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root/libghemical/trunk/ChangeLog
Revision: 245
Committed: Wed Oct 12 18:00:37 2011 UTC (7 years, 8 months ago) by thassine
File size: 69356 byte(s)
Log Message:
update the Changelog
Line File contents
1 2011-09-14 16:49 thassine
2
3 * Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in,
4 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
5 bin/param_mm/default/Makefile.in,
6 bin/param_mm/prmfit/Makefile.in,
7 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
8 bin/param_sf/default/Makefile.in, configure, po/LINGUAS,
9 po/Makefile.in, po/Makefile.in.in, po/de.po, src/Makefile.in,
10 src/libghemical-features.h, src/libghemicalconfig.h.in: add
11 german translation + configuration scripts updated.
12
13 2009-11-02 15:02 thassine
14
15 * po/LINGUAS, po/fi.po, po/ru.po: russian translation added.
16
17 2009-09-11 12:51 thassine
18
19 * configure, configure.ac, po/Makefile.in, src/Makefile.am,
20 src/Makefile.in, src/libghemical-features.h: version 2.99.1
21 released due to a missing file.
22
23 2009-09-04 12:41 thassine
24
25 * ChangeLog: ChangeLog update
26
27 2009-09-04 12:28 thassine
28
29 * configure, configure.ac, po/Makefile.in, src/Makefile.am,
30 src/Makefile.in, src/libghemical-features.h: release the version
31 2.99.1
32
33 2009-08-10 11:22 thassine
34
35 * po/LINGUAS, po/pt_BR.po, src/libghemical-features.h: translation
36 pt_BR added (thanks to Ulisses)
37
38 2009-04-30 11:01 thassine
39
40 * po/mk.po, po/sq.po, src/tab_mm_default.cpp: an AMBER-param error
41 fixed.
42
43 2009-04-21 11:33 thassine
44
45 * po/LINGUAS, po/POTFILES, po/POTFILES.in, po/fi.po, po/mk.po,
46 po/sq.po, src/bond.cpp, src/bond.h, src/conjgrad.cpp,
47 src/eng1_mm.cpp, src/eng1_qm_mopac.cpp, src/mfinder.cpp,
48 src/model.cpp, src/seqbuild.cpp, src/seqbuild.h,
49 src/typerule.cpp, src/utility.cpp: added translations mk + po ;
50 translation fi updated.
51
52 2009-04-01 05:48 thassine
53
54 * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
55 src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp,
56 src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp,
57 src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h,
58 src/engine.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp,
59 src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h,
60 src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
61 src/typerule.cpp: added assertion_failed() method for fatal error
62 reporting.
63
64 2008-12-09 10:41 thassine
65
66 * INSTALL, po/Makefile.in, po/fi.po, src/atom.cpp, src/bond.cpp,
67 src/chn_info.cpp, src/conjgrad.cpp, src/eng1_mm.cpp,
68 src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
69 src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp,
70 src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/engine.cpp,
71 src/intcrd.cpp, src/libghemical-features.h, src/mfinder.cpp,
72 src/model.cpp, src/notice.cpp, src/notice.h, src/pop_ana.cpp,
73 src/sasaeval.cpp, src/sasaeval.h, src/search.cpp,
74 src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
75 src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp:
76 translations added ; Vlado Peshov.
77
78 2008-11-26 11:03 thassine
79
80 * Makefile.am, Makefile.in, autogen.sh, bin/Makefile.in,
81 bin/amber/Makefile.in, bin/builder/Makefile.in,
82 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
83 bin/param_mm/prmfit/Makefile.in,
84 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
85 bin/param_sf/default/Makefile.in, configure, configure.ac, po,
86 po/LINGUAS, po/Makefile.in, po/Makefile.in.in, po/POTFILES,
87 po/POTFILES.in, po/fi.po, po/stamp-it, src/Makefile.am,
88 src/Makefile.in, src/libghemicalconfig.h.in, src/local_i18n.h,
89 src/model.cpp: started adding gettext()-translations ; Vlado
90 Peshov + others.
91
92 2008-11-18 19:19 thassine
93
94 * src/simple_test/Makefile, src/simple_test/example1.cpp,
95 src/simple_test/example1.h, src/simple_test/example2.cpp,
96 src/simple_test/example2.h, src/simple_test/example3.cpp,
97 src/simple_test/example3.h, src/simple_test/fileio.cpp,
98 src/simple_test/streamio.cpp: the examples are now tested and
99 updated ; TODO : example3 suffers from libghemical_init() output.
100
101 2008-10-22 09:41 thassine
102
103 * INSTALL, Makefile.in, autogen.sh, bin/Makefile.in,
104 bin/amber/Makefile.in, bin/builder/Makefile.in,
105 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
106 bin/param_mm/prmfit/Makefile.in,
107 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
108 bin/param_sf/default/Makefile.in, configure, configure.ac,
109 src/Makefile.in, src/libghemicalconfig.h.in, src/sasaeval.h,
110 src/tab_mm_default.h: configuration update (Daniel Leidert) +
111 minor fixes
112
113 2008-08-06 12:15 thassine
114
115 * Makefile.am, Makefile.in, src/libghemical-features.h: added
116 autogen.sh to EXTRA_DIST.
117
118 2008-08-01 06:56 thassine
119
120 * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in,
121 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
122 bin/param_mm/default/Makefile.in,
123 bin/param_mm/prmfit/Makefile.in,
124 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
125 bin/param_sf/default/Makefile.in, configure, configure.ac,
126 src/Makefile.in: configuration fix.
127
128 2008-08-01 06:36 thassine
129
130 * src/sasaeval.cpp, src/sasaeval.h: patched sasaeval to make it
131 compile more reliably.
132
133 2008-07-31 10:29 thassine
134
135 * configure, configure.ac, src/libghemical-features.h: forgot the
136 releasedate
137
138 2008-07-31 10:06 thassine
139
140 * configure, configure.ac, src/Makefile.am, src/Makefile.in,
141 src/libghemical-features.h, src/typedef.h: version number changed
142 to 2.98
143
144 2008-07-31 07:59 thassine
145
146 * src/typedef.h: removed dependencies to GL/glut.h data types ;
147 GL/gl.h data types dependency is optional.
148
149 2008-07-30 20:18 thassine
150
151 * bin/amber/Makefile.in, bin/builder/Makefile.in,
152 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
153 bin/param_mm/prmfit/Makefile.in,
154 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
155 bin/param_sf/default/Makefile.in: added Makefile.in files for
156 clarity...
157
158 2008-07-30 20:11 thassine
159
160 * bin/Makefile.in: added bin/Makefile.in
161
162 2008-07-30 20:10 thassine
163
164 * src/Makefile.in: added src/Makefile.in for clarity.
165
166 2008-07-30 20:07 thassine
167
168 * Makefile.in, configure, configure.ac, src/eng1_mm.cpp,
169 src/eng1_mm.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp,
170 src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h,
171 src/engine.h, src/geomopt.h, src/model.cpp, src/model.h,
172 src/moldyn.h, src/seqbuild.cpp, src/tab_mm_default.cpp,
173 src/tab_mm_default.h, src/tab_mm_tripos52.cpp,
174 src/tab_mm_tripos52.h, src/typedef.h, src/utility.h,
175 src/win32_hacks.cpp, src/win32_hacks.h: renamed AddAtom_lg() and
176 GetClassName_lg() ; libghemical_init() added ; win32-related
177 changes mostly.
178
179 2008-07-18 08:24 thassine
180
181 * src/engine.cpp, src/engine.h, src/model.cpp, src/moldyn.cpp,
182 src/moldyn.h: langevin dynamics is pulled out ; no applications
183 so the implementation is not well tested...
184
185 2008-05-22 10:59 thassine
186
187 * src/Makefile.am, src/engine.h, src/sasaeval.cpp, src/sasaeval.h:
188 added a SASA evaluator ; transferred from the eng1_sf_cg.cpp
189 file.
190
191 2008-04-28 12:11 thassine
192
193 * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_sf.cpp,
194 src/eng1_sf.h: some stuff renamed ; unfortunately this will
195 affect ghemical as well...
196
197 2008-02-26 11:32 thassine
198
199 * src/atom.cpp, src/chn_info.cpp, src/eng1_mm.cpp,
200 src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp,
201 src/notice.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
202 src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp,
203 src/utility.cpp, src/win32_hacks.cpp: should now compile with g++
204 v4.3
205
206 2008-01-07 13:06 thassine
207
208 * src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h,
209 src/chn_info.cpp, src/chn_info.h, src/conjgrad.cpp,
210 src/conjgrad.h, src/constraint.cpp, src/constraint.h,
211 src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp,
212 src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp,
213 src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp,
214 src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h,
215 src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp,
216 src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h,
217 src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp,
218 src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h,
219 src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h,
220 src/intcrd.cpp, src/intcrd.h, src/libghemicaldefine.h,
221 src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h,
222 src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h,
223 src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp,
224 src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp,
225 src/seqbuild.h, src/simple_test/example1.cpp,
226 src/simple_test/example1.h, src/simple_test/example2.cpp,
227 src/simple_test/example2.h, src/simple_test/example3.cpp,
228 src/simple_test/example3.h, src/simple_test/fileio.cpp,
229 src/simple_test/streamio.cpp, src/tab_mm_default.cpp,
230 src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
231 src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h,
232 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h,
233 src/v3d.h, src/win32_hacks.cpp, src/win32_hacks.h: copyright
234 notice update
235
236 2008-01-07 11:28 thassine
237
238 * autogen.sh, src/libghemicaldefine.h, src/model.cpp,
239 src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
240 src/tab_mm_tripos52.cpp: do not use NEWLINE anymore (but simply
241 endl). autogen.sh update.
242
243 2007-10-24 08:43 thassine
244
245 * src/moldyn.h: added a fix for gcc4
246
247 2007-10-09 06:10 thassine
248
249 * configure.ac, src/Makefile.am, src/libghemical-features.h: fixed
250 the libtool versioninfo
251
252 2007-09-21 09:59 thassine
253
254 * bin/amber/Makefile.am, bin/amber/all_amino02.in,
255 bin/amber/all_amino94_MOD.in, bin/amber/all_aminoct02.in,
256 bin/amber/all_aminoct94.in, bin/amber/all_aminont02.in,
257 bin/amber/all_aminont94.in, bin/amber/all_nuc02.in,
258 bin/amber/all_nuc94_MOD.in, bin/amber/original,
259 bin/amber/original/all_amino94.in,
260 bin/amber/original/all_nuc94.in,
261 bin/amber/original/frcmod.ff99SB, bin/amber/original/parm99.dat,
262 bin/amber/parm99.dat, bin/amber/parm99_frcmod_ff99SB.dat,
263 configure.ac, src/atom.h, src/libghemical-features.h,
264 src/model.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp,
265 src/win32_hacks.cpp: commit 20070921
266
267 2007-05-04 09:23 thassine
268
269 * src/tab_mm_default.cpp: an another set of AMBER checks/fixes ;
270 should be OK now.
271
272 2007-05-03 09:04 thassine
273
274 * bin/amber/all_nuc02.in, src/tab_mm_default.cpp: added more fixes
275 for the AMBER forcefield
276
277 2007-04-30 10:51 thassine
278
279 * src/libghemical-features.h, src/tab_mm_default.cpp: some AMBER
280 atom type fixes added.
281
282 2007-03-13 08:54 thassine
283
284 * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
285 src/eng1_mm_tripos52.cpp: checked the nonbonded 1,4-scalings ;
286 should be/have been ok ; debug stuff added.
287
288 2007-02-13 08:22 thassine
289
290 * bin/builder/amino.txt, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
291 src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/engine.cpp,
292 src/engine.h, src/model.cpp, src/model.h, src/search.cpp,
293 src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h,
294 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
295 src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: changes in
296 seq-builder and in engine classes.
297
298 2007-02-01 13:16 thassine
299
300 * bin/builder/amino.txt, bin/builder/nucleic.txt,
301 src/libghemical-features.h, src/seqbuild.cpp, src/seqbuild.h:
302 some sequencebuilder tweaks.
303
304 2007-01-30 09:12 thassine
305
306 * src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
307 src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/intcrd.cpp,
308 src/mfinder.cpp, src/model.cpp, src/model.h, src/seqbuild.cpp,
309 src/seqbuild.h, src/tab_mm_default.cpp, src/typerule.cpp,
310 src/utility.cpp: atom::cr_list is protected now ;
311 model::UpdateChains() may ask nucl-acid detection skipped.
312
313 2007-01-25 10:17 thassine
314
315 * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
316 src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp,
317 src/eng1_qm_mpqc.cpp, src/engine.cpp, src/engine.h,
318 src/model.cpp, src/model.h, src/utility.h: added code for
319 collecting energy components using atom groups.
320
321 2007-01-16 09:05 thassine
322
323 * bin/builder/amino.txt, src/chn_info.h, src/eng1_sf.cpp,
324 src/eng1_sf.h, src/model.cpp, src/model.h, src/seqbuild.h,
325 src/tab_mm_prmfit.h, src/win32_hacks.h: various small changes.
326
327 2007-01-15 10:24 thassine
328
329 * src/eng1_mm_default.cpp, src/eng1_mm_default.h,
330 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h,
331 src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.h,
332 src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.h, src/engine.h,
333 src/libghemical-features.h: changed the SetTorsionConstraint()
334 method parameters.
335
336 2007-01-15 07:53 thassine
337
338 * src/libghemical-features.h, src/model.cpp: changes for the win32
339 version.
340
341 2006-12-21 10:40 thassine
342
343 * configure.ac, src/Makefile.am, src/eng1_mm.cpp, src/geomopt.h,
344 src/libghemicaldefine.h, src/model.cpp, src/model.h,
345 src/moldyn.h, src/search.cpp, src/win32_hacks.cpp,
346 src/win32_hacks.h: minor changes + additions for win32
347 compilation.
348
349 2006-11-08 12:26 thassine
350
351 * AUTHORS, configure.ac, libghemical.pc.in: some configuration
352 fixes added (thanks Jean).
353
354 2006-10-31 10:48 thassine
355
356 * src/atom.h: added a new atomflag ; the atomflag values below 256
357 should be internal (not saved).
358
359 2006-10-26 12:38 thassine
360
361 * src/conjgrad.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h,
362 src/engine.cpp, src/search.cpp, src/search.h: TSS bugfixes added.
363
364 2006-10-24 12:21 thassine
365
366 * src/stamp-h1.in, src/stamp-h2.in: removed unnecessary files.
367
368 2006-10-24 12:19 thassine
369
370 * src/stamp-h2: removed unnecessary files.
371
372 2006-10-24 11:54 thassine
373
374 * src/stamp-h1.in, src/stamp-h2.in: added the new files
375 (libghemical-features.h)...
376
377 2006-10-24 11:52 thassine
378
379 * src/stamp-h2: added the new files (libghemical-features.h)...
380
381 2006-10-24 11:50 thassine
382
383 * src/libghemical-features.h, src/libghemical-features.h.in: added
384 the new files (libghemical-features.h).
385
386 2006-10-24 11:48 thassine
387
388 * configure.ac, src/Makefile.am, src/atom.cpp, src/atom.h,
389 src/bond.cpp, src/bond.h, src/chn_info.cpp, src/chn_info.h,
390 src/conjgrad.cpp, src/conjgrad.h, src/constraint.cpp,
391 src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h,
392 src/eng1_mm_default.cpp, src/eng1_mm_default.h,
393 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h,
394 src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h,
395 src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp,
396 src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h,
397 src/eng1_sf.cpp, src/eng1_sf.h, src/eng1_sf_cg.cpp,
398 src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h,
399 src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp,
400 src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp,
401 src/intcrd.h, src/libghemicalconfig.h.in, src/mfinder.cpp,
402 src/mfinder.h, src/model.cpp, src/model.h, src/moldyn.cpp,
403 src/moldyn.h, src/notice.cpp, src/notice.h, src/pop_ana.cpp,
404 src/pop_ana.h, src/resonance.cpp, src/resonance.h,
405 src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h,
406 src/tab_mm_default.cpp, src/tab_mm_default.h,
407 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h,
408 src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h,
409 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
410 libghemical-features.h implemented (thanks to Jean Brefort).
411
412 2006-10-19 12:16 thassine
413
414 * src/Makefile.am: versioninfo added.
415
416 2006-10-11 10:47 thassine
417
418 * src/engine.cpp, src/engine.h: added a method engine::ReadCRD()
419 for looking at engine::crd.
420
421 2006-08-31 11:03 thassine
422
423 * src/model.cpp, src/utility.cpp: minor bugfixes added + few
424 comments.
425
426 2006-08-29 08:11 thassine
427
428 * ChangeLog, src/seqbuild.cpp: changelog update
429
430 2006-08-28 12:22 thassine
431
432 * src/chn_info.cpp, src/chn_info.h, src/seqbuild.cpp: fixed a
433 memory bug.
434
435 2006-08-28 11:18 thassine
436
437 * INSTALL, bin/builder/amino.txt, bin/builder/nucleic.txt,
438 src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/model.cpp,
439 src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/typedef.h:
440 many changes at sequencebuilder
441
442 2006-08-07 12:28 thassine
443
444 * ChangeLog, configure.ac, src/seqbuild.cpp, src/seqbuild.h:
445 version number change
446
447 2006-08-07 11:49 thassine
448
449 * .cvsignore, bin/.cvsignore, bin/amber/.cvsignore,
450 bin/builder/.cvsignore, bin/param_mm/.cvsignore,
451 bin/param_mm/default/.cvsignore, bin/param_mm/prmfit/.cvsignore,
452 bin/param_mm/tripos52/.cvsignore, bin/param_sf/.cvsignore,
453 bin/param_sf/default/.cvsignore, src/.cvsignore: removed the
454 .cvsignore files.
455
456 2006-07-31 10:45 thassine
457
458 * bin/param_mm/tripos52/atomtypes.txt, src/seqbuild.cpp,
459 src/seqbuild.h: more changes at seqbuild code.
460
461 2006-07-24 11:40 thassine
462
463 * bin/builder/amino.txt, configure.ac, src/Makefile.am,
464 src/chn_info.cpp, src/chn_info.h, src/eng1_sf.cpp,
465 src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h,
466 src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp,
467 src/utility.cpp: the sequence builder code has been updated (no
468 longer compatible with the old one.
469
470 2006-07-12 10:01 thassine
471
472 * bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_sf.cpp,
473 src/seqbuild.cpp, src/seqbuild.h: changes in sequence-builder
474 code and data files.
475
476 2006-04-24 12:02 thassine
477
478 * configure.ac: changed version number after a release.
479
480 2006-04-24 12:00 thassine
481
482 * ChangeLog, configure.ac: this is v2.00
483
484 2006-04-11 09:04 thassine
485
486 * ChangeLog, INSTALL, configure.ac: this is v2.00rc1
487
488 2006-03-29 08:41 thassine
489
490 * INSTALL, src/model.cpp: documentation update.
491
492 2006-03-28 16:19 hutchisn
493
494 * src/model.cpp: Check for selected atoms before adding hydrogens.
495 If the user has selected atoms,
496 only add to those atoms.
497
498 2006-03-28 10:49 thassine
499
500 * ., .cvsignore: cvsignore update.
501
502 2006-03-28 10:36 thassine
503
504 * config.guess, config.sub, ltmain.sh: removed some unnecessary
505 files.
506
507 2006-03-23 11:42 thassine
508
509 * src/model.cpp: fixed a text string.
510
511 2006-03-22 13:01 thassine
512
513 * src/model.cpp: a change in mol.dyn.
514
515 2006-03-22 12:21 thassine
516
517 * src/Makefile.am, src/atom.cpp, src/atom.h, src/constraint.cpp,
518 src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h,
519 src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
520 src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp,
521 src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/engine.h,
522 src/model.cpp, src/model.h: added (distance)constraints ; Donald
523 Curtis.
524
525 2006-03-18 17:02 thassine
526
527 * src/eng1_mm_default.cpp, src/model.cpp, src/moldyn.cpp: some
528 mol.dyn. changes.
529
530 2006-03-14 13:47 thassine
531
532 * src/moldyn.h: a few more mol.dyn. changes.
533
534 2006-03-14 08:45 thassine
535
536 * src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/search.cpp,
537 src/tab_mm_prmfit.cpp: added some mol.dyn. improvements ; some
538 missing srand() calls added.
539
540 2006-03-10 12:12 thassine
541
542 * src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h,
543 src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.cpp, src/model.h:
544 added a mopac/mpqc patch (Jean Br�fort), and a new Orient()
545 method.
546
547 2006-03-08 10:33 thassine
548
549 * ., .cvsignore, aclocal.m4, src/eng1_mm.cpp, src/engine.cpp:
550 aclocal.m4 removed ; some mol.dyn. related changes added.
551
552 2006-03-07 13:42 thassine
553
554 * aclocal.m4, src/engine.cpp: a bugfix for CheckLocations().
555
556 2006-03-07 13:22 thassine
557
558 * aclocal.m4, src/eng1_mm.cpp, src/engine.cpp, src/engine.h:
559 CheckLocations() changed.
560
561 2006-03-07 10:49 thassine
562
563 * aclocal.m4, autogen.sh, config.guess, config.sub, ltmain.sh:
564 updated autogen.sh
565
566 2006-03-07 08:44 thassine
567
568 * aclocal.m4, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
569 src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h, src/model.cpp:
570 added engine::RequestNeighborListUpdate().
571
572 2006-03-06 08:53 thassine
573
574 * aclocal.m4, src/engine.h, src/model.cpp: added a method
575 RequestUpdateTerms().
576
577 2006-03-06 07:46 thassine
578
579 * aclocal.m4, src/moldyn.cpp: a minor fix in mol.dyn.
580
581 2006-03-03 12:56 thassine
582
583 * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed atom
584 changes.
585
586 2006-03-03 12:24 thassine
587
588 * ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, bin,
589 bin/.cvsignore, bin/Makefile.in, bin/amber, bin/amber/.cvsignore,
590 bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore,
591 bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore,
592 bin/param_mm/Makefile.in, bin/param_mm/default,
593 bin/param_mm/default/.cvsignore,
594 bin/param_mm/default/Makefile.in, bin/param_mm/prmfit,
595 bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.in,
596 bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore,
597 bin/param_mm/tripos52/Makefile.in, bin/param_sf,
598 bin/param_sf/.cvsignore, bin/param_sf/Makefile.in,
599 bin/param_sf/default, bin/param_sf/default/.cvsignore,
600 bin/param_sf/default/Makefile.in, configure, src, src/.cvsignore,
601 src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
602 src/engine.cpp, src/engine.h, src/model.cpp, src/model.h,
603 src/moldyn.cpp, src/moldyn.h: many changes ; especially at
604 mol.dyn. code ; autogen.sh added
605
606 2006-03-01 12:15 thassine
607
608 * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h,
609 src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
610 src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp,
611 src/model.h, src/moldyn.cpp, src/moldyn.h: many changes in
612 mol.dyn. code.
613
614 2006-02-28 12:14 thassine
615
616 * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h,
617 src/eng1_mm_default.cpp, src/eng1_mm_default.h,
618 src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h,
619 src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.cpp,
620 src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h,
621 src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: added
622 cleanups/changes for virial/pressure calculations.
623
624 2006-02-27 11:25 thassine
625
626 * aclocal.m4, src/eng1_mm.cpp, src/eng1_qm_mpqc.cpp, src/model.cpp,
627 src/search.cpp, src/tab_mm_prmfit.cpp: tried to do a bit safer
628 stringstream code ; only take the c_str out for copying into a
629 buffer or for passing as a parameter.
630
631 2006-02-27 08:29 thassine
632
633 * aclocal.m4, src/eng1_sf.h: a bugfix added...
634
635 2006-02-24 13:50 thassine
636
637 * aclocal.m4, src/model.cpp: fixed a bug in box solvation.
638
639 2006-02-20 12:34 thassine
640
641 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
642 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
643 bin/param_mm/default/Makefile.in,
644 bin/param_mm/prmfit/Makefile.in,
645 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
646 bin/param_sf/default/Makefile.in, configure, src/Makefile.in,
647 src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp,
648 src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp,
649 src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp,
650 src/model.cpp, src/notice.cpp, src/search.cpp,
651 src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
652 src/tab_mm_tripos52.cpp, src/typedef.h: output-streams-code
653 changed.
654
655 2006-02-17 19:14 hutchisn
656
657 * ChangeLog, src/atom.cpp, src/eng1_mm.cpp,
658 src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
659 src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp,
660 src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp,
661 src/moldyn.cpp, src/notice.cpp, src/search.cpp, src/seqbuild.cpp,
662 src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
663 src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: *
664 src/*.cpp: Update to use stringstream and <sstream> headers --
665 fixes backwards-compatibility warnings using GCC.
666
667 2006-02-17 16:18 hutchisn
668
669 * ChangeLog, Makefile.in, acinclude.m4, aclocal.m4,
670 bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in,
671 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
672 bin/param_mm/prmfit/Makefile.in,
673 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
674 bin/param_sf/default/Makefile.in, config.guess, config.sub,
675 configure, depcomp, install-sh, ltmain.sh, missing,
676 mkinstalldirs, src, src/.cvsignore, src/Makefile.in: *
677 acinclude.m4: Fix underquoted macros to prevent warnings.
678
679 * aclocal.m4, config.guess, config.sub, configure
680 depcomp, install-sh, ltmain.sh, missing, mkinstalldirs
681 */Makefile.in: Update with latest automake (1.9.6), libtool
682 (1.5.22).
683
684 2006-02-16 09:20 thassine
685
686 * aclocal.m4, config.guess, config.sub, ltmain.sh: configure
687 updates.
688
689 2006-02-10 14:22 thassine
690
691 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
692 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
693 bin/param_mm/default/Makefile.in,
694 bin/param_mm/prmfit/Makefile.in,
695 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
696 bin/param_sf/default/Makefile.in, configure, configure.ac,
697 libghemical.pc.in, src/Makefile.am, src/Makefile.in,
698 src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
699 src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp,
700 src/libghemicalconfig.h.in, src/model.cpp, src/pop_ana.cpp,
701 src/seqbuild.cpp, src/seqbuild.h, src/typedef.h, src/utility.cpp,
702 src/utility.h, src/v3d.h: many changes...
703
704 2006-02-07 12:44 thassine
705
706 * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h,
707 src/model.cpp, src/model.h, src/moldyn.h: data hiding fixes ; no
708 longer need to declare classes of the ghemical app as friend
709 classes ; still no perfect but a good start.
710
711 2006-02-06 14:02 thassine
712
713 * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h,
714 src/model.h, src/moldyn.h: fixed some friend statements ; these
715 should be cleaned away in future...
716
717 2006-02-06 09:40 thassine
718
719 * src/utility.cpp: some comments added.
720
721 2006-02-06 08:29 thassine
722
723 * src/eng1_sf.cpp, src/eng1_sf.h, src/model.h: minor changes.
724
725 2006-01-19 13:38 thassine
726
727 * src/eng1_sf.cpp, src/eng1_sf.h: removed some unnecessary changes.
728
729 2006-01-19 07:41 thassine
730
731 * src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h,
732 src/conjgrad.h, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h,
733 src/intcrd.cpp, src/intcrd.h, src/libdefine.h,
734 src/libghemicaldefine.h, src/model.cpp, src/model.h,
735 src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/seqbuild.h,
736 src/tab_mm_default.h, src/tab_mm_tripos52.h, src/typedef.h,
737 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
738 libdefine.h was renamed to libghemicaldefine.h
739
740 2005-12-14 14:10 thassine
741
742 * src, src/.cvsignore: minor changes.
743
744 2005-11-29 10:54 thassine
745
746 * src/geomopt.cpp: oops ; geomopt.cpp pathed wrong way.
747
748 2005-11-29 10:39 thassine
749
750 * src/atom.h, src/geomopt.cpp, src/model.cpp, src/moldyn.cpp,
751 src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
752 src/tab_mm_tripos52.cpp: some changes in the atom flags ; need to
753 separate the user/system level hidden atoms.
754
755 2005-11-17 12:31 thassine
756
757 * src/eng1_sf.h: added an another table.
758
759 2005-11-17 11:56 thassine
760
761 * src/eng1_sf.h: a new table was added for visualization params.
762
763 2005-11-10 10:00 thassine
764
765 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
766 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
767 bin/param_mm/default/Makefile.in,
768 bin/param_mm/prmfit/Makefile.in,
769 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
770 bin/param_sf/default/Makefile.in, configure, configure.ac,
771 ltmain.sh, src/Makefile.in: changed the version number into 1.92
772 after a release.
773
774 2005-11-02 12:24 thassine
775
776 * configure, src/model.h: minor changes ; needed for the app.
777
778 2005-10-26 21:44 hutchisn
779
780 * ., .cvsignore, ChangeLog, Makefile.in, aclocal.m4,
781 bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in,
782 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
783 bin/param_mm/prmfit/Makefile.in,
784 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
785 bin/param_sf/default/Makefile.in, config.guess, config.sub,
786 configure, configure.ac, ltmain.sh, src, src/.cvsignore,
787 src/Makefile.in: * configure.ac, configure: Update to use
788 openbabel-2.0 check,
789 rather than openbabel.
790
791 * ltmain.sh, aclocal.m4, */Makefile.in: Update with latest
792 autoconf, libtool (1.5.20).
793
794 2005-10-08 15:12 thassine
795
796 * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in,
797 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
798 bin/param_mm/default/Makefile.in,
799 bin/param_mm/prmfit/Makefile.in,
800 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
801 bin/param_sf/default/Makefile.in, configure, configure.ac,
802 src/Makefile.in, src/atom.cpp, src/atom.h, src/libdefine.h,
803 src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms ;
804 just a new value stored in atom objects
805
806 2005-09-26 08:46 thassine
807
808 * src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp,
809 src/eng1_sf_ua.h: oops! forgot to add some files...
810
811 2005-09-19 09:21 thassine
812
813 * src/eng1_qm_mopac.cpp, src/search.cpp: minor tweaks ; now should
814 compile with the FC4 compiler.
815
816 2005-08-24 09:55 thassine
817
818 * src/Makefile.am, src/Makefile.in, src/eng2_mm_sf.cpp,
819 src/eng2_mm_sf.h, src/model.cpp: removed the mm_sf model type.
820
821 2005-08-23 11:27 thassine
822
823 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
824 bin/builder/Makefile.in, bin/builder/amino.txt,
825 bin/builder/nucleic.txt, bin/param_mm/Makefile.in,
826 bin/param_mm/default/Makefile.in,
827 bin/param_mm/prmfit/Makefile.in,
828 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
829 bin/param_sf/default/Makefile.in, configure, configure.ac,
830 depcomp, src/Makefile.am, src/Makefile.in, src/eng1_qm_mopac.cpp,
831 src/search.h, src/seqbuild.cpp, src/seqbuild.h: now depends on
832 mopac7-1.10 ; also other smaller changes here and there.
833
834 2005-07-06 08:59 thassine
835
836 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
837 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
838 bin/param_mm/default/Makefile.in,
839 bin/param_mm/prmfit/Makefile.in,
840 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
841 bin/param_sf/default/Makefile.in, configure, configure.ac,
842 src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h,
843 src/conjgrad.h, src/eng1_mm.h, src/eng1_mm_default.h,
844 src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.h, src/eng1_qm.h,
845 src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h,
846 src/eng2_mm_sf.h, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h,
847 src/intcrd.h, src/libconfig.h.in, src/libdefine.h,
848 src/libghemicalconfig.h.in, src/model.h, src/moldyn.h,
849 src/notice.h, src/pop_ana.h, src/resonance.h, src/search.h,
850 src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h,
851 src/tab_mm_tripos52.h, src/typedef.h, src/typerule.h,
852 src/utility.h, src/v3d.h: config headers changed to avoid
853 multiple PACKAGE definitions.
854
855 2005-07-05 08:01 thassine
856
857 * INSTALL, Makefile.in, aclocal.m4, configure, configure.ac,
858 src/Doxyfile, src/eng1_qm_mopac.cpp, src/libconfig.h.in: a fix
859 for the f2c.h/g2c.h issue ported form libmopac7 ; tested to
860 compile with g++-3.4 ok
861
862 2005-07-01 12:48 thassine
863
864 * Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h,
865 src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h,
866 src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_qm_mopac.h,
867 src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h,
868 src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h,
869 src/libdefine.h, src/model.h, src/moldyn.h, src/notice.h,
870 src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h,
871 src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h,
872 src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: some
873 last-minute changes before release.
874
875 2005-07-01 10:49 thassine
876
877 * ChangeLog, INSTALL, aclocal.m4, configure, configure.ac: did the
878 final changes for a release 1.90.
879
880 2005-06-30 13:01 thassine
881
882 * Makefile.in, acconfig.h, acinclude.m4, aclocal.m4,
883 bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in,
884 bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in,
885 bin/param_mm/prmfit/Makefile.in,
886 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
887 bin/param_sf/default/Makefile.in, configure, configure.ac,
888 configure.in, libghemical.pc.in, src/Makefile.in,
889 src/eng1_qm.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h,
890 src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng2_qm_mm.cpp,
891 src/eng2_qm_mm.h, src/libconfig.h.in: a lot of changes in
892 configuration.
893
894 2005-06-23 13:19 thassine
895
896 * src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/model.cpp,
897 src/model.h: the lib/app interface changed.
898
899 2005-06-21 08:14 thassine
900
901 * src/engine.h, src/geomopt.h, src/model.cpp, src/moldyn.cpp,
902 src/moldyn.h, src/utility.cpp, src/utility.h: added some old
903 fixes.
904
905 2005-06-20 13:07 thassine
906
907 * src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp:
908 disabled some options/features that are not yet usable.
909
910 2005-06-20 10:57 thassine
911
912 * src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mpqc.cpp,
913 src/seqbuild.h, src/typerule.cpp: added some older fixes.
914
915 2005-06-20 09:29 thassine
916
917 * src/geomopt.h, src/model.cpp, src/model.h: minor changes related
918 to app multithreading.
919
920 2005-06-14 10:23 thassine
921
922 * src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: started
923 converting GO and MD into multithreaded versions.
924
925 2005-06-13 10:17 thassine
926
927 * src/model.cpp, src/model.h: a complete multi-threaded Random
928 Search added ; others will follow.
929
930 2005-06-13 07:13 thassine
931
932 * config.guess, config.sub, ltmain.sh, src, src/.cvsignore,
933 src/model.cpp, src/model.h, src/search.cpp, src/search.h: added
934 an initial framework for multithreading.
935
936 2005-06-08 08:40 thassine
937
938 * src/eng1_sf.cpp, src/eng1_sf.h, src/search.cpp: some formatting
939 changes and a macro changed in eng1_sf.h
940
941 2005-05-11 15:14 thassine
942
943 * src/atom.h, src/eng1_mm.h, src/eng1_sf.h, src/engine.h,
944 src/model.h: minor changes ; added some friend definitions for
945 the app.
946
947 2005-05-09 06:50 thassine
948
949 * src/atom.h, src/moldyn.cpp, src/moldyn.h: an initial
950 implementation for a LOCKED atom flag.
951
952 2005-05-06 10:05 thassine
953
954 * src/atom.cpp, src/atom.h, src/model.cpp, src/model.h,
955 src/search.cpp, src/seqbuild.cpp: a speed optimization in the
956 CenterCRDSet() function.
957
958 2005-05-03 12:12 thassine
959
960 * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
961 src/eng1_sf.cpp, src/model.cpp: some bugfixes added for solvation
962 functions.
963
964 2005-04-28 10:17 thassine
965
966 * src/eng1_mm.cpp, src/eng1_mm_default.cpp,
967 src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp,
968 src/eng1_qm_mpqc.cpp, src/engine.h, src/model.cpp: added an
969 initial version for getting the energy in MM as its components.
970
971 2005-04-26 07:20 thassine
972
973 * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
974 src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp,
975 src/model.h: some changes added in boundary potential code.
976
977 2005-04-22 13:41 thassine
978
979 * Makefile.in, aclocal.m4, src/model.h: some class names changed in
980 the app ; sync here.
981
982 2005-04-21 12:24 thassine
983
984 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
985 bin/builder/Makefile.in, bin/param_mm/Makefile.in,
986 bin/param_mm/default/Makefile.in,
987 bin/param_mm/prmfit/Makefile.in,
988 bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
989 bin/param_sf/default/Makefile.in, configure, configure.in,
990 src/Makefile.in, src/libconfig.h.in, src/libdefine.h,
991 src/notice.cpp, src/notice.h, src/simple_test/example1.cpp,
992 src/simple_test/example2.cpp, src/simple_test/example3.cpp: made
993 some changes in copyright notices for easier output in the
994 application.
995
996 2005-04-19 12:23 thassine
997
998 * src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h,
999 src/simple_test/example1.cpp, src/tab_mm_tripos52.cpp,
1000 src/tab_mm_tripos52.h: some files were forgotten from the
1001 previous commits ; added them.
1002
1003 2005-04-19 12:20 thassine
1004
1005 * Makefile.in, aclocal.m4, src/simple_test/Makefile,
1006 src/simple_test/example1.h, src/simple_test/example2.cpp,
1007 src/simple_test/example2.h, src/simple_test/example3.cpp,
1008 src/simple_test/example3.h, src/simple_test/example3_extra,
1009 src/simple_test/example3_extra/TestForm.html,
1010 src/simple_test/example3_extra/dumpdata.sh,
1011 src/simple_test/example3_extra/input_example,
1012 src/simple_test/example3_extra/printenv.sh,
1013 src/simple_test/st_main.cpp, src/simple_test/st_main.h,
1014 src/simple_test/streamio.cpp: updated the example(s) and added
1015 some new ones.
1016
1017 2005-04-19 08:48 thassine
1018
1019 * Makefile.in, aclocal.m4, bin/README, bin/param_mm/Makefile.am,
1020 bin/param_mm/Makefile.in, bin/param_mm/prmfit/Makefile.in,
1021 bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore,
1022 bin/param_mm/tripos52/Makefile.am,
1023 bin/param_mm/tripos52/Makefile.in,
1024 bin/param_mm/tripos52/atomtypes.txt,
1025 bin/param_mm/tripos52/parameters1.txt,
1026 bin/param_mm/tripos52/parameters2.txt,
1027 bin/param_mm/tripos52/parameters3.txt,
1028 bin/param_mm/tripos52/parameters4.txt,
1029 bin/param_mm/tripos52/parameters5.txt, config.guess, config.sub,
1030 configure, configure.in, ltmain.sh, src/Makefile.am,
1031 src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm.h,
1032 src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/engine.h,
1033 src/libconfig.h.in, src/model.h: ported the tripos5.2 force field
1034 implementation from ghemical-1.01 into libghemical.
1035
1036 2005-04-08 14:59 thassine
1037
1038 * src/model.cpp, src/model.h: added an utility function.
1039
1040 2005-03-21 12:52 thassine
1041
1042 * src/Makefile.SIMPLE: added an alternative simple makefile in
1043 src/.
1044
1045 2005-02-08 07:12 thassine
1046
1047 * src/conjgrad.cpp: some updates in conjgrad.cpp Simple linesearch.
1048
1049 2005-02-03 11:44 thassine
1050
1051 * src/atom.h, src/bond.h, src/engine.cpp, src/search.cpp,
1052 src/typedef.h: minor changes to make it compile at FC3.
1053
1054 2005-01-19 11:29 thassine
1055
1056 * Makefile.in, src/model.cpp, src/model.h: some minor changes for
1057 new stuff of my own ; not yet functional.
1058
1059 2005-01-04 11:28 thassine
1060
1061 * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added a
1062 new virtual method DoSHAKE() in engine class.
1063
1064 2004-12-10 15:14 thassine
1065
1066 * Makefile.in, aclocal.m4, configure, configure.in,
1067 src/eng1_qm_mopac.cpp, src/libconfig.h.in, src/model.h: small
1068 fixes added ; depends on libg2c only etc.
1069
1070 2004-09-13 09:17 thassine
1071
1072 * Makefile.in, src/atom.cpp, src/atom.h, src/eng1_sf.h,
1073 src/model.cpp: the atom objects now are aware of the model object
1074 ; added some stuff to make everything compile.
1075
1076 2004-08-30 09:28 thassine
1077
1078 * Makefile.in, aclocal.m4, bin/Makefile.in, configure,
1079 configure.in: the include dir is changed into
1080 <prefix>/include/ghemical.
1081
1082 2004-08-27 12:07 thassine
1083
1084 * Makefile.am, Makefile.in, aclocal.m4, libghemical.pc.in,
1085 src/Makefile.am, src/Makefile.in: changed includedir to /ghemical
1086 and some other changes ; .pc file not updated?
1087
1088 2004-08-26 12:34 thassine
1089
1090 * aclocal.m4, configure, configure.in, src/Makefile.am,
1091 src/Makefile.in, src/Makefile.include, src/libconfig.h.in: added
1092 patches to configure/makefiles (Michael Banck).
1093
1094 2004-08-25 11:13 thassine
1095
1096 * AUTHORS, aclocal.m4, bin, bin/.cvsignore, bin/amber,
1097 bin/amber/.cvsignore, bin/amber/Makefile.am,
1098 bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore,
1099 bin/builder/Makefile.am, bin/builder/Makefile.in, bin/param_mm,
1100 bin/param_mm/.cvsignore, bin/param_mm/Makefile.am,
1101 bin/param_mm/default, bin/param_mm/default/.cvsignore,
1102 bin/param_mm/default/Makefile.am,
1103 bin/param_mm/default/Makefile.in, bin/param_mm/prmfit,
1104 bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.am,
1105 bin/param_mm/prmfit/Makefile.in, bin/param_sf,
1106 bin/param_sf/.cvsignore, bin/param_sf/default,
1107 bin/param_sf/default/.cvsignore,
1108 bin/param_sf/default/Makefile.am,
1109 bin/param_sf/default/Makefile.in, config.guess, config.sub,
1110 configure, configure.in, ltmain.sh, src/Makefile.am,
1111 src/Makefile.in, src/Makefile.include, src/model.cpp: added
1112 automake-based configuration scripts (M. Banck and J. Brefort).
1113
1114 2004-08-13 12:14 thassine
1115
1116 * CHANGES, ChangeLog, Makefile.am, Makefile.in, NEWS, README,
1117 acinclude.m4, aclocal.m4, bin/Makefile.am, bin/Makefile.in,
1118 bin/amber/Makefile.am, bin/amber/Makefile.in,
1119 bin/builder/Makefile.am, bin/builder/Makefile.in,
1120 bin/param_mm/Makefile.am, bin/param_mm/Makefile.in,
1121 bin/param_mm/default/Makefile.am,
1122 bin/param_mm/default/Makefile.in, bin/param_sf/Makefile.am,
1123 bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.am,
1124 bin/param_sf/default/Makefile.in, configure, configure.in,
1125 ltmain.sh, missing, src/Makefile.am, src/Makefile.in,
1126 src/libconfig.h.in: added an improved configuration system
1127 (Michael Banck and Jean Brefort).
1128
1129 2004-06-07 19:54 hutchisn
1130
1131 * src/atom.cpp: Updated with standardized element colors.
1132
1133 2004-05-28 15:10 thassine
1134
1135 * src/typerule.cpp: some checks added to typerule class.
1136
1137 2004-05-13 11:45 thassine
1138
1139 * acinclude.m4, aclocal.m4, configure, configure.in,
1140 libghemical.pc.in: some improvements in configure.in
1141
1142 2004-04-16 09:24 thassine
1143
1144 * src/seqbuild.cpp: added a fix for TRP-residues in
1145 sequencebuilder::Identify().
1146
1147 2004-04-08 10:13 thassine
1148
1149 * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1150 src/eng1_qm_mopac.cpp, src/eng1_sf.cpp, src/eng2_mm_sf.cpp,
1151 src/eng2_qm_mm.cpp: fixed some compiler warnings.
1152
1153 2004-03-26 09:05 thassine
1154
1155 * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a new
1156 GetRange() method for bonds in model class.
1157
1158 2004-03-18 12:04 thassine
1159
1160 * src/model.cpp, src/resonance.h: minor changes in
1161 resonance_structures class (just a framework, under
1162 construction).
1163
1164 2004-03-15 13:01 thassine
1165
1166 * src/typerule.cpp: implemented the fc=? test in the typerule
1167 class.
1168
1169 2004-03-09 08:44 thassine
1170
1171 * src/model.cpp, src/model.h: added model::GetRS().
1172
1173 2004-03-03 13:13 thassine
1174
1175 * src/eng1_mm.cpp, src/engine.cpp, src/engine.h,
1176 src/simple_test/Makefile, src/simple_test/st_main.cpp: updated
1177 simple_test and other minor changes.
1178
1179 2004-02-18 11:47 thassine
1180
1181 * Makefile.in, configure, configure.in, src/Makefile.in,
1182 src/libconfig.h.in, src/model.cpp: some tweaks/cleanups in
1183 configure/makefiles.
1184
1185 2004-01-28 08:56 thassine
1186
1187 * libghemical.pc.in, src/pop_ana.cpp, src/pop_ana.h,
1188 src/resonance.cpp, src/resonance.h: added the .pc.in file, a
1189 simple QM population analysis code, and some framework for
1190 resonance structure determination (to be added later).
1191
1192 2004-01-28 08:53 thassine
1193
1194 * Makefile.in, bin/param_mm/default/atomtypes.txt,
1195 bin/param_mm/default/parameters1.txt,
1196 bin/param_mm/default/parameters2.txt,
1197 bin/param_mm/default/parameters3.txt,
1198 bin/param_mm/default/parameters4.txt,
1199 bin/param_mm/prmfit/atomtypes.txt,
1200 bin/param_mm/prmfit/parameters1.txt,
1201 bin/param_mm/prmfit/parameters2.txt,
1202 bin/param_mm/prmfit/parameters3.txt,
1203 bin/param_mm/prmfit/parameters4.txt, configure, configure.in,
1204 src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_qm_mopac.cpp,
1205 src/miniMOPAC, src/model.cpp, src/model.h: remove the mopac
1206 sources ; moved into a separate library.
1207
1208 2003-11-06 11:59 thassine
1209
1210 * src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp,
1211 src/eng2_mm_sf.h, src/engine.h: added convert_crd for eng1_sf.
1212
1213 2003-09-24 06:47 thassine
1214
1215 * src/conjgrad.cpp: minor improvements in conjgrad search.
1216
1217 2003-09-11 11:56 thassine
1218
1219 * src/typerule.cpp, src/typerule.h: some changes in typerules.
1220
1221 2003-09-01 09:25 thassine
1222
1223 * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp: some
1224 bugfixes added.
1225
1226 2003-08-29 07:39 thassine
1227
1228 * bin/param_mm/default/atomtypes.txt,
1229 bin/param_mm/default/parameters1.txt,
1230 bin/param_mm/default/parameters2.txt,
1231 bin/param_mm/default/parameters3.txt,
1232 bin/param_mm/default/parameters4.txt,
1233 bin/param_mm/prmfit/atomtypes.txt,
1234 bin/param_mm/prmfit/parameters1.txt,
1235 bin/param_mm/prmfit/parameters2.txt,
1236 bin/param_mm/prmfit/parameters3.txt,
1237 bin/param_mm/prmfit/parameters4.txt: added a new set of mol.mech.
1238 parameters for testing ; less default force constants than in the
1239 prev. one.
1240
1241 2003-08-21 09:09 thassine
1242
1243 * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/engine.cpp,
1244 src/engine.h: some changes in bp (boundary potential) details.
1245
1246 2003-08-21 05:35 thassine
1247
1248 * src/tab_mm_default.cpp: a bug related to out-of-plane terms is
1249 fixed.
1250
1251 2003-08-19 13:12 thassine
1252
1253 * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1254 src/tab_mm_default.cpp: removed some type checks ; (temporarily).
1255
1256 2003-08-19 11:20 thassine
1257
1258 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: the langevin switch
1259 works now better in GUI.
1260
1261 2003-08-18 12:58 thassine
1262
1263 * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp:
1264 changed the function switch value for angle bending term.
1265
1266 2003-08-14 09:51 thassine
1267
1268 * bin/param_mm/default/atomtypes.txt,
1269 bin/param_mm/default/parameters1.txt, src/eng1_mm.cpp,
1270 src/eng1_mm_default.h, src/model.cpp: added a tool for exporting
1271 solvent boxes as gromacs input files.
1272
1273 2003-08-08 06:33 thassine
1274
1275 * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp,
1276 src/eng1_mm_default.h, src/model.cpp, src/model.h: some changes
1277 in Solvate???() functions and eng1_mm_default_mim.
1278
1279 2003-08-04 06:45 thassine
1280
1281 * bin/param_mm/default/atomtypes.txt,
1282 bin/param_mm/default/parameters1.txt,
1283 bin/param_mm/default/parameters2.txt,
1284 bin/param_mm/default/parameters3.txt,
1285 bin/param_mm/default/parameters4.txt,
1286 bin/param_mm/default/parameters5.txt,
1287 bin/param_mm/default/parameters6.txt,
1288 bin/param_mm/prmfit/atomtypes.txt,
1289 bin/param_mm/prmfit/parameters1.txt,
1290 bin/param_mm/prmfit/parameters2.txt,
1291 bin/param_mm/prmfit/parameters3.txt,
1292 bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp,
1293 src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1294 src/eng1_mm_prmfit.cpp, src/tab_mm_default.cpp,
1295 src/tab_mm_default.h: the new force field parameters added for
1296 testing; the old ones are tagged WITH_TRIPOS_FF
1297
1298 2003-07-29 13:41 thassine
1299
1300 * src/model.h: some small changes due to changes in app.
1301
1302 2003-07-24 08:37 thassine
1303
1304 * src/model.h: some changes added due to changes in the app.
1305
1306 2003-07-15 12:13 thassine
1307
1308 * src/model.cpp, src/model.h: some changes added to model class
1309 (required by the app).
1310
1311 2003-07-11 11:56 thassine
1312
1313 * AUTHORS, CHANGES, configure, src/atom.cpp, src/atom.h,
1314 src/bond.cpp, src/bond.h, src/eng1_mm.cpp, src/eng1_mm.h,
1315 src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1316 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp,
1317 src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h,
1318 src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp,
1319 src/eng1_sf.h, src/engine.cpp, src/engine.h, src/geomopt.cpp,
1320 src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/model.cpp,
1321 src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp,
1322 src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp,
1323 src/seqbuild.h, src/simple_test/fileio.cpp,
1324 src/tab_mm_default.cpp, src/tab_mm_default.h,
1325 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp,
1326 src/typerule.h, src/utility.cpp, src/utility.h: changed the
1327 copyright notices a bit; now its just the year when the file was
1328 created plus names of the authors.
1329
1330 2003-06-17 12:53 thassine
1331
1332 * src/typerule.cpp: bugfixes added to the typerule class ; the next
1333 rule was not checked in many cases earlier.
1334
1335 2003-06-13 10:15 thassine
1336
1337 * AUTHORS, acconfig.h, src/Doxyfile, src/eng1_sf.h, src/geomopt.h,
1338 src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp: added
1339 more checks where/how the atom_list is sorted. that is important
1340 because sorting atom_list may change atom numbering (problem for
1341 example TSS).
1342
1343 2003-06-12 12:53 thassine
1344
1345 * src/bond.cpp, src/bond.h, src/model.cpp, src/search.cpp,
1346 src/search.h: added improvements to transition_state_search ;
1347 should now work pretty well.
1348
1349 2003-06-11 10:40 thassine
1350
1351 * src/conjgrad.cpp, src/conjgrad.h, src/eng1_qm.cpp, src/eng1_qm.h,
1352 src/eng1_qm_mopac.cpp, src/engine.h, src/geomopt.cpp,
1353 src/geomopt.h, src/model.cpp, src/search.cpp, src/search.h,
1354 src/utility.cpp: added transition_state_search and
1355 stationary_state_search + many related changes here and there.
1356 still need to do some testing, and after that add docs in
1357 user-docs and some example molecules.
1358
1359 2003-06-05 03:08 thassine
1360
1361 * bin/param_mm/prmfit, bin/param_mm/prmfit/atomtypes.txt,
1362 bin/param_mm/prmfit/parameters1.txt,
1363 bin/param_mm/prmfit/parameters2.txt,
1364 bin/param_mm/prmfit/parameters3.txt,
1365 bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp,
1366 src/model.cpp: added an initial version of the experimental FF
1367 parameters; for hydrocarbons only and still incomplete.
1368
1369 2003-06-02 15:20 thassine
1370
1371 * src/eng1_mm.cpp, src/eng1_mm_prmfit.h, src/tab_mm_default.cpp,
1372 src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h:
1373 some changes in output at force fields and tabs.
1374
1375 2003-06-02 14:29 thassine
1376
1377 * bin/builder/amino.txt, bin/builder/nucleic.txt,
1378 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h,
1379 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp,
1380 src/typerule.h: some changes in MM force fields.
1381
1382 2003-05-21 14:32 thassine
1383
1384 * src/eng1_mm_prmfit.cpp, src/tab_mm_prmfit.cpp,
1385 src/tab_mm_prmfit.h: added misc changes in mol mech stuff.
1386
1387 2003-05-19 07:05 thassine
1388
1389 * src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1390 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/model.cpp,
1391 src/tab_mm_default.cpp, src/tab_mm_default.h,
1392 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: many changes in MM
1393 force fields/tables; the AMBER implementation should be OK now.
1394
1395 2003-05-16 10:20 thassine
1396
1397 * bin/param_mm/default/parameters6.txt: changes to MM force field ;
1398 added one input file.
1399
1400 2003-05-16 10:19 thassine
1401
1402 * bin/param_mm/default/parameters4.txt,
1403 bin/param_mm/default/parameters5.txt, src/eng1_mm_default.cpp,
1404 src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp,
1405 src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp,
1406 src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h:
1407 changes to MM force field ; need to make it AMBER-compatible.
1408
1409 2003-05-12 09:11 thassine
1410
1411 * src/eng1_sf.h: minor changes to ribbon, etc.
1412
1413 2003-04-29 10:14 thassine
1414
1415 * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/model.h,
1416 src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp,
1417 src/utility.cpp: many changes; now AddHydrogens() is more
1418 compatible with seq-builder and forcefield.
1419
1420 2003-04-25 10:20 thassine
1421
1422 * bin/param_mm/default/parameters5.txt, src/atom.cpp, src/atom.h,
1423 src/eng1_mm.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h:
1424 added an option to molecular mechanics, so that one can use AMBER
1425 forcefield charges/parameters for amino/nucleic acids. charges
1426 are OK now but other params not yet added. the option is very
1427 nifty about correctness of topology, but that will be fixed
1428 later.
1429
1430 2003-04-17 07:34 thassine
1431
1432 * src/model.cpp, src/seqbuild.cpp: setup objects were not deleted,
1433 causing MOPAC to leave some files around and also memory leaking;
1434 fixed now.
1435
1436 2003-04-16 13:43 thassine
1437
1438 * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_sf.cpp, src/eng1_sf.h,
1439 src/model.cpp, src/moldyn.cpp, src/moldyn.h,
1440 src/tab_mm_default.cpp: many small changes (including trajectory
1441 writing).
1442
1443 2003-04-10 13:49 thassine
1444
1445 * src/libconfig.h.in: only whitespace changed.
1446
1447 2003-04-10 12:50 thassine
1448
1449 * src/bond.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1450 src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.h,
1451 src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h,
1452 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp:
1453 many changes in molmech tables and parameters (not ready yet).
1454
1455 2003-04-10 12:48 thassine
1456
1457 * Makefile.in, configure, configure.in, src/libconfig.h.in:
1458 configuration files updated.
1459
1460 2003-04-10 12:46 thassine
1461
1462 * bin/amber, bin/amber/README, bin/amber/all_amino02.in,
1463 bin/amber/all_aminoct02.in, bin/amber/all_aminont02.in,
1464 bin/amber/all_nuc02.in, bin/amber/parm99.dat,
1465 bin/builder/amino.txt, bin/builder/nucleic.txt: changes/additions
1466 in data files.
1467
1468 2003-04-02 06:12 thassine
1469
1470 * src/atom.cpp, src/atom.h, src/eng1_sf.cpp, src/seqbuild.cpp,
1471 src/utility.cpp: some changes/additions in the atom class.
1472
1473 2003-03-18 10:08 thassine
1474
1475 * src/eng1_sf.cpp, src/eng1_sf.h: just minor rearrangements.
1476
1477 2003-03-17 10:13 thassine
1478
1479 * src/eng1_sf.cpp: added a notice about solvation model (not yet
1480 automatically set).
1481
1482 2003-03-17 10:11 thassine
1483
1484 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for ribbons
1485 added, and some changes in moldyn.
1486
1487 2003-03-12 07:19 thassine
1488
1489 * src/eng1_sf.cpp: just some cleanups in comments etc.
1490
1491 2003-03-11 14:22 thassine
1492
1493 * src/model.cpp: added the frame_save_frq variable to
1494 model::DoMoldyn()
1495
1496 2003-03-11 07:58 thassine
1497
1498 * src/model.h: ooops; a function was missing.
1499
1500 2003-03-07 10:39 thassine
1501
1502 * src/simple_test, src/simple_test/Makefile,
1503 src/simple_test/example_file.gpr, src/simple_test/fileio.cpp,
1504 src/simple_test/st_main.cpp, src/simple_test/st_main.h: added a
1505 simple test suite (with a Makefile of it's own).
1506
1507 2003-02-14 10:56 thassine
1508
1509 * src/eng1_sf.cpp: slight changes in output.
1510
1511 2003-02-14 07:59 thassine
1512
1513 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: many
1514 molecular-dynamics-related changes.
1515
1516 2003-02-11 14:44 thassine
1517
1518 * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/eng1_sf.h,
1519 src/eng2_mm_sf.cpp, src/engine.h, src/model.cpp, src/model.h,
1520 src/moldyn.cpp, src/moldyn.h: sf will (later) support both
1521 implicit and explicit solvation model; work started now.
1522
1523 2003-02-08 07:35 thassine
1524
1525 * src/atom.h, src/bond.cpp, src/bond.h, src/eng1_mm.cpp,
1526 src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1527 src/eng1_mm_prmfit.h, src/eng1_sf.cpp, src/eng1_sf.h,
1528 src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp, src/engine.cpp,
1529 src/engine.h, src/model.cpp, src/model.h, src/tab_mm_default.cpp:
1530 make separate subclasses for boundary-potential and
1531 periodic-boundary eng-classes; also some comments added etc.
1532
1533 2003-02-06 14:50 thassine
1534
1535 * bin/param_mm/default/parameters1.txt,
1536 bin/param_mm/default/parameters2.txt,
1537 bin/param_mm/default/parameters5.txt, src/atom.h,
1538 src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1539 src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp,
1540 src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp,
1541 src/model.h, src/moldyn.h, src/tab_mm_default.cpp: many changes
1542 (computations-related).
1543
1544 2003-02-03 09:50 thassine
1545
1546 * bin/param_mm/default/parameters5.txt, src/eng1_mm.cpp,
1547 src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1548 src/model.cpp, src/model.h, src/moldyn.cpp,
1549 src/tab_mm_default.cpp: some changes to MM force field parameters
1550 (for H2O) and some important bugfixes in MM connectivity records
1551 code; this will affect nonbonded interactions.
1552
1553 2003-01-31 12:24 thassine
1554
1555 * src/engine.cpp, src/geomopt.cpp, src/model.h, src/moldyn.cpp,
1556 src/utility.cpp, src/utility.h: many bugfixes added; it is
1557 important to note that model::GetAtomCount() may now be different
1558 from engine::GetAtomCount().
1559
1560 2003-01-31 09:25 thassine
1561
1562 * src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp: an
1563 important bugfix was added to engine::engine(); also some minor
1564 fixes.
1565
1566 2003-01-30 16:31 thassine
1567
1568 * src/eng1_sf.cpp, src/eng1_sf.h: several fixes to SF; should now
1569 work more or less again.
1570
1571 2003-01-30 14:14 thassine
1572
1573 * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp: many changes in
1574 SF.
1575
1576 2003-01-30 08:29 thassine
1577
1578 * src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_mm.cpp,
1579 src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1580 src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h,
1581 src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp,
1582 src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp,
1583 src/model.h: many changes in the way how data is stored in
1584 different models; compiles but SF-stuff does not work yet; QM and
1585 MM should work.
1586
1587 2003-01-27 13:43 thassine
1588
1589 * src/atom.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_qm.cpp,
1590 src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h,
1591 src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp,
1592 src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp,
1593 src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/utility.cpp:
1594 many changes in the way how the setup classes work (not even
1595 ready yet but compiles and qm/mm works).
1596
1597 2003-01-24 08:01 thassine
1598
1599 * src/seqbuild.cpp: a fix to sequence-builder: identify now also
1600 includes H atoms to residues that it detects, so that selecting
1601 by chain/residue now works as expected.
1602
1603 2003-01-23 12:55 thassine
1604
1605 * src/atom.h, src/model.cpp, src/model.h, src/seqbuild.cpp,
1606 src/seqbuild.h: some improvements to seqbuilder.
1607
1608 2003-01-22 11:09 thassine
1609
1610 * src, src/.cvsignore: minor cleanups.
1611
1612 2003-01-22 09:25 thassine
1613
1614 * src/eng1_mm_prmfit.h: minor cleanups.
1615
1616 2003-01-22 09:11 thassine
1617
1618 * src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some cleanups, again.
1619
1620 2003-01-22 08:28 thassine
1621
1622 * src/typedef.h: added a missing file
1623
1624 2003-01-22 08:28 thassine
1625
1626 * src/model.cpp, src/model.h: minor cleanups.
1627
1628 2003-01-22 07:18 thassine
1629
1630 * Makefile.in, src/Makefile.in, src/eng1_sf.cpp, src/libdefine.h,
1631 src/model.cpp, src/model.h, src/notice.cpp, src/notice.h,
1632 src/seqbuild.cpp, src/tab_mm_default.cpp: now also make install
1633 works.
1634
1635 2003-01-21 11:42 thassine
1636
1637 * src/eng2_qm_mm.h, src/errutil.cpp, src/errutil.h,
1638 src/libdefine.h: various improvements...
1639
1640 2003-01-21 11:19 thassine
1641
1642 * Makefile.in, configure, configure.in, src/Makefile.in,
1643 src/atom.h, src/bond.h, src/config.h.in, src/conjgrad.h,
1644 src/define.h, src/eng1_mm.h, src/eng1_mm_default.h,
1645 src/eng1_mm_prmfit.h, src/eng1_qm.h, src/eng1_qm_mopac.h,
1646 src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h,
1647 src/engine.h, src/geomopt.h, src/intcrd.cpp, src/intcrd.h,
1648 src/libconfig.h.in, src/libdefine.h, src/model.cpp, src/model.h,
1649 src/moldyn.h, src/notice.cpp, src/notice.h, src/search.h,
1650 src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.h,
1651 src/tab_mm_prmfit.h, src/typedef.h, src/typerule.cpp,
1652 src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h: many
1653 improvements added but make install does not work yet.
1654
1655 2003-01-20 14:05 thassine
1656
1657 * configure, src/engine.h: minor fixes; not ready yet...
1658
1659 2003-01-20 08:38 thassine
1660
1661 * ., .cvsignore, AUTHORS, CHANGES, COPYING, INSTALL, Makefile.in,
1662 TODO, acconfig.h, aclocal.m4, bin, bin/.cvsignore, bin/builder,
1663 bin/builder/amino.txt, bin/builder/nucleic.txt, bin/param_mm,
1664 bin/param_mm/default, bin/param_mm/default/atomtypes.txt,
1665 bin/param_mm/default/parameters1.txt,
1666 bin/param_mm/default/parameters2.txt,
1667 bin/param_mm/default/parameters3.txt,
1668 bin/param_mm/default/parameters4.txt,
1669 bin/param_mm/default/parameters5.txt, bin/param_sf,
1670 bin/param_sf/default, bin/param_sf/default/loopdip.txt,
1671 bin/param_sf/default/looptor.txt,
1672 bin/param_sf/default/nonbonded.txt, config.guess, config.sub,
1673 configure, configure.in, install-sh, libghemical.spec,
1674 mkinstalldirs, src, src/.cvsignore, src/Doxyfile,
1675 src/Makefile.in, src/atom.cpp, src/atom.h, src/bond.cpp,
1676 src/bond.h, src/config.h.in, src/conjgrad.cpp, src/conjgrad.h,
1677 src/define.h, src/eng1_mm.cpp, src/eng1_mm.h,
1678 src/eng1_mm_default.cpp, src/eng1_mm_default.h,
1679 src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp,
1680 src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h,
1681 src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp,
1682 src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h,
1683 src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp,
1684 src/engine.h, src/errutil.cpp, src/errutil.h, src/geomopt.cpp,
1685 src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/miniMOPAC,
1686 src/miniMOPAC/.cvsignore, src/miniMOPAC/Makefile.in,
1687 src/miniMOPAC/README, src/miniMOPAC/aababc.c,
1688 src/miniMOPAC/addfck.c, src/miniMOPAC/addhcr.c,
1689 src/miniMOPAC/addnuc.c, src/miniMOPAC/analyt.c,
1690 src/miniMOPAC/anavib.c, src/miniMOPAC/axis.c,
1691 src/miniMOPAC/block.c, src/miniMOPAC/bonds.c,
1692 src/miniMOPAC/brlzon.c, src/miniMOPAC/btoc.c,
1693 src/miniMOPAC/calpar.c, src/miniMOPAC/capcor.c,
1694 src/miniMOPAC/cdiag.c, src/miniMOPAC/chrge.c,
1695 src/miniMOPAC/cnvg.c, src/miniMOPAC/compfg.c,
1696 src/miniMOPAC/config.log, src/miniMOPAC/consts.c,
1697 src/miniMOPAC/cqden.c, src/miniMOPAC/datin.c,
1698 src/miniMOPAC/dcart.c, src/miniMOPAC/delmol.c,
1699 src/miniMOPAC/delri.c, src/miniMOPAC/denrot.c,
1700 src/miniMOPAC/densit.c, src/miniMOPAC/depvar.c,
1701 src/miniMOPAC/deri0.c, src/miniMOPAC/deri1.c,
1702 src/miniMOPAC/deri2.c, src/miniMOPAC/deri21.c,
1703 src/miniMOPAC/deri22.c, src/miniMOPAC/deri23.c,
1704 src/miniMOPAC/deritr.c, src/miniMOPAC/deriv.c,
1705 src/miniMOPAC/dernvo.c, src/miniMOPAC/ders.c,
1706 src/miniMOPAC/dfock2.c, src/miniMOPAC/dfpsav.c,
1707 src/miniMOPAC/dgemm.c, src/miniMOPAC/dgemv.c,
1708 src/miniMOPAC/dger.c, src/miniMOPAC/dgetf2.c,
1709 src/miniMOPAC/dgetrf.c, src/miniMOPAC/dgetri.c,
1710 src/miniMOPAC/diag.c, src/miniMOPAC/diat.c,
1711 src/miniMOPAC/diat2.c, src/miniMOPAC/diegrd.c,
1712 src/miniMOPAC/dielen.c, src/miniMOPAC/diis.c,
1713 src/miniMOPAC/dijkl1.c, src/miniMOPAC/dijkl2.c,
1714 src/miniMOPAC/dipind.c, src/miniMOPAC/dipole.c,
1715 src/miniMOPAC/dlaswp.c, src/miniMOPAC/dofs.c,
1716 src/miniMOPAC/dot.c, src/miniMOPAC/drc.c, src/miniMOPAC/drcout.c,
1717 src/miniMOPAC/dtrmm.c, src/miniMOPAC/dtrmv.c,
1718 src/miniMOPAC/dtrsm.c, src/miniMOPAC/dtrti2.c,
1719 src/miniMOPAC/dtrtri.c, src/miniMOPAC/dvfill.c,
1720 src/miniMOPAC/ef.c, src/miniMOPAC/enpart.c, src/miniMOPAC/esp.c,
1721 src/miniMOPAC/etime.c, src/miniMOPAC/exchng.c,
1722 src/miniMOPAC/fdate.c, src/miniMOPAC/ffhpol.c,
1723 src/miniMOPAC/flepo.c, src/miniMOPAC/fmat.c,
1724 src/miniMOPAC/fock1.c, src/miniMOPAC/fock2.c,
1725 src/miniMOPAC/force.c, src/miniMOPAC/formxy.c,
1726 src/miniMOPAC/forsav.c, src/miniMOPAC/fortran,
1727 src/miniMOPAC/fortran/SIZES, src/miniMOPAC/fortran/aababc.f,
1728 src/miniMOPAC/fortran/addfck.f, src/miniMOPAC/fortran/addhcr.f,
1729 src/miniMOPAC/fortran/addnuc.f, src/miniMOPAC/fortran/analyt.f,
1730 src/miniMOPAC/fortran/anavib.f, src/miniMOPAC/fortran/axis.f,
1731 src/miniMOPAC/fortran/block.f, src/miniMOPAC/fortran/bonds.f,
1732 src/miniMOPAC/fortran/brlzon.f, src/miniMOPAC/fortran/btoc.f,
1733 src/miniMOPAC/fortran/calpar.f, src/miniMOPAC/fortran/capcor.f,
1734 src/miniMOPAC/fortran/cdiag.f, src/miniMOPAC/fortran/chrge.f,
1735 src/miniMOPAC/fortran/cnvg.f, src/miniMOPAC/fortran/compfg.f,
1736 src/miniMOPAC/fortran/consts.f, src/miniMOPAC/fortran/cqden.f,
1737 src/miniMOPAC/fortran/datin.f, src/miniMOPAC/fortran/dcart.f,
1738 src/miniMOPAC/fortran/delmol.f, src/miniMOPAC/fortran/delri.f,
1739 src/miniMOPAC/fortran/denrot.f, src/miniMOPAC/fortran/densit.f,
1740 src/miniMOPAC/fortran/depvar.f, src/miniMOPAC/fortran/deri0.f,
1741 src/miniMOPAC/fortran/deri1.f, src/miniMOPAC/fortran/deri2.f,
1742 src/miniMOPAC/fortran/deri21.f, src/miniMOPAC/fortran/deri22.f,
1743 src/miniMOPAC/fortran/deri23.f, src/miniMOPAC/fortran/deritr.f,
1744 src/miniMOPAC/fortran/deriv.f, src/miniMOPAC/fortran/dernvo.f,
1745 src/miniMOPAC/fortran/ders.f, src/miniMOPAC/fortran/dfock2.f,
1746 src/miniMOPAC/fortran/dfpsav.f, src/miniMOPAC/fortran/dgemm.f,
1747 src/miniMOPAC/fortran/dgemv.f, src/miniMOPAC/fortran/dger.f,
1748 src/miniMOPAC/fortran/dgetf2.f, src/miniMOPAC/fortran/dgetrf.f,
1749 src/miniMOPAC/fortran/dgetri.f, src/miniMOPAC/fortran/diag.f,
1750 src/miniMOPAC/fortran/diat.f, src/miniMOPAC/fortran/diat2.f,
1751 src/miniMOPAC/fortran/diegrd.f, src/miniMOPAC/fortran/dielen.f,
1752 src/miniMOPAC/fortran/diis.f, src/miniMOPAC/fortran/dijkl1.f,
1753 src/miniMOPAC/fortran/dijkl2.f, src/miniMOPAC/fortran/dipind.f,
1754 src/miniMOPAC/fortran/dipole.f, src/miniMOPAC/fortran/dlaswp.f,
1755 src/miniMOPAC/fortran/dofs.f, src/miniMOPAC/fortran/dot.f,
1756 src/miniMOPAC/fortran/drc.f, src/miniMOPAC/fortran/drcout.f,
1757 src/miniMOPAC/fortran/dtrmm.f, src/miniMOPAC/fortran/dtrmv.f,
1758 src/miniMOPAC/fortran/dtrsm.f, src/miniMOPAC/fortran/dtrti2.f,
1759 src/miniMOPAC/fortran/dtrtri.f, src/miniMOPAC/fortran/dvfill.f,
1760 src/miniMOPAC/fortran/ef.f, src/miniMOPAC/fortran/enpart.f,
1761 src/miniMOPAC/fortran/esp.f, src/miniMOPAC/fortran/etime.c,
1762 src/miniMOPAC/fortran/exchng.f, src/miniMOPAC/fortran/fdate.c,
1763 src/miniMOPAC/fortran/ffhpol.f, src/miniMOPAC/fortran/flepo.f,
1764 src/miniMOPAC/fortran/fmat.f, src/miniMOPAC/fortran/fock1.f,
1765 src/miniMOPAC/fortran/fock2.f, src/miniMOPAC/fortran/force.f,
1766 src/miniMOPAC/fortran/formxy.f, src/miniMOPAC/fortran/forsav.f,
1767 src/miniMOPAC/fortran/frame.f, src/miniMOPAC/fortran/freqcy.f,
1768 src/miniMOPAC/fortran/geout.f, src/miniMOPAC/fortran/geoutg.f,
1769 src/miniMOPAC/fortran/getgeg.f, src/miniMOPAC/fortran/getgeo.f,
1770 src/miniMOPAC/fortran/getsym.f, src/miniMOPAC/fortran/gettxt.f,
1771 src/miniMOPAC/fortran/gmetry.f, src/miniMOPAC/fortran/gover.f,
1772 src/miniMOPAC/fortran/greenf.f, src/miniMOPAC/fortran/grid.f,
1773 src/miniMOPAC/fortran/h1elec.f, src/miniMOPAC/fortran/haddon.f,
1774 src/miniMOPAC/fortran/hcore.f, src/miniMOPAC/fortran/helect.f,
1775 src/miniMOPAC/fortran/hqrii.f, src/miniMOPAC/fortran/ijkl.f,
1776 src/miniMOPAC/fortran/ilaenv.f, src/miniMOPAC/fortran/initsv.f,
1777 src/miniMOPAC/fortran/interp.f, src/miniMOPAC/fortran/iter.f,
1778 src/miniMOPAC/fortran/jcarin.f, src/miniMOPAC/fortran/linmin.f,
1779 src/miniMOPAC/fortran/local.f, src/miniMOPAC/fortran/locmin.f,
1780 src/miniMOPAC/fortran/lsame.f, src/miniMOPAC/fortran/makpol.f,
1781 src/miniMOPAC/fortran/mamult.f, src/miniMOPAC/fortran/matou1.f,
1782 src/miniMOPAC/fortran/matout.f, src/miniMOPAC/fortran/matpak.f,
1783 src/miniMOPAC/fortran/meci.f, src/miniMOPAC/fortran/mecid.f,
1784 src/miniMOPAC/fortran/mecih.f, src/miniMOPAC/fortran/mecip.f,
1785 src/miniMOPAC/fortran/minimopac.f,
1786 src/miniMOPAC/fortran/moldat.f, src/miniMOPAC/fortran/molval.f,
1787 src/miniMOPAC/fortran/mopac.f, src/miniMOPAC/fortran/mullik.f,
1788 src/miniMOPAC/fortran/mult.f, src/miniMOPAC/fortran/nllsq.f,
1789 src/miniMOPAC/fortran/nuchar.f, src/miniMOPAC/fortran/parsav.f,
1790 src/miniMOPAC/fortran/partxy.f, src/miniMOPAC/fortran/pathk.f,
1791 src/miniMOPAC/fortran/paths.f, src/miniMOPAC/fortran/perm.f,
1792 src/miniMOPAC/fortran/polar.f, src/miniMOPAC/fortran/powsav.f,
1793 src/miniMOPAC/fortran/powsq.f, src/miniMOPAC/fortran/prtdrc.f,
1794 src/miniMOPAC/fortran/quadr.f, src/miniMOPAC/fortran/react1.f,
1795 src/miniMOPAC/fortran/reada.f, src/miniMOPAC/fortran/readmo.f,
1796 src/miniMOPAC/fortran/refer.f, src/miniMOPAC/fortran/repp.f,
1797 src/miniMOPAC/fortran/rotat.f, src/miniMOPAC/fortran/rotate.f,
1798 src/miniMOPAC/fortran/rsp.f, src/miniMOPAC/fortran/search.f,
1799 src/miniMOPAC/fortran/second.f, src/miniMOPAC/fortran/setupg.f,
1800 src/miniMOPAC/fortran/solrot.f, src/miniMOPAC/fortran/swap.f,
1801 src/miniMOPAC/fortran/sympro.f, src/miniMOPAC/fortran/symtry.f,
1802 src/miniMOPAC/fortran/symtrz.f, src/miniMOPAC/fortran/thermo.f,
1803 src/miniMOPAC/fortran/timer.f, src/miniMOPAC/fortran/timout.f,
1804 src/miniMOPAC/fortran/update.f, src/miniMOPAC/fortran/upsurf.f,
1805 src/miniMOPAC/fortran/vecprt.f, src/miniMOPAC/fortran/writmo.f,
1806 src/miniMOPAC/fortran/wrtkey.f, src/miniMOPAC/fortran/wrttxt.f,
1807 src/miniMOPAC/fortran/xerbla.f, src/miniMOPAC/fortran/xyzint.f,
1808 src/miniMOPAC/frame.c, src/miniMOPAC/freqcy.c,
1809 src/miniMOPAC/geout.c, src/miniMOPAC/geoutg.c,
1810 src/miniMOPAC/getgeg.c, src/miniMOPAC/getgeo.c,
1811 src/miniMOPAC/getsym.c, src/miniMOPAC/gettxt.c,
1812 src/miniMOPAC/gmetry.c, src/miniMOPAC/gover.c,
1813 src/miniMOPAC/greenf.c, src/miniMOPAC/grid.c,
1814 src/miniMOPAC/h1elec.c, src/miniMOPAC/haddon.c,
1815 src/miniMOPAC/hcore.c, src/miniMOPAC/helect.c,
1816 src/miniMOPAC/hqrii.c, src/miniMOPAC/ijkl.c,
1817 src/miniMOPAC/ilaenv.c, src/miniMOPAC/initsv.c,
1818 src/miniMOPAC/interp.c, src/miniMOPAC/iter.c,
1819 src/miniMOPAC/jcarin.c, src/miniMOPAC/linmin.c,
1820 src/miniMOPAC/local.c, src/miniMOPAC/locmin.c,
1821 src/miniMOPAC/lsame.c, src/miniMOPAC/makpol.c,
1822 src/miniMOPAC/mamult.c, src/miniMOPAC/matou1.c,
1823 src/miniMOPAC/matout.c, src/miniMOPAC/matpak.c,
1824 src/miniMOPAC/meci.c, src/miniMOPAC/mecid.c,
1825 src/miniMOPAC/mecih.c, src/miniMOPAC/mecip.c,
1826 src/miniMOPAC/minimopac.c, src/miniMOPAC/moldat.c,
1827 src/miniMOPAC/molval.c, src/miniMOPAC/mullik.c,
1828 src/miniMOPAC/mult.c, src/miniMOPAC/nllsq.c,
1829 src/miniMOPAC/nuchar.c, src/miniMOPAC/parsav.c,
1830 src/miniMOPAC/partxy.c, src/miniMOPAC/pathk.c,
1831 src/miniMOPAC/paths.c, src/miniMOPAC/perm.c,
1832 src/miniMOPAC/polar.c, src/miniMOPAC/powsav.c,
1833 src/miniMOPAC/powsq.c, src/miniMOPAC/prtdrc.c,
1834 src/miniMOPAC/quadr.c, src/miniMOPAC/react1.c,
1835 src/miniMOPAC/reada.c, src/miniMOPAC/readmo.c,
1836 src/miniMOPAC/refer.c, src/miniMOPAC/repp.c,
1837 src/miniMOPAC/rotat.c, src/miniMOPAC/rotate.c,
1838 src/miniMOPAC/rsp.c, src/miniMOPAC/search.c,
1839 src/miniMOPAC/second.c, src/miniMOPAC/setupg.c,
1840 src/miniMOPAC/solrot.c, src/miniMOPAC/swap.c,
1841 src/miniMOPAC/sympro.c, src/miniMOPAC/symtry.c,
1842 src/miniMOPAC/symtrz.c, src/miniMOPAC/thermo.c,
1843 src/miniMOPAC/timer.c, src/miniMOPAC/timout.c,
1844 src/miniMOPAC/update.c, src/miniMOPAC/upsurf.c,
1845 src/miniMOPAC/vecprt.c, src/miniMOPAC/writmo.c,
1846 src/miniMOPAC/wrtkey.c, src/miniMOPAC/wrttxt.c,
1847 src/miniMOPAC/xerbla.c, src/miniMOPAC/xyzint.c, src/model.cpp,
1848 src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp,
1849 src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp,
1850 src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h,
1851 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typedef.h,
1852 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h,
1853 src/v3d.h: Initial revision
1854
1855 2003-01-20 08:38
1856
1857 * .: New repository initialized by cvs2svn.

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