1 |
+ |
2003-12-29 14:56 chuckv |
2 |
+ |
|
3 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
4 |
+ |
third-party directory for code not written by us. Also added |
5 |
+ |
Mersenne Twister random number generator code. This will eventually |
6 |
+ |
replace sprng as the random number generator used by OOPSE. |
7 |
+ |
|
8 |
+ |
2003-12-22 16:26 chuckv |
9 |
+ |
|
10 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
11 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
12 |
+ |
Fixes to profile code. |
13 |
+ |
|
14 |
+ |
2003-12-19 15:36 mmeineke |
15 |
+ |
|
16 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
17 |
+ |
timing.F90, timing.f90: More profiling fixes. |
18 |
+ |
|
19 |
+ |
2003-12-19 15:19 chuckv |
20 |
+ |
|
21 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
22 |
+ |
|
23 |
+ |
2003-12-19 15:17 chuckv |
24 |
+ |
|
25 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
26 |
+ |
|
27 |
+ |
2003-12-19 13:53 mmeineke |
28 |
+ |
|
29 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
30 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
31 |
+ |
the code |
32 |
+ |
|
33 |
+ |
2003-12-19 12:25 mmeineke |
34 |
+ |
|
35 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
36 |
+ |
some profiling routines |
37 |
+ |
|
38 |
+ |
2003-12-19 10:12 mmeineke |
39 |
+ |
|
40 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
41 |
+ |
and GofRomega |
42 |
+ |
|
43 |
+ |
additional work on randomBilayer |
44 |
+ |
|
45 |
+ |
2003-12-19 10:12 mmeineke |
46 |
+ |
|
47 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
48 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
49 |
+ |
GofRomega |
50 |
+ |
|
51 |
+ |
2003-12-18 16:47 mmeineke |
52 |
+ |
|
53 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
54 |
+ |
some profile functionality |
55 |
+ |
|
56 |
+ |
2003-12-18 15:46 chuckv |
57 |
+ |
|
58 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
59 |
+ |
Added functions for simple profiling in fortran. |
60 |
+ |
|
61 |
+ |
2003-12-17 15:13 chuckv |
62 |
+ |
|
63 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
64 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
65 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
66 |
+ |
zeros the array between scatters so half of the sum was being lost. |
67 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
68 |
+ |
nlocal. |
69 |
+ |
|
70 |
+ |
2003-12-16 15:49 mmeineke |
71 |
+ |
|
72 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
73 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
74 |
+ |
gofRomega. both need to be debugged and tested. |
75 |
+ |
|
76 |
+ |
2003-12-12 10:42 gezelter |
77 |
+ |
|
78 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
79 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
80 |
+ |
gradients (to do minimizations) |
81 |
+ |
|
82 |
+ |
2003-12-12 10:33 mmeineke |
83 |
+ |
|
84 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
85 |
+ |
header |
86 |
+ |
|
87 |
+ |
2003-12-10 11:52 mmeineke |
88 |
+ |
|
89 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
90 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
91 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
92 |
+ |
from bilayerSys to randomBilayer |
93 |
+ |
|
94 |
+ |
2003-11-25 10:44 mmeineke |
95 |
+ |
|
96 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
97 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
98 |
+ |
TB3 in DUFF.frc |
99 |
+ |
|
100 |
+ |
2003-11-21 15:09 mmeineke |
101 |
+ |
|
102 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
103 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
104 |
+ |
message in SimInfo. Added a more informative error message in |
105 |
+ |
InitializeFromFile |
106 |
+ |
|
107 |
+ |
2003-11-21 15:07 mmeineke |
108 |
+ |
|
109 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
110 |
+ |
ing in the GofR,CosTheta |
111 |
+ |
|
112 |
+ |
2003-11-21 14:31 chrisfen |
113 |
+ |
|
114 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
115 |
+ |
a bug in SimInfo ordering of radii |
116 |
+ |
|
117 |
+ |
2003-11-11 12:20 mmeineke |
118 |
+ |
|
119 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
120 |
+ |
a min function. |
121 |
+ |
|
122 |
+ |
2003-11-10 16:50 mmeineke |
123 |
+ |
|
124 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
125 |
+ |
reordered the rcut/ecr/boxSize initialization |
126 |
+ |
|
127 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
128 |
+ |
now exit when it runs into rcut or ecr. |
129 |
+ |
|
130 |
+ |
2003-11-07 16:46 chuckv |
131 |
+ |
|
132 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
133 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
134 |
+ |
use of mpich modules. We use mpif.h instead.: |
135 |
+ |
|
136 |
+ |
2003-11-07 12:09 mmeineke |
137 |
+ |
|
138 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
139 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
140 |
+ |
the atom loop in the NPT family of integrators. |
141 |
+ |
|
142 |
+ |
2003-11-06 17:01 mmeineke |
143 |
+ |
|
144 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
145 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
146 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
147 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
148 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
149 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
150 |
+ |
* useIntiTime => useInitialTime |
151 |
+ |
|
152 |
+ |
2003-11-06 14:24 mmeineke |
153 |
+ |
|
154 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
155 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
156 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
157 |
+ |
|
158 |
+ |
2003-11-06 14:11 mmeineke |
159 |
+ |
|
160 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
161 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
162 |
+ |
new-templateless branch to the main trunk. |
163 |
+ |
|
164 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
165 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
166 |
+ |
sudden deaths we saw. * some formating in the string when we |
167 |
+ |
write out the extended system state. * added NPT.cpp to the |
168 |
+ |
makefile.in |
169 |
+ |
|
170 |
+ |
2003-11-06 13:20 mmeineke |
171 |
+ |
|
172 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
173 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
174 |
+ |
bug. The box was not switching between orthorhombic and |
175 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
176 |
+ |
the check.which should fix it. |
177 |
+ |
|
178 |
+ |
2003-11-05 14:16 mmeineke |
179 |
+ |
|
180 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
181 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
182 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
183 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
184 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
185 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
186 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
187 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
188 |
+ |
some work on trying to find the compression bug |
189 |
+ |
|
190 |
+ |
2003-11-03 17:07 mmeineke |
191 |
+ |
|
192 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
193 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
194 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
195 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
196 |
+ |
most of standard template library from OOPSE. |
197 |
+ |
|
198 |
+ |
2003-10-31 16:06 mmeineke |
199 |
+ |
|
200 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
201 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
202 |
+ |
SimSetup.cpp: started work on template removal. |
203 |
+ |
|
204 |
+ |
2003-10-31 13:28 mmeineke |
205 |
+ |
|
206 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
207 |
+ |
added template stuff to the Maikefile template |
208 |
+ |
|
209 |
+ |
little changes to some printf format statements |
210 |
+ |
|
211 |
+ |
2003-10-31 13:28 mmeineke |
212 |
+ |
|
213 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
214 |
+ |
template |
215 |
+ |
|
216 |
+ |
2003-10-30 13:59 gezelter |
217 |
+ |
|
218 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
219 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
220 |
+ |
rList problems |
221 |
+ |
|
222 |
+ |
2003-10-30 09:11 gezelter |
223 |
+ |
|
224 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
225 |
+ |
queried before q0 was allocated. |
226 |
+ |
|
227 |
+ |
2003-10-29 15:41 mmeineke |
228 |
+ |
|
229 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
230 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
231 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
232 |
+ |
in bass.l |
233 |
+ |
|
234 |
+ |
fixed a little bug in the first time step, regarding the setting of |
235 |
+ |
ecr and est in fortran |
236 |
+ |
|
237 |
+ |
2003-10-29 15:40 mmeineke |
238 |
+ |
|
239 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
240 |
+ |
|
241 |
+ |
2003-10-29 12:55 mmeineke |
242 |
+ |
|
243 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
244 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
245 |
+ |
rcut is setup, as well as additional debugging comments. |
246 |
+ |
|
247 |
+ |
2003-10-29 09:28 gezelter |
248 |
+ |
|
249 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
250 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
251 |
+ |
templates |
252 |
+ |
|
253 |
+ |
2003-10-28 22:16 gezelter |
254 |
+ |
|
255 |
+ |
* src/Makefile.in: Refixed broken makefile |
256 |
+ |
|
257 |
+ |
2003-10-28 22:06 gezelter |
258 |
+ |
|
259 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
260 |
+ |
fixes |
261 |
+ |
|
262 |
+ |
2003-10-28 19:19 tim |
263 |
+ |
|
264 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
265 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
266 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
267 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
268 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
269 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
270 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
271 |
+ |
file. |
272 |
+ |
|
273 |
+ |
2003-10-28 17:25 mmeineke |
274 |
+ |
|
275 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
276 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
277 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
278 |
+ |
how c calls fortran. All function pointers and fortran calls are |
279 |
+ |
rigidly typecast now. |
280 |
+ |
|
281 |
+ |
2003-10-28 15:42 gezelter |
282 |
+ |
|
283 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
284 |
+ |
Portability fixes |
285 |
+ |
|
286 |
+ |
2003-10-28 15:09 gezelter |
287 |
+ |
|
288 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
289 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
290 |
+ |
src/Makefile.in: Compatibility fixes |
291 |
+ |
|
292 |
+ |
2003-10-28 12:08 mmeineke |
293 |
+ |
|
294 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
295 |
+ |
started work on template removal |
296 |
+ |
|
297 |
+ |
2003-10-28 12:04 gezelter |
298 |
+ |
|
299 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
300 |
+ |
trying to understand extern "C" stuff for pointers |
301 |
+ |
|
302 |
+ |
2003-10-28 11:20 gezelter |
303 |
+ |
|
304 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
305 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
306 |
+ |
|
307 |
+ |
2003-10-28 11:03 gezelter |
308 |
+ |
|
309 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
310 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
311 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
312 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
313 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
314 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
315 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
316 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
317 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
318 |
+ |
more portable c header stuff Also, mod file fixes and portability |
319 |
+ |
changes Some fortran changes will need to be reversed. |
320 |
+ |
|
321 |
+ |
2003-10-28 11:03 gezelter |
322 |
+ |
|
323 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
324 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
325 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
326 |
+ |
portable c header stuff Also, mod file fixes and portability |
327 |
+ |
changes |
328 |
+ |
|
329 |
+ |
2003-10-28 11:02 gezelter |
330 |
+ |
|
331 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
332 |
+ |
stuff |
333 |
+ |
|
334 |
+ |
2003-10-27 18:00 gezelter |
335 |
+ |
|
336 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
337 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
338 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
339 |
+ |
|
340 |
+ |
2003-10-27 17:08 mmeineke |
341 |
+ |
|
342 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
343 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
344 |
+ |
added routines for the sysbuilder to work with simSetup |
345 |
+ |
|
346 |
+ |
remved the QuickBass routines, and had all parsing go through |
347 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
348 |
+ |
|
349 |
+ |
2003-10-27 17:07 mmeineke |
350 |
+ |
|
351 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
352 |
+ |
routines for the sysbuilder to work with simSetup |
353 |
+ |
|
354 |
+ |
2003-10-27 11:20 gezelter |
355 |
+ |
|
356 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
357 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
358 |
+ |
|
359 |
+ |
2003-10-24 17:17 mmeineke |
360 |
+ |
|
361 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
362 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
363 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
364 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
365 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
366 |
+ |
from the Makefile |
367 |
+ |
|
368 |
+ |
2003-10-24 12:36 gezelter |
369 |
+ |
|
370 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
371 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
372 |
+ |
builder |
373 |
+ |
|
374 |
+ |
2003-10-24 12:35 gezelter |
375 |
+ |
|
376 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
377 |
+ |
merge problem |
378 |
+ |
|
379 |
+ |
2003-10-23 14:57 mmeineke |
380 |
+ |
|
381 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
382 |
+ |
init |
383 |
+ |
|
384 |
+ |
fixed an eam mpi parmeter setup bug |
385 |
+ |
|
386 |
+ |
added the init file to the makefile |
387 |
+ |
|
388 |
+ |
2003-10-23 14:57 mmeineke |
389 |
+ |
|
390 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
391 |
+ |
to the init |
392 |
+ |
|
393 |
+ |
fixed an eam mpi parmeter setup bug |
394 |
+ |
|
395 |
+ |
2003-10-23 14:57 mmeineke |
396 |
+ |
|
397 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
398 |
+ |
|
399 |
+ |
2003-10-22 16:17 mmeineke |
400 |
+ |
|
401 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
402 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
403 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
404 |
+ |
no box skew allowed. |
405 |
+ |
|
406 |
+ |
2003-10-21 14:33 mmeineke |
407 |
+ |
|
408 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
409 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
410 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
411 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
412 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
413 |
+ |
true; |
414 |
+ |
|
415 |
+ |
2003-10-17 16:19 mmeineke |
416 |
+ |
|
417 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
418 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
419 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
420 |
+ |
to the build list for both configure and configure.in |
421 |
+ |
|
422 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
423 |
+ |
working. |
424 |
+ |
|
425 |
+ |
2003-10-17 16:18 mmeineke |
426 |
+ |
|
427 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
428 |
+ |
build list for both configure and configure.in |
429 |
+ |
|
430 |
+ |
2003-10-17 16:17 mmeineke |
431 |
+ |
|
432 |
+ |
* configure: added the staticProps directory to the build list |
433 |
+ |
|
434 |
+ |
2003-10-16 14:16 mmeineke |
435 |
+ |
|
436 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
437 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
438 |
+ |
use linked lists instead of a vector. |
439 |
+ |
|
440 |
+ |
Fixed the makefile to build DumpReader.cpp |
441 |
+ |
|
442 |
+ |
Removed a comment output in Exclude.cpp |
443 |
+ |
|
444 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
445 |
+ |
a frame is written. This lets the .eor file represent the last |
446 |
+ |
written frame of a simulation. |
447 |
+ |
|
448 |
+ |
2003-10-10 12:10 mmeineke |
449 |
+ |
|
450 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
451 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
452 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
453 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
454 |
+ |
over to staticProps |
455 |
+ |
|
456 |
+ |
2003-10-09 17:09 mmeineke |
457 |
+ |
|
458 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
459 |
+ |
a position where it will compile and run first runs. |
460 |
+ |
|
461 |
+ |
2003-10-04 13:46 chuckv |
462 |
+ |
|
463 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
464 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
465 |
+ |
|
466 |
+ |
2003-10-04 13:08 chuckv |
467 |
+ |
|
468 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
469 |
+ |
|
470 |
+ |
2003-10-03 17:11 mmeineke |
471 |
+ |
|
472 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
473 |
+ |
entahlpy from the statwriter and thermo. |
474 |
+ |
|
475 |
+ |
2003-10-03 17:02 mmeineke |
476 |
+ |
|
477 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
478 |
+ |
statements in simError |
479 |
+ |
|
480 |
+ |
added a function to get the maxCutoff |
481 |
+ |
|
482 |
+ |
2003-10-03 17:01 mmeineke |
483 |
+ |
|
484 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
485 |
+ |
statements in simError |
486 |
+ |
|
487 |
+ |
2003-09-30 11:00 mmeineke |
488 |
+ |
|
489 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
490 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
491 |
+ |
|
492 |
+ |
2003-09-29 17:06 mmeineke |
493 |
+ |
|
494 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
495 |
+ |
for conifig.in |
496 |
+ |
|
497 |
+ |
fixed wrappers to extern "C" |
498 |
+ |
|
499 |
+ |
2003-09-29 17:06 mmeineke |
500 |
+ |
|
501 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
502 |
+ |
conifig.in |
503 |
+ |
|
504 |
+ |
2003-09-29 17:05 mmeineke |
505 |
+ |
|
506 |
+ |
* configure: added mpif90 mod check back |
507 |
+ |
|
508 |
+ |
2003-09-29 16:16 mmeineke |
509 |
+ |
|
510 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
511 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
512 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
513 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
514 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
515 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
516 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
517 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
518 |
+ |
found with SUN's SUNWspro.s1s7 |
519 |
+ |
|
520 |
+ |
2003-09-29 12:38 mmeineke |
521 |
+ |
|
522 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
523 |
+ |
signifigant change. |
524 |
+ |
|
525 |
+ |
2003-09-25 16:17 mmeineke |
526 |
+ |
|
527 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
528 |
+ |
additional remarks from icc -w3 (extra verbose output) |
529 |
+ |
|
530 |
+ |
2003-09-25 14:27 mmeineke |
531 |
+ |
|
532 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
533 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
534 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
535 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
536 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
537 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
538 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
539 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
540 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
541 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
542 |
+ |
gcc -Wall and g++ -Wall |
543 |
+ |
|
544 |
+ |
2003-09-25 13:54 gezelter |
545 |
+ |
|
546 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
547 |
+ |
|
548 |
+ |
2003-09-25 11:42 gezelter |
549 |
+ |
|
550 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
551 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
552 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
553 |
+ |
fixes for configure |
554 |
+ |
|
555 |
+ |
2003-09-24 14:34 mmeineke |
556 |
+ |
|
557 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
558 |
+ |
that it is called before the first Statistics are written. |
559 |
+ |
|
560 |
+ |
2003-09-23 15:36 gezelter |
561 |
+ |
|
562 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
563 |
+ |
bunch of Make.dep files to CVS |
564 |
+ |
|
565 |
+ |
2003-09-23 15:34 mmeineke |
566 |
+ |
|
567 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
568 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
569 |
+ |
|
570 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
571 |
+ |
|
572 |
+ |
2003-09-22 18:07 tim |
573 |
+ |
|
574 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
575 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
576 |
+ |
|
577 |
+ |
2003-09-22 16:23 mmeineke |
578 |
+ |
|
579 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
580 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
581 |
+ |
Converted NPTf to work with the NPT base class. |
582 |
+ |
|
583 |
+ |
Removed NPTfm and NPTim from cvs |
584 |
+ |
|
585 |
+ |
2003-09-19 15:00 mmeineke |
586 |
+ |
|
587 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
588 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
589 |
+ |
class. NPTi is up to date. NPTf is not. |
590 |
+ |
|
591 |
+ |
2003-09-19 11:03 mmeineke |
592 |
+ |
|
593 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
594 |
+ |
makefile |
595 |
+ |
|
596 |
+ |
2003-09-19 11:01 gezelter |
597 |
+ |
|
598 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
599 |
+ |
|
600 |
+ |
2003-09-19 11:01 gezelter |
601 |
+ |
|
602 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
603 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
604 |
+ |
|
605 |
+ |
2003-09-19 10:20 mmeineke |
606 |
+ |
|
607 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
608 |
+ |
|
609 |
+ |
2003-09-19 09:55 gezelter |
610 |
+ |
|
611 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
612 |
+ |
samples/water/ssd.bass: [no log message] |
613 |
+ |
|
614 |
+ |
2003-09-19 09:22 tim |
615 |
+ |
|
616 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
617 |
+ |
|
618 |
+ |
2003-09-17 09:22 mmeineke |
619 |
+ |
|
620 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
621 |
+ |
work with constraints. |
622 |
+ |
|
623 |
+ |
2003-09-16 15:02 tim |
624 |
+ |
|
625 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
626 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
627 |
+ |
|
628 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
629 |
+ |
|
630 |
+ |
NPTi appears very stable. |
631 |
+ |
|
632 |
+ |
2003-09-15 11:52 tim |
633 |
+ |
|
634 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
635 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
636 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
637 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
638 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
639 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
640 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
641 |
+ |
statWriter fix bug of vector wrapping at NPTi |
642 |
+ |
|
643 |
+ |
2003-09-12 11:20 gezelter |
644 |
+ |
|
645 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
646 |
+ |
Makefile.in |
647 |
+ |
|
648 |
+ |
2003-09-12 11:20 gezelter |
649 |
+ |
|
650 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
651 |
+ |
|
652 |
+ |
2003-09-09 15:35 mmeineke |
653 |
+ |
|
654 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
655 |
+ |
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
656 |
+ |
|
657 |
+ |
added two new NPT integrators, they still need work. |
658 |
+ |
|
659 |
+ |
2003-09-09 15:34 mmeineke |
660 |
+ |
|
661 |
+ |
* ChangeLog: updated the ChangeLog |
662 |
+ |
|
663 |
+ |
2003-09-05 17:45 gezelter |
664 |
+ |
|
665 |
+ |
* libmdtools/Make.dep: dependency on config.h |
666 |
+ |
|
667 |
+ |
2003-09-05 17:36 gezelter |
668 |
+ |
|
669 |
+ |
* configure, ac-tools/aclocal.m4: fixed sprng problem |
670 |
+ |
|
671 |
+ |
2003-09-05 16:29 gezelter |
672 |
+ |
|
673 |
+ |
* samples/metals/Makefile.in: New Makefile for metals sample |
674 |
+ |
|
675 |
+ |
2003-09-05 16:27 gezelter |
676 |
+ |
|
677 |
+ |
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
678 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
679 |
+ |
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
680 |
+ |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
681 |
+ |
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
682 |
+ |
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
683 |
+ |
libmdtools/Makefile, libmdtools/Makefile.in, |
684 |
+ |
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
685 |
+ |
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
686 |
+ |
libmdtools/fortranWrappers.cpp, |
687 |
+ |
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
688 |
+ |
libmdtools/simulation_module.F90, samples/Makefile, |
689 |
+ |
samples/Makefile.in, samples/alkane/Makefile, |
690 |
+ |
samples/alkane/Makefile.in, samples/argon/Makefile, |
691 |
+ |
samples/argon/Makefile.in, samples/argon/argon.bass, |
692 |
+ |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
693 |
+ |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
694 |
+ |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
695 |
+ |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
696 |
+ |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
697 |
+ |
autoconf / configure method of configuring OOPSE |
698 |
+ |
|
699 |
+ |
2003-09-04 16:48 mmeineke |
700 |
+ |
|
701 |
+ |
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
702 |
+ |
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
703 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
704 |
+ |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
705 |
+ |
added resetTime to the Global namespace. |
706 |
+ |
|
707 |
+ |
added ability to reset the integrators in the NVT and NPT family. |
708 |
+ |
|
709 |
+ |
2003-09-04 16:48 mmeineke |
710 |
+ |
|
711 |
+ |
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
712 |
+ |
namespace. |
713 |
+ |
|
714 |
+ |
2003-09-02 09:30 tim |
715 |
+ |
|
716 |
+ |
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
717 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
718 |
+ |
PolicyByMass |
719 |
+ |
|
720 |
+ |
2003-08-28 16:09 tim |
721 |
+ |
|
722 |
+ |
* ChangeLog, libmdtools/GenericData.cpp, |
723 |
+ |
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
724 |
+ |
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
725 |
+ |
|
726 |
+ |
2003-08-27 14:23 tim |
727 |
+ |
|
728 |
+ |
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
729 |
+ |
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
730 |
+ |
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
731 |
+ |
turn on the optimization flag, it causes a seg fault |
732 |
+ |
|
733 |
+ |
2003-08-27 11:25 gezelter |
734 |
+ |
|
735 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
736 |
+ |
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
737 |
+ |
stress tensor parallel bug. |
738 |
+ |
|
739 |
+ |
2003-08-27 11:16 tim |
740 |
+ |
|
741 |
+ |
* ChangeLog, libmdtools/DUFF.cpp, |
742 |
+ |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
743 |
+ |
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
744 |
+ |
molMembershipList use global index instead of local index |
745 |
+ |
|
746 |
|
2003-08-26 15:37 tim |
747 |
|
|
748 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
993 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
994 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
995 |
|
works..... |
251 |
– |
|
252 |
– |
2003-08-08 13:32 mmeineke |
253 |
– |
|
254 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
255 |
– |
moved frameCount's functionality into DumpReader. also split props |
256 |
– |
into staticProps and dynamicProps. (currently only have |
257 |
– |
staticProps) |
996 |
|
|
997 |
|
2003-08-08 12:48 mmeineke |
998 |
|
|
1050 |
|
2003-07-29 11:32 mmeineke |
1051 |
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1052 |
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* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1053 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1054 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
317 |
< |
src/Makefile: working on the props code |
1053 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1054 |
> |
working on the props code |
1055 |
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1056 |
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2003-07-29 11:32 mmeineke |
1057 |
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