1 |
+ |
2004-01-12 15:37 tim |
2 |
+ |
|
3 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
4 |
+ |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
5 |
+ |
master nodes |
6 |
+ |
|
7 |
+ |
2004-01-10 04:46 tim |
8 |
+ |
|
9 |
+ |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
10 |
+ |
roll it back fix a bug of copying string to a pointer Still have |
11 |
+ |
Seg fault, it looks like a random MPI seg fault in totalview |
12 |
+ |
|
13 |
+ |
2004-01-09 21:15 tim |
14 |
+ |
|
15 |
+ |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
16 |
+ |
|
17 |
+ |
2004-01-09 15:29 gezelter |
18 |
+ |
|
19 |
+ |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
20 |
+ |
|
21 |
+ |
2004-01-08 17:25 chuckv |
22 |
+ |
|
23 |
+ |
* libmdtools/DumpWriter.cpp: A work in progress... |
24 |
+ |
|
25 |
+ |
2004-01-08 13:59 gezelter |
26 |
+ |
|
27 |
+ |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
28 |
+ |
case |
29 |
+ |
|
30 |
+ |
2004-01-08 13:13 mmeineke |
31 |
+ |
|
32 |
+ |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
33 |
+ |
state bug. |
34 |
+ |
|
35 |
+ |
2004-01-08 13:05 gezelter |
36 |
+ |
|
37 |
+ |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
38 |
+ |
|
39 |
+ |
2004-01-08 12:57 mmeineke |
40 |
+ |
|
41 |
+ |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
42 |
+ |
exstended state bug |
43 |
+ |
|
44 |
+ |
2004-01-08 12:40 gezelter |
45 |
+ |
|
46 |
+ |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
47 |
+ |
|
48 |
+ |
2004-01-08 10:44 mmeineke |
49 |
+ |
|
50 |
+ |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
51 |
+ |
XS state info flag |
52 |
+ |
|
53 |
+ |
2004-01-07 14:26 tim |
54 |
+ |
|
55 |
+ |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
56 |
+ |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
57 |
+ |
sending message from master node to itself in DumpWriter.cpp and |
58 |
+ |
InitializeFromFile.cpp |
59 |
+ |
|
60 |
+ |
2004-01-06 14:49 chuckv |
61 |
+ |
|
62 |
+ |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
63 |
+ |
performance fixes in the dipole dipole and reaction field code |
64 |
+ |
|
65 |
+ |
2004-01-06 13:54 chuckv |
66 |
+ |
|
67 |
+ |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
68 |
+ |
little more sane |
69 |
+ |
|
70 |
+ |
2004-01-05 17:49 chuckv |
71 |
+ |
|
72 |
+ |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
73 |
+ |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
74 |
+ |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
75 |
+ |
performance by reducing spurious function calls |
76 |
+ |
|
77 |
+ |
2004-01-05 17:18 chuckv |
78 |
+ |
|
79 |
+ |
* libmdtools/do_Forces.F90: mangling forces even further |
80 |
+ |
|
81 |
+ |
2004-01-05 17:18 chuckv |
82 |
+ |
|
83 |
+ |
* configure, ac-tools/configure.in: mpich mucking |
84 |
+ |
|
85 |
+ |
2004-01-05 17:12 chuckv |
86 |
+ |
|
87 |
+ |
* libmdtools/do_Forces.F90: mangled do_forces... |
88 |
+ |
|
89 |
+ |
2004-01-05 16:00 chuckv |
90 |
+ |
|
91 |
+ |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
92 |
+ |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
93 |
+ |
lookup |
94 |
+ |
|
95 |
+ |
2003-12-29 14:56 chuckv |
96 |
+ |
|
97 |
+ |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
98 |
+ |
third-party directory for code not written by us. Also added |
99 |
+ |
Mersenne Twister random number generator code. This will eventually |
100 |
+ |
replace sprng as the random number generator used by OOPSE. |
101 |
+ |
|
102 |
+ |
2003-12-22 16:26 chuckv |
103 |
+ |
|
104 |
+ |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
105 |
+ |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
106 |
+ |
Fixes to profile code. |
107 |
+ |
|
108 |
+ |
2003-12-19 15:36 mmeineke |
109 |
+ |
|
110 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
111 |
+ |
timing.F90, timing.f90: More profiling fixes. |
112 |
+ |
|
113 |
+ |
2003-12-19 15:19 chuckv |
114 |
+ |
|
115 |
+ |
* libmdtools/timing.f90: Another change for MPI in timing. |
116 |
+ |
|
117 |
+ |
2003-12-19 15:17 chuckv |
118 |
+ |
|
119 |
+ |
* libmdtools/timing.f90: Small update to timing in MPI |
120 |
+ |
|
121 |
+ |
2003-12-19 13:53 mmeineke |
122 |
+ |
|
123 |
+ |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
124 |
+ |
profiling commands work now. Will start adding PROFILE ifdefs into |
125 |
+ |
the code |
126 |
+ |
|
127 |
+ |
2003-12-19 12:25 mmeineke |
128 |
+ |
|
129 |
+ |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
130 |
+ |
some profiling routines |
131 |
+ |
|
132 |
+ |
2003-12-19 10:12 mmeineke |
133 |
+ |
|
134 |
+ |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
135 |
+ |
and GofRomega |
136 |
+ |
|
137 |
+ |
additional work on randomBilayer |
138 |
+ |
|
139 |
+ |
2003-12-19 10:12 mmeineke |
140 |
+ |
|
141 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
142 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
143 |
+ |
GofRomega |
144 |
+ |
|
145 |
+ |
2003-12-18 16:47 mmeineke |
146 |
+ |
|
147 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
148 |
+ |
some profile functionality |
149 |
+ |
|
150 |
+ |
2003-12-18 15:46 chuckv |
151 |
+ |
|
152 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
153 |
+ |
Added functions for simple profiling in fortran. |
154 |
+ |
|
155 |
+ |
2003-12-17 15:13 chuckv |
156 |
+ |
|
157 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
158 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
159 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
160 |
+ |
zeros the array between scatters so half of the sum was being lost. |
161 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
162 |
+ |
nlocal. |
163 |
+ |
|
164 |
+ |
2003-12-16 15:49 mmeineke |
165 |
+ |
|
166 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
167 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
168 |
+ |
gofRomega. both need to be debugged and tested. |
169 |
+ |
|
170 |
+ |
2003-12-12 10:42 gezelter |
171 |
+ |
|
172 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
173 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
174 |
+ |
gradients (to do minimizations) |
175 |
+ |
|
176 |
+ |
2003-12-12 10:33 mmeineke |
177 |
+ |
|
178 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
179 |
+ |
header |
180 |
+ |
|
181 |
+ |
2003-12-10 11:52 mmeineke |
182 |
+ |
|
183 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
184 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
185 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
186 |
+ |
from bilayerSys to randomBilayer |
187 |
+ |
|
188 |
+ |
2003-11-25 10:44 mmeineke |
189 |
+ |
|
190 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
191 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
192 |
+ |
TB3 in DUFF.frc |
193 |
+ |
|
194 |
+ |
2003-11-21 15:09 mmeineke |
195 |
+ |
|
196 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
197 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
198 |
+ |
message in SimInfo. Added a more informative error message in |
199 |
+ |
InitializeFromFile |
200 |
+ |
|
201 |
+ |
2003-11-21 15:07 mmeineke |
202 |
+ |
|
203 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
204 |
+ |
ing in the GofR,CosTheta |
205 |
+ |
|
206 |
+ |
2003-11-21 14:31 chrisfen |
207 |
+ |
|
208 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
209 |
+ |
a bug in SimInfo ordering of radii |
210 |
+ |
|
211 |
+ |
2003-11-11 12:20 mmeineke |
212 |
+ |
|
213 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
214 |
+ |
a min function. |
215 |
+ |
|
216 |
+ |
2003-11-10 16:50 mmeineke |
217 |
+ |
|
218 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
219 |
+ |
reordered the rcut/ecr/boxSize initialization |
220 |
+ |
|
221 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
222 |
+ |
now exit when it runs into rcut or ecr. |
223 |
+ |
|
224 |
+ |
2003-11-07 16:46 chuckv |
225 |
+ |
|
226 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
227 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
228 |
+ |
use of mpich modules. We use mpif.h instead.: |
229 |
+ |
|
230 |
+ |
2003-11-07 12:09 mmeineke |
231 |
+ |
|
232 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
233 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
234 |
+ |
the atom loop in the NPT family of integrators. |
235 |
+ |
|
236 |
+ |
2003-11-06 17:01 mmeineke |
237 |
+ |
|
238 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
239 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
240 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
241 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
242 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
243 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
244 |
+ |
* useIntiTime => useInitialTime |
245 |
+ |
|
246 |
+ |
2003-11-06 14:24 mmeineke |
247 |
+ |
|
248 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
249 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
250 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
251 |
+ |
|
252 |
+ |
2003-11-06 14:11 mmeineke |
253 |
+ |
|
254 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
255 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
256 |
+ |
new-templateless branch to the main trunk. |
257 |
+ |
|
258 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
259 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
260 |
+ |
sudden deaths we saw. * some formating in the string when we |
261 |
+ |
write out the extended system state. * added NPT.cpp to the |
262 |
+ |
makefile.in |
263 |
+ |
|
264 |
+ |
2003-11-06 13:20 mmeineke |
265 |
+ |
|
266 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
267 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
268 |
+ |
bug. The box was not switching between orthorhombic and |
269 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
270 |
+ |
the check.which should fix it. |
271 |
+ |
|
272 |
+ |
2003-11-05 14:16 mmeineke |
273 |
+ |
|
274 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
275 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
276 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
277 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
278 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
279 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
280 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
281 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
282 |
+ |
some work on trying to find the compression bug |
283 |
+ |
|
284 |
+ |
2003-11-03 17:07 mmeineke |
285 |
+ |
|
286 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
287 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
288 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
289 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
290 |
+ |
most of standard template library from OOPSE. |
291 |
+ |
|
292 |
+ |
2003-10-31 16:06 mmeineke |
293 |
+ |
|
294 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
295 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
296 |
+ |
SimSetup.cpp: started work on template removal. |
297 |
+ |
|
298 |
+ |
2003-10-31 13:28 mmeineke |
299 |
+ |
|
300 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
301 |
+ |
added template stuff to the Maikefile template |
302 |
+ |
|
303 |
+ |
little changes to some printf format statements |
304 |
+ |
|
305 |
+ |
2003-10-31 13:28 mmeineke |
306 |
+ |
|
307 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
308 |
+ |
template |
309 |
+ |
|
310 |
+ |
2003-10-30 13:59 gezelter |
311 |
+ |
|
312 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
313 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
314 |
+ |
rList problems |
315 |
+ |
|
316 |
+ |
2003-10-30 09:11 gezelter |
317 |
+ |
|
318 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
319 |
+ |
queried before q0 was allocated. |
320 |
+ |
|
321 |
+ |
2003-10-29 15:41 mmeineke |
322 |
+ |
|
323 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
324 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
325 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
326 |
+ |
in bass.l |
327 |
+ |
|
328 |
+ |
fixed a little bug in the first time step, regarding the setting of |
329 |
+ |
ecr and est in fortran |
330 |
+ |
|
331 |
+ |
2003-10-29 15:40 mmeineke |
332 |
+ |
|
333 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
334 |
+ |
|
335 |
+ |
2003-10-29 12:55 mmeineke |
336 |
+ |
|
337 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
338 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
339 |
+ |
rcut is setup, as well as additional debugging comments. |
340 |
+ |
|
341 |
+ |
2003-10-29 09:28 gezelter |
342 |
+ |
|
343 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
344 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
345 |
+ |
templates |
346 |
+ |
|
347 |
+ |
2003-10-28 22:16 gezelter |
348 |
+ |
|
349 |
+ |
* src/Makefile.in: Refixed broken makefile |
350 |
+ |
|
351 |
+ |
2003-10-28 22:06 gezelter |
352 |
+ |
|
353 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
354 |
+ |
fixes |
355 |
+ |
|
356 |
+ |
2003-10-28 19:19 tim |
357 |
+ |
|
358 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
359 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
360 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
361 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
362 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
363 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
364 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
365 |
+ |
file. |
366 |
+ |
|
367 |
+ |
2003-10-28 17:25 mmeineke |
368 |
+ |
|
369 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
370 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
371 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
372 |
+ |
how c calls fortran. All function pointers and fortran calls are |
373 |
+ |
rigidly typecast now. |
374 |
+ |
|
375 |
+ |
2003-10-28 15:42 gezelter |
376 |
+ |
|
377 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
378 |
+ |
Portability fixes |
379 |
+ |
|
380 |
+ |
2003-10-28 15:09 gezelter |
381 |
+ |
|
382 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
383 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
384 |
+ |
src/Makefile.in: Compatibility fixes |
385 |
+ |
|
386 |
+ |
2003-10-28 12:08 mmeineke |
387 |
+ |
|
388 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
389 |
+ |
started work on template removal |
390 |
+ |
|
391 |
+ |
2003-10-28 12:04 gezelter |
392 |
+ |
|
393 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
394 |
+ |
trying to understand extern "C" stuff for pointers |
395 |
+ |
|
396 |
+ |
2003-10-28 11:20 gezelter |
397 |
+ |
|
398 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
399 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
400 |
+ |
|
401 |
+ |
2003-10-28 11:03 gezelter |
402 |
+ |
|
403 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
404 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
405 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
406 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
407 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
408 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
409 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
410 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
411 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
412 |
+ |
more portable c header stuff Also, mod file fixes and portability |
413 |
+ |
changes Some fortran changes will need to be reversed. |
414 |
+ |
|
415 |
+ |
2003-10-28 11:03 gezelter |
416 |
+ |
|
417 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
418 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
419 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
420 |
+ |
portable c header stuff Also, mod file fixes and portability |
421 |
+ |
changes |
422 |
+ |
|
423 |
+ |
2003-10-28 11:02 gezelter |
424 |
+ |
|
425 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
426 |
+ |
stuff |
427 |
+ |
|
428 |
+ |
2003-10-27 18:00 gezelter |
429 |
+ |
|
430 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
431 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
432 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
433 |
+ |
|
434 |
+ |
2003-10-27 17:08 mmeineke |
435 |
+ |
|
436 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
437 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
438 |
+ |
added routines for the sysbuilder to work with simSetup |
439 |
+ |
|
440 |
+ |
remved the QuickBass routines, and had all parsing go through |
441 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
442 |
+ |
|
443 |
+ |
2003-10-27 17:07 mmeineke |
444 |
+ |
|
445 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
446 |
+ |
routines for the sysbuilder to work with simSetup |
447 |
+ |
|
448 |
+ |
2003-10-27 11:20 gezelter |
449 |
+ |
|
450 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
451 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
452 |
+ |
|
453 |
+ |
2003-10-24 17:17 mmeineke |
454 |
+ |
|
455 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
456 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
457 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
458 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
459 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
460 |
+ |
from the Makefile |
461 |
+ |
|
462 |
+ |
2003-10-24 12:36 gezelter |
463 |
+ |
|
464 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
465 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
466 |
+ |
builder |
467 |
+ |
|
468 |
+ |
2003-10-24 12:35 gezelter |
469 |
+ |
|
470 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
471 |
+ |
merge problem |
472 |
+ |
|
473 |
+ |
2003-10-23 14:57 mmeineke |
474 |
+ |
|
475 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
476 |
+ |
init |
477 |
+ |
|
478 |
+ |
fixed an eam mpi parmeter setup bug |
479 |
+ |
|
480 |
+ |
added the init file to the makefile |
481 |
+ |
|
482 |
+ |
2003-10-23 14:57 mmeineke |
483 |
+ |
|
484 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
485 |
+ |
to the init |
486 |
+ |
|
487 |
+ |
fixed an eam mpi parmeter setup bug |
488 |
+ |
|
489 |
+ |
2003-10-23 14:57 mmeineke |
490 |
+ |
|
491 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
492 |
+ |
|
493 |
+ |
2003-10-22 16:17 mmeineke |
494 |
+ |
|
495 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
496 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
497 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
498 |
+ |
no box skew allowed. |
499 |
+ |
|
500 |
+ |
2003-10-21 14:33 mmeineke |
501 |
+ |
|
502 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
503 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
504 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
505 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
506 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
507 |
+ |
true; |
508 |
+ |
|
509 |
+ |
2003-10-17 16:19 mmeineke |
510 |
+ |
|
511 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
512 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
513 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
514 |
+ |
to the build list for both configure and configure.in |
515 |
+ |
|
516 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
517 |
+ |
working. |
518 |
+ |
|
519 |
+ |
2003-10-17 16:18 mmeineke |
520 |
+ |
|
521 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
522 |
+ |
build list for both configure and configure.in |
523 |
+ |
|
524 |
+ |
2003-10-17 16:17 mmeineke |
525 |
+ |
|
526 |
+ |
* configure: added the staticProps directory to the build list |
527 |
+ |
|
528 |
+ |
2003-10-16 14:16 mmeineke |
529 |
+ |
|
530 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
531 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
532 |
+ |
use linked lists instead of a vector. |
533 |
+ |
|
534 |
+ |
Fixed the makefile to build DumpReader.cpp |
535 |
+ |
|
536 |
+ |
Removed a comment output in Exclude.cpp |
537 |
+ |
|
538 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
539 |
+ |
a frame is written. This lets the .eor file represent the last |
540 |
+ |
written frame of a simulation. |
541 |
+ |
|
542 |
+ |
2003-10-10 12:10 mmeineke |
543 |
+ |
|
544 |
+ |
* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
545 |
+ |
props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
546 |
+ |
props/PairCorrList.hpp, props/PairCorrType.cpp, |
547 |
+ |
props/PairCorrType.hpp, props/staticProps.cpp, |
548 |
+ |
staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
549 |
+ |
staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
550 |
+ |
staticProps/GofR.cpp, staticProps/Makefile.in, |
551 |
+ |
staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
552 |
+ |
staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
553 |
+ |
staticProps/staticProps.cpp: removed the props directory, and moved |
554 |
+ |
everything over to staticProps |
555 |
+ |
|
556 |
+ |
2003-10-09 17:09 mmeineke |
557 |
+ |
|
558 |
+ |
* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
559 |
+ |
props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
560 |
+ |
props/PairCorrType.cpp, props/PairCorrType.hpp, |
561 |
+ |
props/staticProps.cpp: Contiuned work on staticProps. should be in |
562 |
+ |
a position where it will compile and run first runs. |
563 |
+ |
|
564 |
+ |
2003-10-04 13:46 chuckv |
565 |
+ |
|
566 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
567 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
568 |
+ |
|
569 |
+ |
2003-10-04 13:08 chuckv |
570 |
+ |
|
571 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
572 |
+ |
|
573 |
+ |
2003-10-03 17:11 mmeineke |
574 |
+ |
|
575 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
576 |
+ |
entahlpy from the statwriter and thermo. |
577 |
+ |
|
578 |
+ |
2003-10-03 17:02 mmeineke |
579 |
+ |
|
580 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
581 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
582 |
+ |
staticProps.cpp: changed the formating ogf the error statements in |
583 |
+ |
simError |
584 |
+ |
|
585 |
+ |
added a function to get the maxCutoff |
586 |
+ |
|
587 |
+ |
near completion of the staticProps code. still needs the pair loop, |
588 |
+ |
and the loop to allocate and read each frame. |
589 |
+ |
|
590 |
+ |
2003-10-03 17:02 mmeineke |
591 |
+ |
|
592 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
593 |
+ |
statements in simError |
594 |
+ |
|
595 |
+ |
added a function to get the maxCutoff |
596 |
+ |
|
597 |
+ |
2003-10-03 17:01 mmeineke |
598 |
+ |
|
599 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
600 |
+ |
statements in simError |
601 |
+ |
|
602 |
+ |
2003-10-02 17:06 mmeineke |
603 |
+ |
|
604 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
605 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
606 |
+ |
staticProps.cpp: finishing up the constructs needed to get this |
607 |
+ |
program up and running |
608 |
+ |
|
609 |
+ |
2003-09-30 11:00 mmeineke |
610 |
+ |
|
611 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
612 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
613 |
+ |
|
614 |
+ |
2003-09-29 17:06 mmeineke |
615 |
+ |
|
616 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
617 |
+ |
for conifig.in |
618 |
+ |
|
619 |
+ |
fixed wrappers to extern "C" |
620 |
+ |
|
621 |
+ |
2003-09-29 17:06 mmeineke |
622 |
+ |
|
623 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
624 |
+ |
conifig.in |
625 |
+ |
|
626 |
+ |
2003-09-29 17:05 mmeineke |
627 |
+ |
|
628 |
+ |
* configure: added mpif90 mod check back |
629 |
+ |
|
630 |
+ |
2003-09-29 16:16 mmeineke |
631 |
+ |
|
632 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
633 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
634 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
635 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
636 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
637 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
638 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
639 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
640 |
+ |
found with SUN's SUNWspro.s1s7 |
641 |
+ |
|
642 |
+ |
2003-09-29 12:38 mmeineke |
643 |
+ |
|
644 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
645 |
+ |
signifigant change. |
646 |
+ |
|
647 |
+ |
2003-09-25 16:17 mmeineke |
648 |
+ |
|
649 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
650 |
+ |
additional remarks from icc -w3 (extra verbose output) |
651 |
+ |
|
652 |
+ |
2003-09-25 14:27 mmeineke |
653 |
+ |
|
654 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
655 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
656 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
657 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
658 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
659 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
660 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
661 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
662 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
663 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
664 |
+ |
gcc -Wall and g++ -Wall |
665 |
+ |
|
666 |
+ |
2003-09-25 13:54 gezelter |
667 |
+ |
|
668 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
669 |
+ |
|
670 |
+ |
2003-09-25 11:42 gezelter |
671 |
+ |
|
672 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
673 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
674 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
675 |
+ |
fixes for configure |
676 |
+ |
|
677 |
+ |
2003-09-24 14:34 mmeineke |
678 |
+ |
|
679 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
680 |
+ |
that it is called before the first Statistics are written. |
681 |
+ |
|
682 |
+ |
2003-09-23 15:36 gezelter |
683 |
+ |
|
684 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
685 |
+ |
bunch of Make.dep files to CVS |
686 |
+ |
|
687 |
+ |
2003-09-23 15:34 mmeineke |
688 |
+ |
|
689 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
690 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
691 |
+ |
|
692 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
693 |
+ |
|
694 |
+ |
2003-09-22 18:07 tim |
695 |
+ |
|
696 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
697 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
698 |
+ |
|
699 |
+ |
2003-09-22 16:23 mmeineke |
700 |
+ |
|
701 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
702 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
703 |
+ |
Converted NPTf to work with the NPT base class. |
704 |
+ |
|
705 |
+ |
Removed NPTfm and NPTim from cvs |
706 |
+ |
|
707 |
+ |
2003-09-19 15:00 mmeineke |
708 |
+ |
|
709 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
710 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
711 |
+ |
class. NPTi is up to date. NPTf is not. |
712 |
+ |
|
713 |
+ |
2003-09-19 11:03 mmeineke |
714 |
+ |
|
715 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
716 |
+ |
makefile |
717 |
+ |
|
718 |
+ |
2003-09-19 11:01 gezelter |
719 |
+ |
|
720 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
721 |
+ |
|
722 |
+ |
2003-09-19 11:01 gezelter |
723 |
+ |
|
724 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
725 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
726 |
+ |
|
727 |
+ |
2003-09-19 10:20 mmeineke |
728 |
+ |
|
729 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
730 |
+ |
|
731 |
+ |
2003-09-19 09:55 gezelter |
732 |
+ |
|
733 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
734 |
+ |
samples/water/ssd.bass: [no log message] |
735 |
+ |
|
736 |
+ |
2003-09-19 09:22 tim |
737 |
+ |
|
738 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
739 |
+ |
|
740 |
+ |
2003-09-17 09:22 mmeineke |
741 |
+ |
|
742 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
743 |
+ |
work with constraints. |
744 |
+ |
|
745 |
+ |
2003-09-16 15:02 tim |
746 |
+ |
|
747 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
748 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
749 |
+ |
|
750 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
751 |
+ |
|
752 |
+ |
NPTi appears very stable. |
753 |
+ |
|
754 |
+ |
2003-09-15 11:52 tim |
755 |
+ |
|
756 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
757 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
758 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
759 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
760 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
761 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
762 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
763 |
+ |
statWriter fix bug of vector wrapping at NPTi |
764 |
+ |
|
765 |
+ |
2003-09-12 15:51 mmeineke |
766 |
+ |
|
767 |
+ |
* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
768 |
+ |
PairCorrType.hpp: added AllCorr. It eill still need some work |
769 |
+ |
|
770 |
+ |
2003-09-12 11:20 gezelter |
771 |
+ |
|
772 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
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Makefile.in |
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2003-09-12 11:20 gezelter |
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* ChangeLog: Entered changes for configure into ChangeLog |
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2003-09-10 16:28 mmeineke |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |