |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
7444 |
DUFF parser |
7445 |
|
7446 |
2004-11-18 16:42 tim |
7447 |
|
7448 |
* forceFields/newDUFF.frc: adding new format DUFF force field |
7449 |
|
7450 |
2004-11-18 10:57 chrisfen |
7451 |
|
7452 |
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
7453 |
slowed down the force loop |
7454 |
|
7455 |
2004-11-18 00:42 tim |
7456 |
|
7457 |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
7458 |
initially added on branch new_design. |
7459 |
|
7460 |
2004-11-18 00:42 tim |
7461 |
|
7462 |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
7463 |
initially added on branch new_design. |
7464 |
|
7465 |
2004-11-18 00:42 tim |
7466 |
|
7467 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
7468 |
primitives/Bend.cpp, utils/NumericConstant.cpp, |
7469 |
utils/NumericConstant.hpp: Adding NumericConstant class |
7470 |
|
7471 |
2004-11-17 23:16 tim |
7472 |
|
7473 |
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
7474 |
UseTheForce/ForceFields.hpp: remove more junk files |
7475 |
|
7476 |
2004-11-17 23:12 tim |
7477 |
|
7478 |
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
7479 |
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
7480 |
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
7481 |
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
7482 |
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
7483 |
primitives/TorsionExtensions.cpp: remove some junk files |
7484 |
|
7485 |
2004-11-17 23:07 tim |
7486 |
|
7487 |
* src/primitives/BendExtensions.cpp: remove some junk files |
7488 |
|
7489 |
2004-11-17 23:04 tim |
7490 |
|
7491 |
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
7492 |
QuadraticBondType.hpp: refine QudraticBond |
7493 |
|
7494 |
2004-11-17 22:57 tim |
7495 |
|
7496 |
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
7497 |
|
7498 |
2004-11-17 22:57 tim |
7499 |
|
7500 |
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
7501 |
initially added on branch new_design. |
7502 |
|
7503 |
2004-11-17 16:47 tim |
7504 |
|
7505 |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
7506 |
was initially added on branch new_design. |
7507 |
|
7508 |
2004-11-17 16:47 tim |
7509 |
|
7510 |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
7511 |
added on branch new_design. |
7512 |
|
7513 |
2004-11-17 16:47 tim |
7514 |
|
7515 |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
7516 |
added on branch new_design. |
7517 |
|
7518 |
2004-11-17 16:47 tim |
7519 |
|
7520 |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
7521 |
initially added on branch new_design. |
7522 |
|
7523 |
2004-11-17 16:47 tim |
7524 |
|
7525 |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
7526 |
initially added on branch new_design. |
7527 |
|
7528 |
2004-11-17 16:47 tim |
7529 |
|
7530 |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
7531 |
initially added on branch new_design. |
7532 |
|
7533 |
2004-11-17 16:47 tim |
7534 |
|
7535 |
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
7536 |
added on branch new_design. |
7537 |
|
7538 |
2004-11-17 16:47 tim |
7539 |
|
7540 |
* src/: math/ChebyshevPolynomials.cpp, |
7541 |
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
7542 |
primitives/Bend.hpp, primitives/GhostBend.cpp, |
7543 |
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
7544 |
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
7545 |
types/CubicBendType.hpp, types/CubicBondType.hpp, |
7546 |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
7547 |
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
7548 |
UreyBradleyBend and GhostBend |
7549 |
|
7550 |
2004-11-17 13:58 tim |
7551 |
|
7552 |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
7553 |
was initially added on branch new_design. |
7554 |
|
7555 |
2004-11-17 13:58 tim |
7556 |
|
7557 |
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
7558 |
was initially added on branch new_design. |
7559 |
|
7560 |
2004-11-17 13:58 tim |
7561 |
|
7562 |
* src/: math/ChebyshevPolynomials.cpp, |
7563 |
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
7564 |
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
7565 |
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
7566 |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
7567 |
stuff and Chebyshev Polynomial |
7568 |
|
7569 |
2004-11-17 13:58 tim |
7570 |
|
7571 |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
7572 |
initially added on branch new_design. |
7573 |
|
7574 |
2004-11-17 01:37 tim |
7575 |
|
7576 |
* src/types/PolynomialTorsionType.hpp: file |
7577 |
PolynomialTorsionType.hpp was initially added on branch new_design. |
7578 |
|
7579 |
2004-11-17 01:37 tim |
7580 |
|
7581 |
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
7582 |
initially added on branch new_design. |
7583 |
|
7584 |
2004-11-17 01:37 tim |
7585 |
|
7586 |
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
7587 |
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
7588 |
types/BondType.hpp, types/CharmmTorsionType.cpp, |
7589 |
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
7590 |
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
7591 |
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
7592 |
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
7593 |
utils/StringTokenizer.hpp: add PolynomialBondType, |
7594 |
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
7595 |
CharmmTorsionType. Need to refine the design and add document for |
7596 |
them |
7597 |
|
7598 |
2004-11-17 01:37 tim |
7599 |
|
7600 |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
7601 |
initially added on branch new_design. |
7602 |
|
7603 |
2004-11-17 01:37 tim |
7604 |
|
7605 |
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
7606 |
initially added on branch new_design. |
7607 |
|
7608 |
2004-11-17 01:37 tim |
7609 |
|
7610 |
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
7611 |
initially added on branch new_design. |
7612 |
|
7613 |
2004-11-16 20:11 tim |
7614 |
|
7615 |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
7616 |
TorsionType.hpp: add PolynomialBondType |
7617 |
|
7618 |
2004-11-16 20:11 tim |
7619 |
|
7620 |
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
7621 |
initially added on branch new_design. |
7622 |
|
7623 |
2004-11-16 18:20 tim |
7624 |
|
7625 |
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
7626 |
on branch new_design. |
7627 |
|
7628 |
2004-11-16 18:20 tim |
7629 |
|
7630 |
* src/math/Polynomial.hpp: Adding Polynomial class |
7631 |
|
7632 |
2004-11-16 17:04 gezelter |
7633 |
|
7634 |
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
7635 |
added on branch new_design. |
7636 |
|
7637 |
2004-11-16 17:04 gezelter |
7638 |
|
7639 |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
7640 |
initially added on branch new_design. |
7641 |
|
7642 |
2004-11-16 17:04 gezelter |
7643 |
|
7644 |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
7645 |
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
7646 |
|
7647 |
2004-11-16 15:36 tim |
7648 |
|
7649 |
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
7650 |
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
7651 |
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
7652 |
TorsionType |
7653 |
|
7654 |
2004-11-15 21:07 tim |
7655 |
|
7656 |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
7657 |
branch new_design. |
7658 |
|
7659 |
2004-11-15 21:07 tim |
7660 |
|
7661 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
7662 |
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
7663 |
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
7664 |
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
7665 |
|
7666 |
2004-11-15 18:00 tim |
7667 |
|
7668 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
7669 |
UseTheForce/ForceFieldFactory.cpp, |
7670 |
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
7671 |
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
7672 |
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
7673 |
|
7674 |
2004-11-15 18:00 tim |
7675 |
|
7676 |
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
7677 |
was initially added on branch new_design. |
7678 |
|
7679 |
2004-11-15 18:00 tim |
7680 |
|
7681 |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
7682 |
was initially added on branch new_design. |
7683 |
|
7684 |
2004-11-15 18:00 tim |
7685 |
|
7686 |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
7687 |
branch new_design. |
7688 |
|
7689 |
2004-11-15 13:02 tim |
7690 |
|
7691 |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
7692 |
initially added on branch new_design. |
7693 |
|
7694 |
2004-11-15 13:02 tim |
7695 |
|
7696 |
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
7697 |
branch new_design. |
7698 |
|
7699 |
2004-11-15 13:02 tim |
7700 |
|
7701 |
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
7702 |
branch new_design. |
7703 |
|
7704 |
2004-11-15 13:02 tim |
7705 |
|
7706 |
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
7707 |
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
7708 |
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
7709 |
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
7710 |
DumpWriter.Next Step is LJFF and integrators |
7711 |
|
7712 |
2004-11-13 00:08 tim |
7713 |
|
7714 |
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
7715 |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
7716 |
brains/SimInfo.hpp, primitives/Molecule.cpp, |
7717 |
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
7718 |
refactory, refactory |
7719 |
|
7720 |
2004-11-12 17:43 tim |
7721 |
|
7722 |
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
7723 |
StringTokenizer.cpp: bug fix in hasMoreTokens |
7724 |
|
7725 |
2004-11-12 17:28 tim |
7726 |
|
7727 |
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
7728 |
initially added on branch new_design. |
7729 |
|
7730 |
2004-11-12 17:28 tim |
7731 |
|
7732 |
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
7733 |
StringUtils, a c-style strtok like class, need unit test |
7734 |
|
7735 |
2004-11-12 12:40 tim |
7736 |
|
7737 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
7738 |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
7739 |
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
7740 |
|
7741 |
2004-11-12 02:05 tim |
7742 |
|
7743 |
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
7744 |
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
7745 |
MoleculeCreator forget to create CutoffGroups for free atoms |
7746 |
|
7747 |
2004-11-12 01:19 tim |
7748 |
|
7749 |
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
7750 |
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
7751 |
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
7752 |
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
7753 |
OOPSE = Object-Obfuscated Parallel Simulation Engine |
7754 |
|
7755 |
2004-11-11 16:48 chrisfen |
7756 |
|
7757 |
* samples/water/tip3p_ice/tp3.md: working sample |
7758 |
|
7759 |
2004-11-11 16:47 chrisfen |
7760 |
|
7761 |
* src/restraints/Restraints.cpp: working towards parallel |
7762 |
restraints |
7763 |
|
7764 |
2004-11-11 16:47 chrisfen |
7765 |
|
7766 |
* src/integrators/Integrator.cpp: Commented out some write |
7767 |
statements |
7768 |
|
7769 |
2004-11-11 16:46 chrisfen |
7770 |
|
7771 |
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
7772 |
write statements |
7773 |
|
7774 |
2004-11-11 16:46 chrisfen |
7775 |
|
7776 |
* samples/water/tip3p_ice/tp3.md: Fun with ice |
7777 |
|
7778 |
2004-11-11 11:41 tim |
7779 |
|
7780 |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
7781 |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
7782 |
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
7783 |
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
7784 |
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
7785 |
useless mpiSimulation |
7786 |
|
7787 |
2004-11-11 11:41 tim |
7788 |
|
7789 |
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
7790 |
branch new_design. |
7791 |
|
7792 |
2004-11-10 17:50 tim |
7793 |
|
7794 |
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
7795 |
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
7796 |
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
7797 |
|
7798 |
2004-11-10 17:01 tim |
7799 |
|
7800 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
7801 |
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
7802 |
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
7803 |
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
7804 |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
7805 |
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
7806 |
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
7807 |
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
7808 |
File will be removed) (3) ForceField (at least LJ) and BondType, |
7809 |
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
7810 |
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
7811 |
|
7812 |
2004-11-10 09:52 tim |
7813 |
|
7814 |
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
7815 |
configurable StatWriter |
7816 |
|
7817 |
2004-11-10 09:52 tim |
7818 |
|
7819 |
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
7820 |
branch new_design. |
7821 |
|
7822 |
2004-11-09 21:58 tim |
7823 |
|
7824 |
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
7825 |
in progress |
7826 |
|
7827 |
2004-11-09 18:11 tim |
7828 |
|
7829 |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
7830 |
added on branch new_design. |
7831 |
|
7832 |
2004-11-09 18:11 tim |
7833 |
|
7834 |
* src/integrators/VelocityVerletIntegrator.cpp: file |
7835 |
VelocityVerletIntegrator.cpp was initially added on branch |
7836 |
new_design. |
7837 |
|
7838 |
2004-11-09 18:11 tim |
7839 |
|
7840 |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
7841 |
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
7842 |
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
7843 |
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
7844 |
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
7845 |
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
7846 |
|
7847 |
2004-11-09 18:11 tim |
7848 |
|
7849 |
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
7850 |
added on branch new_design. |
7851 |
|
7852 |
2004-11-09 18:11 tim |
7853 |
|
7854 |
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
7855 |
branch new_design. |
7856 |
|
7857 |
2004-11-08 20:08 tim |
7858 |
|
7859 |
* src/integrators/VelocityVerletIntegrator.hpp: file |
7860 |
VelocityVerletIntegrator.hpp was initially added on branch |
7861 |
new_design. |
7862 |
|
7863 |
2004-11-08 20:08 tim |
7864 |
|
7865 |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
7866 |
branch new_design. |
7867 |
|
7868 |
2004-11-08 20:08 tim |
7869 |
|
7870 |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
7871 |
integrators/Integrator.hpp, integrators/NVE.hpp, |
7872 |
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
7873 |
utils/TypeContainer.hpp: More to break |
7874 |
|
7875 |
2004-11-06 00:21 tim |
7876 |
|
7877 |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
7878 |
added on branch new_design. |
7879 |
|
7880 |
2004-11-06 00:21 tim |
7881 |
|
7882 |
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
7883 |
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
7884 |
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
7885 |
ForceField and TypeContainer classes |
7886 |
|
7887 |
2004-11-05 18:38 tim |
7888 |
|
7889 |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
7890 |
initially added on branch new_design. |
7891 |
|
7892 |
2004-11-05 18:38 tim |
7893 |
|
7894 |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
7895 |
initially added on branch new_design. |
7896 |
|
7897 |
2004-11-05 18:38 tim |
7898 |
|
7899 |
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
7900 |
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
7901 |
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
7902 |
brains/SimInfo.hpp, primitives/Molecule.hpp, |
7903 |
utils/LocalndexManager.hpp: Fix Exclude class etc. |
7904 |
|
7905 |
2004-11-05 16:45 chrisfen |
7906 |
|
7907 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
7908 |
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
7909 |
linear visitor |
7910 |
|
7911 |
2004-11-05 16:04 chrisfen |
7912 |
|
7913 |
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
7914 |
debugging process |
7915 |
|
7916 |
2004-11-05 16:04 chrisfen |
7917 |
|
7918 |
* make/Makefile.in: included visitors and minimizer |
7919 |
|
7920 |
2004-11-05 16:03 chrisfen |
7921 |
|
7922 |
* ChangeLog: new changes |
7923 |
|
7924 |
2004-11-04 21:56 tim |
7925 |
|
7926 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
7927 |
primitives/Molecule.hpp: Pain...... |
7928 |
|
7929 |
2004-11-04 15:55 tim |
7930 |
|
7931 |
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
7932 |
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
7933 |
src/brains/Stats.hpp: time to break SimSetup |
7934 |
|
7935 |
2004-11-04 15:51 gezelter |
7936 |
|
7937 |
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
7938 |
classes in progress |
7939 |
|
7940 |
2004-11-04 14:48 tim |
7941 |
|
7942 |
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
7943 |
branch new_design. |
7944 |
|
7945 |
2004-11-04 14:48 tim |
7946 |
|
7947 |
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
7948 |
branch new_design. |
7949 |
|
7950 |
2004-11-04 14:48 tim |
7951 |
|
7952 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
7953 |
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
7954 |
class |
7955 |
|
7956 |
2004-11-04 11:22 gezelter |
7957 |
|
7958 |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
7959 |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
7960 |
linearAxis are virtual in StuntDouble, but are implemented by |
7961 |
DirectionalAtom and RigidBody In StuntDouble, they should return |
7962 |
false and "-1" but there should be logic to figure them out in the |
7963 |
other two classes |
7964 |
|
7965 |
2004-11-04 11:20 gezelter |
7966 |
|
7967 |
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
7968 |
remember what I did |
7969 |
|
7970 |
2004-11-04 11:20 gezelter |
7971 |
|
7972 |
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
7973 |
|
7974 |
2004-11-04 11:20 gezelter |
7975 |
|
7976 |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
7977 |
in the entry_plug so that it only is set if the atoms really are in |
7978 |
the simulation |
7979 |
|
7980 |
2004-11-04 11:20 gezelter |
7981 |
|
7982 |
* samples/water/ssd/ssd.md: testing force fields |
7983 |
|
7984 |
2004-11-04 11:19 gezelter |
7985 |
|
7986 |
* samples/shape/linear.in: testing shapes |
7987 |
|
7988 |
2004-11-03 14:56 tim |
7989 |
|
7990 |
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
7991 |
class(similar as SimSetup) |
7992 |
|
7993 |
2004-11-03 14:56 tim |
7994 |
|
7995 |
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
7996 |
added on branch new_design. |
7997 |
|
7998 |
2004-11-03 14:56 tim |
7999 |
|
8000 |
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
8001 |
added on branch new_design. |
8002 |
|
8003 |
2004-11-03 13:00 tim |
8004 |
|
8005 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8006 |
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
8007 |
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
8008 |
brains/DataStorage.hpp, primitives/Atom.hpp, |
8009 |
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
8010 |
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
8011 |
compiled. Still a long way to go ...... |
8012 |
|
8013 |
2004-11-03 11:08 tim |
8014 |
|
8015 |
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
8016 |
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
8017 |
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
8018 |
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
8019 |
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
8020 |
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
8021 |
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
8022 |
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
8023 |
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
8024 |
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
8025 |
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
8026 |
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
8027 |
|
8028 |
2004-11-02 17:41 tim |
8029 |
|
8030 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
8031 |
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
8032 |
Need unit test |
8033 |
|
8034 |
2004-11-02 17:41 tim |
8035 |
|
8036 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
8037 |
initially added on branch new_design. |
8038 |
|
8039 |
2004-11-02 17:41 tim |
8040 |
|
8041 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
8042 |
branch new_design. |
8043 |
|
8044 |
2004-11-02 11:59 tim |
8045 |
|
8046 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
8047 |
branch new_design. |
8048 |
|
8049 |
2004-11-02 11:59 tim |
8050 |
|
8051 |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
8052 |
SimSnapshotManager.hpp: SimModel in progress |
8053 |
|
8054 |
2004-11-02 10:28 chrisfen |
8055 |
|
8056 |
* src/: UseTheForce/DarkSide/shapes.F90, |
8057 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
8058 |
looks like it's working |
8059 |
|
8060 |
2004-11-02 10:27 tim |
8061 |
|
8062 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
8063 |
functions for dealing with memory issue |
8064 |
|
8065 |
2004-11-02 10:27 tim |
8066 |
|
8067 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
8068 |
added on branch new_design. |
8069 |
|
8070 |
2004-11-02 10:23 tim |
8071 |
|
8072 |
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
8073 |
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
8074 |
SimModel(something similar as SimInfo) |
8075 |
|
8076 |
2004-11-01 17:52 tim |
8077 |
|
8078 |
* src/: applications/simpleBuilder/MoLocator.hpp, |
8079 |
applications/simpleBuilder/simpleBuilder.cpp, |
8080 |
brains/DataStorage.hpp, brains/ForceFields.cpp, |
8081 |
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
8082 |
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
8083 |
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
8084 |
math/SquareMatrix3.hpp, math/Vector3.hpp, |
8085 |
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
8086 |
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
8087 |
primitives/Molecule.cpp, primitives/Molecule.hpp, |
8088 |
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
8089 |
restraints/Restraints.cpp, types/TorsionType.hpp, |
8090 |
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
8091 |
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
8092 |
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
8093 |
RigidBody and StuntDouble classes get compiled |
8094 |
|
8095 |
2004-11-01 16:40 tim |
8096 |
|
8097 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
8098 |
on branch new_design. |
8099 |
|
8100 |
2004-11-01 16:40 tim |
8101 |
|
8102 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
8103 |
branch new_design. |
8104 |
|
8105 |
2004-11-01 16:40 tim |
8106 |
|
8107 |
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
8108 |
branch new_design. |
8109 |
|
8110 |
2004-11-01 16:40 tim |
8111 |
|
8112 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
8113 |
version of Bond, Bend and Torsion. |
8114 |
|
8115 |
2004-11-01 16:37 tim |
8116 |
|
8117 |
* src/types/BendType.hpp: file BendType.hpp was initially added on |
8118 |
branch new_design. |
8119 |
|
8120 |
2004-11-01 16:37 tim |
8121 |
|
8122 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
8123 |
BondType, BendType, TorsionType |
8124 |
|
8125 |
2004-11-01 16:37 tim |
8126 |
|
8127 |
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
8128 |
added on branch new_design. |
8129 |
|
8130 |
2004-11-01 16:37 tim |
8131 |
|
8132 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
8133 |
branch new_design. |
8134 |
|
8135 |
2004-11-01 15:15 tim |
8136 |
|
8137 |
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
8138 |
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
8139 |
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
8140 |
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
8141 |
break, break and break..... |
8142 |
|
8143 |
2004-11-01 14:57 tim |
8144 |
|
8145 |
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
8146 |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
8147 |
StuntDouble.hpp: these core classes get compiled |
8148 |
|
8149 |
2004-10-29 18:37 tim |
8150 |
|
8151 |
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
8152 |
class |
8153 |
|
8154 |
2004-10-29 18:28 chrisfen |
8155 |
|
8156 |
* src/: UseTheForce/DarkSide/atype.F90, |
8157 |
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
8158 |
types/ShapeAtomType.cpp: still debugging |
8159 |
|
8160 |
2004-10-29 18:28 chrisfen |
8161 |
|
8162 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
8163 |
shapes rcut calculator added |
8164 |
|
8165 |
2004-10-29 18:27 chrisfen |
8166 |
|
8167 |
* samples/shape/linear.md: shorter run |
8168 |
|
8169 |
2004-10-29 16:54 tim |
8170 |
|
8171 |
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
8172 |
|
8173 |
2004-10-29 12:22 tim |
8174 |
|
8175 |
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
8176 |
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
8177 |
some deprecated files |
8178 |
|
8179 |
2004-10-29 12:20 tim |
8180 |
|
8181 |
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
8182 |
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
8183 |
More painful reconstruction is coming !!! |
8184 |
|
8185 |
2004-10-28 18:34 tim |
8186 |
|
8187 |
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
8188 |
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
8189 |
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
8190 |
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
8191 |
DirectionalAtom and RigidBody |
8192 |
|
8193 |
2004-10-28 18:26 tim |
8194 |
|
8195 |
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
8196 |
src/applications/simpleBuilder/MoLocator.cpp, |
8197 |
src/applications/simpleBuilder/Vector3d.hpp, |
8198 |
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
8199 |
remove old Vector3d.hpp from application/simpleBuilder |
8200 |
|
8201 |
2004-10-28 17:42 tim |
8202 |
|
8203 |
* src/utils/next_combination.hpp: Minor change in next_combination |
8204 |
|
8205 |
2004-10-28 17:28 tim |
8206 |
|
8207 |
* src/utils/next_combination.hpp, |
8208 |
test/utils/NextCombinationTestCase.cpp, |
8209 |
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
8210 |
|
8211 |
2004-10-28 17:11 tim |
8212 |
|
8213 |
* src/utils/next_combination.hpp: change documentation of |
8214 |
next_combination.hpp |
8215 |
|
8216 |
2004-10-28 16:41 tim |
8217 |
|
8218 |
* ChangeLog, src/utils/next_combination.hpp, |
8219 |
test/utils/NextCombinationTestCase.cpp, |
8220 |
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
8221 |
|
8222 |
2004-10-28 16:01 tim |
8223 |
|
8224 |
* src/utils/next_combination.hpp: adding replace wildcard function |
8225 |
|
8226 |
2004-10-28 15:33 tim |
8227 |
|
8228 |
* src/utils/next_combination.hpp: Minor change |
8229 |
|
8230 |
2004-10-28 15:06 tim |
8231 |
|
8232 |
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
8233 |
src/applications/simpleBuilder/simpleBuilder.cpp, |
8234 |
src/utils/next_combination.hpp, test/utils/Makefile, |
8235 |
test/utils/NextCombinationTestCase.cpp, |
8236 |
test/utils/ReplaceWildCardTestCase.cpp, |
8237 |
test/utils/next_combination.hpp: STL next_permutation like |
8238 |
next_combination is working |
8239 |
|
8240 |
2004-10-28 13:22 chrisfen |
8241 |
|
8242 |
* src/UseTheForce/WATER.cpp: fix of setDipoles |
8243 |
|
8244 |
2004-10-28 13:20 gezelter |
8245 |
|
8246 |
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
8247 |
shapeFile |
8248 |
|
8249 |
2004-10-28 13:20 gezelter |
8250 |
|
8251 |
* samples/shape/linear.md: forgot the orientation line |
8252 |
|
8253 |
2004-10-28 12:56 gezelter |
8254 |
|
8255 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8256 |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
8257 |
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
8258 |
declaration foo |
8259 |
|
8260 |
2004-10-28 12:55 gezelter |
8261 |
|
8262 |
* samples/lipid/5x5.md: uncommented .in line |
8263 |
|
8264 |
2004-10-28 11:42 tim |
8265 |
|
8266 |
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
8267 |
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
8268 |
in progress |
8269 |
|
8270 |
2004-10-28 11:15 tim |
8271 |
|
8272 |
* test/utils/: NextCombinationTestCase.cpp, |
8273 |
NextCombinationTestCase.hpp: adding next_combination test case |
8274 |
|
8275 |
2004-10-28 11:02 tim |
8276 |
|
8277 |
* test/utils/next_combination.hpp: STL Compatible combination |
8278 |
sequence generator |
8279 |
|
8280 |
2004-10-28 02:23 tim |
8281 |
|
8282 |
* test/utils/: GenerateCombination.hpp, |
8283 |
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
8284 |
|
8285 |
2004-10-28 02:16 tim |
8286 |
|
8287 |
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
8288 |
next_combination function. |
8289 |
|
8290 |
2004-10-27 23:27 tim |
8291 |
|
8292 |
* test/utils/ReplaceWildCard.hpp: no message |
8293 |
|
8294 |
2004-10-27 23:14 tim |
8295 |
|
8296 |
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
8297 |
ReplaceWildCard(recursive version) is working, need refactoring. An |
8298 |
iterative version is on the way |
8299 |
|
8300 |
2004-10-27 22:28 tim |
8301 |
|
8302 |
* test/utils/: Makefile, ReplaceWildCard.hpp, |
8303 |
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
8304 |
|
8305 |
2004-10-27 22:08 tim |
8306 |
|
8307 |
* test/utils/: ReplaceWildCardTestCase.cpp, |
8308 |
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
8309 |
|
8310 |
2004-10-27 19:17 tim |
8311 |
|
8312 |
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
8313 |
test |
8314 |
|
8315 |
2004-10-27 02:25 tim |
8316 |
|
8317 |
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
8318 |
char matching is on the way |
8319 |
|
8320 |
2004-10-27 02:07 tim |
8321 |
|
8322 |
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
8323 |
|
8324 |
2004-10-26 23:00 gezelter |
8325 |
|
8326 |
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
8327 |
|
8328 |
2004-10-26 22:20 gezelter |
8329 |
|
8330 |
* src/UseTheForce/ForceFields.hpp: subclass foo |
8331 |
|
8332 |
2004-10-26 22:16 gezelter |
8333 |
|
8334 |
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
8335 |
string conversion |
8336 |
|
8337 |
2004-10-26 20:01 gezelter |
8338 |
|
8339 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8340 |
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
8341 |
brains/SimSetup.hpp: char* -> string |
8342 |
|
8343 |
2004-10-26 18:25 gezelter |
8344 |
|
8345 |
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
8346 |
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
8347 |
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
8348 |
isXXX |
8349 |
|
8350 |
2004-10-26 18:25 gezelter |
8351 |
|
8352 |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
8353 |
define name collision |
8354 |
|
8355 |
2004-10-26 18:24 gezelter |
8356 |
|
8357 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8358 |
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
8359 |
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
8360 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8361 |
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
8362 |
forcefield refactoring for shapes |
8363 |
|
8364 |
2004-10-26 18:24 gezelter |
8365 |
|
8366 |
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
8367 |
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
8368 |
linear.md, linear.shape, toluene.shape: adding sample shape |
8369 |
directory |
8370 |
|
8371 |
2004-10-26 18:19 tim |
8372 |
|
8373 |
* ChangeLog, src/brains/DataStorage.cpp, |
8374 |
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
8375 |
test/brains/DataStorageTestCase.cpp, |
8376 |
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
8377 |
DataStorage passes unit test |
8378 |
|
8379 |
2004-10-26 14:03 chrisfen |
8380 |
|
8381 |
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
8382 |
Changes to help advance shapes |
8383 |
|
8384 |
2004-10-26 14:02 chrisfen |
8385 |
|
8386 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
8387 |
Shapes force field reader |
8388 |
|
8389 |
2004-10-26 13:28 tim |
8390 |
|
8391 |
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
8392 |
SnapshotTestCase in progress |
8393 |
|
8394 |
2004-10-25 18:46 tim |
8395 |
|
8396 |
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
8397 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
8398 |
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
8399 |
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
8400 |
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
8401 |
and Vector classes |
8402 |
|
8403 |
2004-10-25 13:03 tim |
8404 |
|
8405 |
* ChangeLog, src/utils/GenericFactory.hpp, |
8406 |
test/utils/GenericFactoryTestCase.cpp, |
8407 |
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
8408 |
GenericFactory Test Case. GenericFactory now can bed used to creat |
8409 |
ForcefieldFactory and IntegratorFactory etc. |
8410 |
|
8411 |
2004-10-25 00:08 tim |
8412 |
|
8413 |
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
8414 |
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
8415 |
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
8416 |
get reconstructed |
8417 |
|
8418 |
2004-10-24 03:55 tim |
8419 |
|
8420 |
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
8421 |
|
8422 |
2004-10-23 19:09 tim |
8423 |
|
8424 |
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
8425 |
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
8426 |
RigidBody.cpp: Refactoring in progress |
8427 |
|
8428 |
2004-10-22 19:09 tim |
8429 |
|
8430 |
* ChangeLog, src/brains/Snapshot.hpp, |
8431 |
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
8432 |
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
8433 |
test/brains/StuntDouble.hpp: more work in Snapshot |
8434 |
|
8435 |
2004-10-22 18:59 chrisfen |
8436 |
|
8437 |
* src/: UseTheForce/LJFF.cpp, |
8438 |
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
8439 |
god! It runs and conserves energy! |
8440 |
|
8441 |
2004-10-22 18:54 chrisfen |
8442 |
|
8443 |
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
8444 |
|
8445 |
2004-10-22 18:53 chrisfen |
8446 |
|
8447 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8448 |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
8449 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8450 |
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
8451 |
breakey |
8452 |
|
8453 |
2004-10-22 18:53 chrisfen |
8454 |
|
8455 |
* make/Makefile.in: compiler flags |
8456 |
|
8457 |
2004-10-22 17:20 gezelter |
8458 |
|
8459 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8460 |
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
8461 |
brains/fSimulation.h, types/AtomType.hpp, |
8462 |
types/DirectionalAtomType.hpp: fixey fixey |
8463 |
|
8464 |
2004-10-22 16:22 gezelter |
8465 |
|
8466 |
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
8467 |
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
8468 |
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
8469 |
fortran files and c/Fortran interfaces |
8470 |
|
8471 |
2004-10-22 16:21 gezelter |
8472 |
|
8473 |
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
8474 |
DirectionalAtomType.hpp, Makefile: More on AtomType and |
8475 |
DirectionalAtomType |
8476 |
|
8477 |
2004-10-22 10:47 gezelter |
8478 |
|
8479 |
* src/types/AtomType.hpp: Adding AtomType |
8480 |
|
8481 |
2004-10-21 17:31 tim |
8482 |
|
8483 |
* ChangeLog, src/brains/Snapshot.hpp, |
8484 |
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
8485 |
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
8486 |
src/math/Vector.hpp, src/math/Vector3.hpp, |
8487 |
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
8488 |
Snapshot and SnapshotManager in progress |
8489 |
|
8490 |
2004-10-21 17:30 tim |
8491 |
|
8492 |
* test/brains/: BrainsTest.cpp, Makefile, |
8493 |
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
8494 |
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
8495 |
Snapshot and snapshotManager. |
8496 |
|
8497 |
2004-10-21 16:15 gezelter |
8498 |
|
8499 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8500 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
8501 |
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
8502 |
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
8503 |
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
8504 |
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
8505 |
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
8506 |
Fixey Fixey. |
8507 |
|
8508 |
2004-10-21 12:32 tim |
8509 |
|
8510 |
* src/utils/GenericData.cpp, src/utils/Makefile, |
8511 |
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
8512 |
|
8513 |
2004-10-21 12:24 tim |
8514 |
|
8515 |
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
8516 |
|
8517 |
2004-10-21 12:22 tim |
8518 |
|
8519 |
* ChangeLog, src/brains/SimSetup.cpp, |
8520 |
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
8521 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
8522 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
8523 |
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
8524 |
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
8525 |
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
8526 |
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
8527 |
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
8528 |
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
8529 |
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
8530 |
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
8531 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
8532 |
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
8533 |
GenericData |
8534 |
|
8535 |
2004-10-21 11:25 chuckv |
8536 |
|
8537 |
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
8538 |
module. |
8539 |
|
8540 |
2004-10-21 11:24 chuckv |
8541 |
|
8542 |
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
8543 |
fortran lj module. |
8544 |
|
8545 |
2004-10-20 18:54 tim |
8546 |
|
8547 |
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
8548 |
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
8549 |
test/utils/PropertyMapTestCase.cpp, |
8550 |
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
8551 |
GenericData and PropertyMap pass unit test. |
8552 |
|
8553 |
2004-10-20 17:52 gezelter |
8554 |
|
8555 |
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
8556 |
DarkSide/sticky_interface.h: fixed a fortran name problem |
8557 |
|
8558 |
2004-10-20 17:38 tim |
8559 |
|
8560 |
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
8561 |
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
8562 |
UtilTest, UtilTest.cpp: adding generic data test case |
8563 |
|
8564 |
2004-10-20 17:16 chuckv |
8565 |
|
8566 |
* configure, ac-tools/aclocal.m4, |
8567 |
src/UseTheForce/DarkSide/Makefile, |
8568 |
src/UseTheForce/DarkSide/mpiSimulation.F90, |
8569 |
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
8570 |
src/UseTheForce/DarkSide/simParallel.F90, |
8571 |
src/UseTheForce/DarkSide/simParallel_interface.h, |
8572 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
8573 |
Fortran/C++ interface de-obfuscation project appears to be |
8574 |
complete! Woo hoo! |
8575 |
|
8576 |
2004-10-20 16:47 chuckv |
8577 |
|
8578 |
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
8579 |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
8580 |
continues |
8581 |
|
8582 |
2004-10-20 16:46 chuckv |
8583 |
|
8584 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
8585 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
8586 |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
8587 |
UseTheForce/doForces_interface.h, |
8588 |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
8589 |
UseTheForce/DarkSide/atype_interface.h, |
8590 |
UseTheForce/DarkSide/eam_interface.h, |
8591 |
UseTheForce/DarkSide/gb_interface.h, |
8592 |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
8593 |
UseTheForce/DarkSide/shapes_interface.h, |
8594 |
UseTheForce/DarkSide/simulation_interface.h, |
8595 |
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
8596 |
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
8597 |
de-obfuscation project (It is a very long story) |
8598 |
|
8599 |
2004-10-20 14:07 tim |
8600 |
|
8601 |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
8602 |
test/math/SquareMatrix3TestCase.cpp, |
8603 |
test/math/SquareMatrixTestCase.cpp, |
8604 |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
8605 |
|
8606 |
2004-10-20 01:52 tim |
8607 |
|
8608 |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
8609 |
SnapshotManager in design phase |
8610 |
|
8611 |
2004-10-20 00:54 gezelter |
8612 |
|
8613 |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
8614 |
problem prevented linking |
8615 |
|
8616 |
2004-10-20 00:54 gezelter |
8617 |
|
8618 |
* src/UseTheForce/Shapes_FF.cpp: fixed include |
8619 |
|
8620 |
2004-10-20 00:26 gezelter |
8621 |
|
8622 |
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
8623 |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
8624 |
more fortran name mangling |
8625 |
|
8626 |
2004-10-20 00:23 gezelter |
8627 |
|
8628 |
* src/profiling/timing.F90: yet more fortran renaming |
8629 |
|
8630 |
2004-10-20 00:19 gezelter |
8631 |
|
8632 |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
8633 |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
8634 |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
8635 |
wrappers.F90: Fortran name cleanup continues |
8636 |
|
8637 |
2004-10-20 00:12 gezelter |
8638 |
|
8639 |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
8640 |
broken fortran stuff |
8641 |
|
8642 |
2004-10-20 00:02 gezelter |
8643 |
|
8644 |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
8645 |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
8646 |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
8647 |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
8648 |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
8649 |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
8650 |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
8651 |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
8652 |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
8653 |
shapes_interface.h, shapes_module.h, simulation.F90, |
8654 |
simulation_interface.h, simulation_module.F90, |
8655 |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
8656 |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
8657 |
name sanity on the fortran side |
8658 |
|
8659 |
2004-10-19 20:18 tim |
8660 |
|
8661 |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
8662 |
|
8663 |
2004-10-19 19:01 tim |
8664 |
|
8665 |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
8666 |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
8667 |
except diagonalize(), all of functions in math library pass the |
8668 |
test |
8669 |
|
8670 |
2004-10-19 18:43 chuckv |
8671 |
|
8672 |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
8673 |
C-fortran interface functions. |
8674 |
|
8675 |
2004-10-19 18:37 chuckv |
8676 |
|
8677 |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
8678 |
eam_module_inteface.h, gb_module_interface.h, |
8679 |
mpisimulation_module_interface.h, simulation_module_interface.h, |
8680 |
sticky_pair_module_interface.h: Added correct prototypes for |
8681 |
C-fortran interface functions. |
8682 |
|
8683 |
2004-10-19 17:28 tim |
8684 |
|
8685 |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
8686 |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
8687 |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
8688 |
test/math/RectMatrixTestCase.cpp, |
8689 |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
8690 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
8691 |
bugs get fixed at math library |
8692 |
|
8693 |
2004-10-19 16:43 chuckv |
8694 |
|
8695 |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
8696 |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
8697 |
DarkSide/mpisimulation_module_interface.h, |
8698 |
DarkSide/simulation_module_interface.h, |
8699 |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
8700 |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
8701 |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
8702 |
DarkSide/simulation_module.F90, do_Forces.F90, |
8703 |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
8704 |
notifycutoffs_module_interface.h: Added new files for fortran |
8705 |
interface. |
8706 |
|
8707 |
2004-10-19 16:43 gezelter |
8708 |
|
8709 |
* src/UseTheForce/Makefile: regressing |
8710 |
|
8711 |
2004-10-19 16:40 gezelter |
8712 |
|
8713 |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
8714 |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
8715 |
working on shapes for portability |
8716 |
|
8717 |
2004-10-19 16:40 gezelter |
8718 |
|
8719 |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
8720 |
|
8721 |
2004-10-19 14:21 chrisfen |
8722 |
|
8723 |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
8724 |
findBegin |
8725 |
|
8726 |
2004-10-19 00:34 tim |
8727 |
|
8728 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
8729 |
are fixed in Vector class |
8730 |
|
8731 |
2004-10-19 00:28 tim |
8732 |
|
8733 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
8734 |
some bugs in RectMatrixTestCase |
8735 |
|
8736 |
2004-10-19 00:21 tim |
8737 |
|
8738 |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
8739 |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
8740 |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
8741 |
test/math/VectorTestCase.hpp: implement more test cases |
8742 |
|
8743 |
2004-10-18 19:13 tim |
8744 |
|
8745 |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
8746 |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
8747 |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
8748 |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
8749 |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
8750 |
tests on math library |
8751 |
|
8752 |
2004-10-18 17:03 tim |
8753 |
|
8754 |
* test/math/: Makefile, QuaternionTestCase.cpp, |
8755 |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
8756 |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
8757 |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
8758 |
more testing units |
8759 |
|
8760 |
2004-10-18 13:07 tim |
8761 |
|
8762 |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
8763 |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
8764 |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
8765 |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
8766 |
|
8767 |
2004-10-18 12:30 gezelter |
8768 |
|
8769 |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
8770 |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
8771 |
\phi) |
8772 |
|
8773 |
2004-10-18 12:29 gezelter |
8774 |
|
8775 |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
8776 |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
8777 |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
8778 |
Shapes into OOPSE |
8779 |
|
8780 |
2004-10-18 11:21 gezelter |
8781 |
|
8782 |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
8783 |
|
8784 |
2004-10-18 01:23 tim |
8785 |
|
8786 |
* test/math/VectorTestCase.hpp: adding vector test case |
8787 |
|
8788 |
2004-10-18 01:23 tim |
8789 |
|
8790 |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
8791 |
test case |
8792 |
|
8793 |
2004-10-16 21:19 tim |
8794 |
|
8795 |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
8796 |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
8797 |
progress |
8798 |
|
8799 |
2004-10-15 21:31 tim |
8800 |
|
8801 |
* src/math/Quaternion.hpp: add quaternion class |
8802 |
|
8803 |
2004-10-15 17:11 tim |
8804 |
|
8805 |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
8806 |
IfstrstreamTestCase.hpp: adding test file |
8807 |
|
8808 |
2004-10-15 17:10 tim |
8809 |
|
8810 |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
8811 |
|
8812 |
2004-10-15 16:42 tim |
8813 |
|
8814 |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
8815 |
|
8816 |
2004-10-15 16:35 tim |
8817 |
|
8818 |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
8819 |
|
8820 |
2004-10-15 16:34 tim |
8821 |
|
8822 |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
8823 |
namespace oopse |
8824 |
|
8825 |
2004-10-15 15:38 chuckv |
8826 |
|
8827 |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
8828 |
XLF and XLC. |
8829 |
|
8830 |
2004-10-15 14:28 tim |
8831 |
|
8832 |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
8833 |
adding ifstrstream test case |
8834 |
|
8835 |
2004-10-15 14:20 tim |
8836 |
|
8837 |
* src/io/basic_ifstrstream.hpp: fix include |
8838 |
|
8839 |
2004-10-15 14:18 tim |
8840 |
|
8841 |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
8842 |
|
8843 |
2004-10-15 14:17 tim |
8844 |
|
8845 |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
8846 |
|
8847 |
2004-10-15 14:16 tim |
8848 |
|
8849 |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
8850 |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
8851 |
|
8852 |
2004-10-15 11:37 tim |
8853 |
|
8854 |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
8855 |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
8856 |
|
8857 |
2004-10-15 11:20 tim |
8858 |
|
8859 |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
8860 |
|
8861 |
2004-10-15 11:19 tim |
8862 |
|
8863 |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
8864 |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
8865 |
SquareMatrixTestCase class |
8866 |
|
8867 |
2004-10-15 03:52 tim |
8868 |
|
8869 |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
8870 |
|
8871 |
2004-10-14 19:28 tim |
8872 |
|
8873 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
8874 |
Vector.hpp: math library in progress |
8875 |
|
8876 |
2004-10-14 19:27 tim |
8877 |
|
8878 |
* src/io/FileReader.hpp: FileReader in progress |
8879 |
|
8880 |
2004-10-13 19:53 tim |
8881 |
|
8882 |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
8883 |
test in isOrthogonal of SquareMatrix is failed by some reasons |
8884 |
|
8885 |
2004-10-13 18:28 tim |
8886 |
|
8887 |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
8888 |
class |
8889 |
|
8890 |
2004-10-13 18:27 tim |
8891 |
|
8892 |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
8893 |
RectMatrixTestCase.hpp: adding testing unit |
8894 |
|
8895 |
2004-10-13 18:24 tim |
8896 |
|
8897 |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
8898 |
|
8899 |
2004-10-13 02:51 tim |
8900 |
|
8901 |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
8902 |
Vector3.hpp: refactory vector and matrix classes |
8903 |
|
8904 |
2004-10-13 02:50 tim |
8905 |
|
8906 |
* src/math/Vector3d.hpp: Remove some Makefile.in |
8907 |
|
8908 |
2004-10-12 19:57 tim |
8909 |
|
8910 |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
8911 |
Matrix3x3d.hpp |
8912 |
|
8913 |
2004-10-12 15:08 tim |
8914 |
|
8915 |
* doc/: cppstyle.html, style.css: adding c++ coding style |
8916 |
|
8917 |
2004-10-11 18:15 tim |
8918 |
|
8919 |
* src/: constraints/AbstractClasses.hpp, |
8920 |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
8921 |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
8922 |
|
8923 |
2004-10-11 17:54 tim |
8924 |
|
8925 |
* scripts/filepp: fix a bug in filepp |
8926 |
|
8927 |
2004-10-11 17:13 tim |
8928 |
|
8929 |
* make/Makefile.in: using filepp to generate dependencies instead |
8930 |
of compilers |
8931 |
|
8932 |
2004-10-11 17:10 tim |
8933 |
|
8934 |
* scripts/filepp: filepp can be used to generate dependencies for |
8935 |
c/c++ now |
8936 |
|
8937 |
2004-10-11 14:40 tim |
8938 |
|
8939 |
* make/Makefile.in: remove -module from F90Options |
8940 |
|
8941 |
2004-10-11 14:01 tim |
8942 |
|
8943 |
* make/Makefile.in: adding rules to move fortran 90 module to |
8944 |
target directory |
8945 |
|
8946 |
2004-10-11 11:43 gezelter |
8947 |
|
8948 |
* make/Makefile.in: fixed makefile.in |
8949 |
|
8950 |
2004-10-11 10:51 tim |
8951 |
|
8952 |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
8953 |
machine |
8954 |
|
8955 |
2004-10-11 10:26 tim |
8956 |
|
8957 |
* forceFields/Makefile: add Makefile |
8958 |
|
8959 |
2004-10-11 10:23 tim |
8960 |
|
8961 |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
8962 |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
8963 |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
8964 |
directory |
8965 |
|
8966 |
2004-10-11 10:23 tim |
8967 |
|
8968 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
8969 |
Makefile |
8970 |
|
8971 |
2004-10-09 02:01 tim |
8972 |
|
8973 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
8974 |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
8975 |
Remove some Makefile.in |
8976 |
|
8977 |
2004-10-08 19:15 tim |
8978 |
|
8979 |
* make/Makefile.in: [no log message] |
8980 |
|
8981 |
2004-10-08 18:51 tim |
8982 |
|
8983 |
* make/Makefile.in: fix make install |
8984 |
|
8985 |
2004-10-08 18:10 tim |
8986 |
|
8987 |
* make/Makefile.in: adding make install |
8988 |
|
8989 |
2004-10-08 18:04 tim |
8990 |
|
8991 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
8992 |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
8993 |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
8994 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
8995 |
water/ssde/Makefile, water/ssde/Makefile.in, |
8996 |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
8997 |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
8998 |
zcons/Makefile.in: add Makefile to sample directory |
8999 |
|
9000 |
2004-10-06 19:03 gezelter |
9001 |
|
9002 |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
9003 |
stuff |
9004 |
|
9005 |
2004-10-06 19:03 gezelter |
9006 |
|
9007 |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
9008 |
make/Doxyfile, src/applications/getopt.c, |
9009 |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
9010 |
build fixes |
9011 |
|
9012 |
2004-10-06 18:20 tim |
9013 |
|
9014 |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
9015 |
|
9016 |
2004-10-06 18:19 tim |
9017 |
|
9018 |
* scripts/filepp: filepp can handle different fortran module case |
9019 |
and suffix |
9020 |
|
9021 |
2004-10-06 17:27 gezelter |
9022 |
|
9023 |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
9024 |
OOPSE-2.0 directory structure yet |
9025 |
|
9026 |
2004-10-06 17:27 gezelter |
9027 |
|
9028 |
* ChangeLog: Yeah yeah, we'lll get around to it later |
9029 |
|
9030 |
2004-10-06 17:22 gezelter |
9031 |
|
9032 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
9033 |
make/Makefile.in: cleaning up build process |
9034 |
|
9035 |
2004-10-06 16:01 chrisfen |
9036 |
|
9037 |
* src/restraints/Restraints.cpp: made the file reading in |
9038 |
restraints more intelligent - no longer gives uninformative seg |
9039 |
faults |
9040 |
|
9041 |
2004-10-06 15:55 gezelter |
9042 |
|
9043 |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
9044 |
|
9045 |
2004-10-06 15:51 gezelter |
9046 |
|
9047 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
9048 |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
9049 |
|
9050 |
2004-10-06 14:53 tim |
9051 |
|
9052 |
* make/: Makefile, Makefile.in: fix make statistics |
9053 |
|
9054 |
2004-10-06 14:18 tim |
9055 |
|
9056 |
* make/: Makefile, Makefile.in: adding GNU make functions to |
9057 |
combine all of the static libraries to a big library |
9058 |
|
9059 |
2004-10-05 18:57 tim |
9060 |
|
9061 |
* make/: Makefile, Makefile.in: adding shared library flag |
9062 |
|
9063 |
2004-10-05 15:37 tim |
9064 |
|
9065 |
* src/: Makefile, UseTheForce/Makefile, |
9066 |
UseTheForce/mpiSimulation_module.F90, |
9067 |
UseTheForce/DarkSide/Makefile, |
9068 |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
9069 |
mpiSimulation_module to DarkSide |
9070 |
|
9071 |
2004-10-05 15:35 tim |
9072 |
|
9073 |
* make/: Makefile, Makefile.in: building MPI version;using static |
9074 |
library instead of shared library |
9075 |
|
9076 |
2004-10-05 10:14 tim |
9077 |
|
9078 |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
9079 |
to filepp |
9080 |
|
9081 |
2004-10-04 16:56 tim |
9082 |
|
9083 |
* make/: Makefile, Makefile.in: add make cvslog |
9084 |
|
9085 |
2004-10-04 12:24 gezelter |
9086 |
|
9087 |
* make/: Makefile, Makefile.in: more work on the parallel build |
9088 |
|
9089 |
2004-10-04 12:06 gezelter |
9090 |
|
9091 |
* make/: Makefile, Makefile.in: changes to backport declare flags |
9092 |
|
9093 |
2004-10-04 11:27 gezelter |
9094 |
|
9095 |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
9096 |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
9097 |
shapes |
9098 |
|
9099 |
2004-10-02 00:40 tim |
9100 |
|
9101 |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
9102 |
|
9103 |
2004-10-02 00:22 tim |
9104 |
|
9105 |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
9106 |
|
9107 |
2004-10-01 17:59 tim |
9108 |
|
9109 |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
9110 |
|
9111 |
2004-10-01 17:22 gezelter |
9112 |
|
9113 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
9114 |
few minor build changes |
9115 |
|
9116 |
2004-10-01 17:11 tim |
9117 |
|
9118 |
* scripts/filepp: adding fortran90 make dependency tool |
9119 |
|
9120 |
2004-09-30 11:41 tim |
9121 |
|
9122 |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
9123 |
remove object files belong to current package. turn off silent |
9124 |
mode |
9125 |
|
9126 |
2004-09-29 17:55 tim |
9127 |
|
9128 |
* src/: Makefile, UseTheForce/Makefile, |
9129 |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
9130 |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
9131 |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
9132 |
integrators/Makefile, io/Makefile, math/Makefile, |
9133 |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
9134 |
restraints/Makefile, types/Makefile, utils/Makefile, |
9135 |
visitors/Makefile: define DEV_ROOT as relative path |
9136 |
|
9137 |
2004-09-29 17:54 tim |
9138 |
|
9139 |
* make/: Makefile, Makefile.in: get the relative path by shell |
9140 |
script |
9141 |
|
9142 |
2004-09-29 17:32 tim |
9143 |
|
9144 |
* make/Makefile: eliminate DEV_ROOT by relative path |
9145 |
|
9146 |
2004-09-29 14:37 tim |
9147 |
|
9148 |
* make/Makefile.in: add PackageLibs; fix dependency rule |
9149 |
|
9150 |
2004-09-29 13:57 gezelter |
9151 |
|
9152 |
* configure, ac-tools/configure.in: updates |
9153 |
|
9154 |
2004-09-29 13:56 gezelter |
9155 |
|
9156 |
* make/: Make.conf.in, Makefile.in, _files/style.css: Working on |
9157 |
make stuff |
9158 |
|
9159 |
2004-09-29 13:46 tim |
9160 |
|
9161 |
* Makefile: If makefile does not exist, print error message |
9162 |
|
9163 |
2004-09-29 13:12 tim |
9164 |
|
9165 |
* make/: Make.conf.in, Makefile: fix dependencies rule |
9166 |
|
9167 |
2004-09-29 11:58 gezelter |
9168 |
|
9169 |
* Makefile, make/Makefile: still working on build process |
9170 |
|
9171 |
2004-09-29 11:00 tim |
9172 |
|
9173 |
* make/Makefile: add print statment to rules |
9174 |
|
9175 |
2004-09-29 10:59 tim |
9176 |
|
9177 |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
9178 |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
9179 |
applications/simpleBuilder/Makefile, brains/Makefile, |
9180 |
constraints/Makefile, integrators/Makefile, io/Makefile, |
9181 |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
9182 |
profiling/Makefile, restraints/Makefile, types/Makefile, |
9183 |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
9184 |
|
9185 |
2004-09-28 22:55 tim |
9186 |
|
9187 |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
9188 |
which cause headache in bulding libutils |
9189 |
|
9190 |
2004-09-28 19:24 tim |
9191 |
|
9192 |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
9193 |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
9194 |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
9195 |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
9196 |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
9197 |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
9198 |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
9199 |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
9200 |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
9201 |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
9202 |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
9203 |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
9204 |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
9205 |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
9206 |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
9207 |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
9208 |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
9209 |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
9210 |
change directory structure of application. Every executable file is |
9211 |
replaced in seperate directory |
9212 |
|
9213 |
2004-09-28 18:15 gezelter |
9214 |
|
9215 |
* lib/dummy: Keep that lib around, please. |
9216 |
|
9217 |
2004-09-28 18:14 gezelter |
9218 |
|
9219 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
9220 |
starting a configure version |
9221 |
|
9222 |
2004-09-28 17:08 tim |
9223 |
|
9224 |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
9225 |
UseTheForce/DarkSide/Makefile, |
9226 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
9227 |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
9228 |
brains/Makefile, brains/simulation_module.F90: move fortran files |
9229 |
around to solve dependency problem |
9230 |
|
9231 |
2004-09-28 16:43 tim |
9232 |
|
9233 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
9234 |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
9235 |
src/applications/Makedepend, src/applications/Makefile, |
9236 |
src/brains/Makedepend, src/brains/simulation_module.F90, |
9237 |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
9238 |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
9239 |
src/utils/Makefile: [no log message] |
9240 |
|
9241 |
2004-09-28 16:41 tim |
9242 |
|
9243 |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
9244 |
problem |
9245 |
|
9246 |
2004-09-28 12:13 tim |
9247 |
|
9248 |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
9249 |
src/io/Makefile: add yacc and lex rules |
9250 |
|
9251 |
2004-09-27 16:24 tim |
9252 |
|
9253 |
* make/Makefile: adding include path to F90Options |
9254 |
|
9255 |
2004-09-27 16:13 tim |
9256 |
|
9257 |
* make/Makefile: change suffix from .cc to .cpp |
9258 |
|
9259 |
2004-09-24 12:27 tim |
9260 |
|
9261 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
9262 |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
9263 |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
9264 |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
9265 |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
9266 |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
9267 |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
9268 |
UseTheForce/DarkSide/notifyCutoffs.F90, |
9269 |
UseTheForce/DarkSide/switch_module.F90, |
9270 |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
9271 |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
9272 |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
9273 |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
9274 |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
9275 |
applications/cmdline.c, applications/nanoBuilder.cpp, |
9276 |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
9277 |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
9278 |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
9279 |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
9280 |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
9281 |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
9282 |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
9283 |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
9284 |
integrators/Integrator.hpp, integrators/NPT.cpp, |
9285 |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
9286 |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
9287 |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
9288 |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
9289 |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
9290 |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
9291 |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
9292 |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
9293 |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
9294 |
math/MatVec3.h, math/randomSPRNG.cpp, |
9295 |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
9296 |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
9297 |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
9298 |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
9299 |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
9300 |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
9301 |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
9302 |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
9303 |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
9304 |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
9305 |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
9306 |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
9307 |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
9308 |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
9309 |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
9310 |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
9311 |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
9312 |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
9313 |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
9314 |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
9315 |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
9316 |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
9317 |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
9318 |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
9319 |
utils/simError.c, visitors/AtomVisitor.cpp, |
9320 |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
9321 |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
9322 |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
9323 |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
9324 |
visitors/ZconsVisitor.hpp: change the #include in source files |
9325 |
|
9326 |
2004-09-24 00:16 gezelter |
9327 |
|
9328 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
9329 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
9330 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
9331 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
9332 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
9333 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
9334 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
9335 |
src/UseTheForce/fForceField.h, |
9336 |
src/UseTheForce/fSwitchingFunction.h, |
9337 |
src/UseTheForce/fortranWrapDefines.hpp, |
9338 |
src/UseTheForce/fortranWrappers.cpp, |
9339 |
src/UseTheForce/fortranWrappers.hpp, |
9340 |
src/UseTheForce/mpiComponentPlan.h, |
9341 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
9342 |
src/UseTheForce/mpiSimulation_module.F90, |
9343 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
9344 |
src/UseTheForce/DarkSide/atype_module.F90, |
9345 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
9346 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
9347 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
9348 |
src/UseTheForce/DarkSide/calc_eam.F90, |
9349 |
src/UseTheForce/DarkSide/calc_gb.F90, |
9350 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
9351 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
9352 |
src/UseTheForce/DarkSide/force_globals.F90, |
9353 |
src/UseTheForce/DarkSide/neighborLists.F90, |
9354 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
9355 |
src/UseTheForce/DarkSide/switch_module.F90, |
9356 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
9357 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
9358 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
9359 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
9360 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
9361 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
9362 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
9363 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
9364 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
9365 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
9366 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
9367 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
9368 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
9369 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
9370 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
9371 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
9372 |
src/types/MakeStamps.hpp, src/types/Makefile, |
9373 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
9374 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
9375 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
9376 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
9377 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
9378 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
9379 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
9380 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
9381 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
9382 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
9383 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
9384 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
9385 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
9386 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
9387 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
9388 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
9389 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
9390 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
9391 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
9392 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
9393 |
src/minimizers/OOPSEMinimizer.cpp, |
9394 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
9395 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
9396 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
9397 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
9398 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
9399 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
9400 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
9401 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
9402 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
9403 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
9404 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
9405 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
9406 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
9407 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
9408 |
src/utils/GenericData.hpp, src/utils/Makefile, |
9409 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
9410 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
9411 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
9412 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
9413 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
9414 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
9415 |
src/utils/simError.c, src/utils/simError.h, |
9416 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
9417 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
9418 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
9419 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
9420 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
9421 |
src/visitors/RigidBodyVisitor.cpp, |
9422 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
9423 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
9424 |
make/_files/style.css, samples/Makefile.in, |
9425 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
9426 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
9427 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
9428 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
9429 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
9430 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
9431 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
9432 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
9433 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
9434 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
9435 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
9436 |
src/applications/LatticeCreator.cpp, |
9437 |
src/applications/LatticeCreator.hpp, |
9438 |
src/applications/LatticeFactory.cpp, |
9439 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
9440 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
9441 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
9442 |
src/applications/cmdline.c, src/applications/cmdline.h, |
9443 |
src/applications/getopt.c, src/applications/getopt1.c, |
9444 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
9445 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
9446 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
9447 |
src/applications/simpleBuilder.ggo, |
9448 |
src/applications/simpleBuilderCmd.c, |
9449 |
src/integrators/AbstractClasses.hpp, |
9450 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
9451 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
9452 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
9453 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
9454 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
9455 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
9456 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
9457 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
9458 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
9459 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
9460 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
9461 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
9462 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
9463 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
9464 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
9465 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
9466 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
9467 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
9468 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
9469 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
9470 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
9471 |
samples/alkane/butane.in, samples/alkane/butane.md, |
9472 |
samples/argon/500.in, samples/argon/500.md, |
9473 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
9474 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
9475 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
9476 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
9477 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
9478 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
9479 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
9480 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
9481 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
9482 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
9483 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
9484 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
9485 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
9486 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
9487 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
9488 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
9489 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
9490 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
9491 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
9492 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
9493 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
9494 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
9495 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
9496 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
9497 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
9498 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
9499 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
9500 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
9501 |
|
9502 |
2004-09-24 00:16 gezelter |
9503 |
|
9504 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
9505 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
9506 |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
9507 |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
9508 |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
9509 |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
9510 |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
9511 |
src/UseTheForce/fForceField.h, |
9512 |
src/UseTheForce/fSwitchingFunction.h, |
9513 |
src/UseTheForce/fortranWrapDefines.hpp, |
9514 |
src/UseTheForce/fortranWrappers.cpp, |
9515 |
src/UseTheForce/fortranWrappers.hpp, |
9516 |
src/UseTheForce/mpiComponentPlan.h, |
9517 |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
9518 |
src/UseTheForce/mpiSimulation_module.F90, |
9519 |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
9520 |
src/UseTheForce/DarkSide/atype_module.F90, |
9521 |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
9522 |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
9523 |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
9524 |
src/UseTheForce/DarkSide/calc_eam.F90, |
9525 |
src/UseTheForce/DarkSide/calc_gb.F90, |
9526 |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
9527 |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
9528 |
src/UseTheForce/DarkSide/force_globals.F90, |
9529 |
src/UseTheForce/DarkSide/neighborLists.F90, |
9530 |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
9531 |
src/UseTheForce/DarkSide/switch_module.F90, |
9532 |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
9533 |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
9534 |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
9535 |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
9536 |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
9537 |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
9538 |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
9539 |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
9540 |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
9541 |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
9542 |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
9543 |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
9544 |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
9545 |
src/types/BondStamp.hpp, src/types/Component.cpp, |
9546 |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
9547 |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
9548 |
src/types/MakeStamps.hpp, src/types/Makefile, |
9549 |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
9550 |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
9551 |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
9552 |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
9553 |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
9554 |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
9555 |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
9556 |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
9557 |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
9558 |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
9559 |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
9560 |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
9561 |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
9562 |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
9563 |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
9564 |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
9565 |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
9566 |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
9567 |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
9568 |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
9569 |
src/minimizers/OOPSEMinimizer.cpp, |
9570 |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
9571 |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
9572 |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
9573 |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
9574 |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
9575 |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
9576 |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
9577 |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
9578 |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
9579 |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
9580 |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
9581 |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
9582 |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
9583 |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
9584 |
src/utils/GenericData.hpp, src/utils/Makefile, |
9585 |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
9586 |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
9587 |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
9588 |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
9589 |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
9590 |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
9591 |
src/utils/simError.c, src/utils/simError.h, |
9592 |
src/utils/status_module.F90, src/utils/vector_class.F90, |
9593 |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
9594 |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
9595 |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
9596 |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
9597 |
src/visitors/RigidBodyVisitor.cpp, |
9598 |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
9599 |
src/visitors/ZconsVisitor.hpp, make/Makefile, |
9600 |
make/_files/style.css, samples/Makefile.in, |
9601 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
9602 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
9603 |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
9604 |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
9605 |
samples/zcons/Makefile.in, samples/zcons/water.md, |
9606 |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
9607 |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
9608 |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
9609 |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
9610 |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
9611 |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
9612 |
src/applications/LatticeCreator.cpp, |
9613 |
src/applications/LatticeCreator.hpp, |
9614 |
src/applications/LatticeFactory.cpp, |
9615 |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
9616 |
src/applications/Makefile, src/applications/MoLocator.cpp, |
9617 |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
9618 |
src/applications/cmdline.c, src/applications/cmdline.h, |
9619 |
src/applications/getopt.c, src/applications/getopt1.c, |
9620 |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
9621 |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
9622 |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
9623 |
src/applications/simpleBuilder.ggo, |
9624 |
src/applications/simpleBuilderCmd.c, |
9625 |
src/integrators/AbstractClasses.hpp, |
9626 |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
9627 |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
9628 |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
9629 |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
9630 |
src/integrators/NVT.cpp, src/profiling/Makefile, |
9631 |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
9632 |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
9633 |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
9634 |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
9635 |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
9636 |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
9637 |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
9638 |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
9639 |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
9640 |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
9641 |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
9642 |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
9643 |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
9644 |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
9645 |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
9646 |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
9647 |
samples/alkane/butane.in, samples/alkane/butane.md, |
9648 |
samples/argon/500.in, samples/argon/500.md, |
9649 |
samples/argon/Makefile.in, samples/argon/ar864.in, |
9650 |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
9651 |
samples/argon/argonNVT.md, samples/argon/lj.md, |
9652 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
9653 |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
9654 |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
9655 |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
9656 |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
9657 |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
9658 |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
9659 |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
9660 |
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
9661 |
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
9662 |
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
9663 |
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
9664 |
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
9665 |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
9666 |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
9667 |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
9668 |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
9669 |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
9670 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
9671 |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
9672 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
9673 |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
9674 |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
9675 |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
9676 |
forceFields/Pt.VC.funcfl: Initial revision |
9677 |
|