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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 User Rev File contents
1 thassine 245 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 thassine 240 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 thassine 245 src/typerule.cpp: added assertion_failed() method for fatal error
62     reporting.
63 thassine 240
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 thassine 245 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 thassine 240
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 thassine 245 src/libghemical-features.h, src/typedef.h: version number changed
142     to 2.98
143 thassine 240
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 thassine 245 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 thassine 240
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 thassine 245 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 thassine 240 src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h,
232 thassine 245 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 thassine 240
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 thassine 245 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 thassine 240
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 thassine 245 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 thassine 240
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 thassine 245 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
410     libghemical-features.h implemented (thanks to Jean Brefort).
411 thassine 240
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 thassine 187 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 thassine 184 2006-08-07 11:49 thassine
448 thassine 178
449 thassine 184 * .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 thassine 178 * ChangeLog, INSTALL, configure.ac: this is v2.00rc1
487    
488 thassine 184 2006-03-29 08:41 thassine
489 hutchisn 149
490 thassine 177 * INSTALL, src/model.cpp: documentation update.
491 hutchisn 149
492 thassine 184 2006-03-28 16:19 hutchisn
493 hutchisn 149
494 thassine 177 * src/model.cpp: Check for selected atoms before adding hydrogens.
495 thassine 184 If the user has selected atoms,
496     only add to those atoms.
497 hutchisn 150
498 thassine 184 2006-03-28 10:49 thassine
499 hutchisn 133
500 thassine 184 * ., .cvsignore: cvsignore update.
501 hutchisn 133
502 thassine 184 2006-03-28 10:36 thassine
503 hutchisn 133
504 thassine 177 * config.guess, config.sub, ltmain.sh: removed some unnecessary
505     files.
506    
507 thassine 184 2006-03-23 11:42 thassine
508 thassine 177
509     * src/model.cpp: fixed a text string.
510    
511 thassine 184 2006-03-22 13:01 thassine
512 thassine 177
513     * src/model.cpp: a change in mol.dyn.
514    
515 thassine 184 2006-03-22 12:21 thassine
516 thassine 177
517 thassine 184 * 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 thassine 177
525 thassine 184 2006-03-18 17:02 thassine
526 thassine 177
527 thassine 184 * src/eng1_mm_default.cpp, src/model.cpp, src/moldyn.cpp: some
528     mol.dyn. changes.
529 thassine 177
530 thassine 184 2006-03-14 13:47 thassine
531 thassine 177
532     * src/moldyn.h: a few more mol.dyn. changes.
533    
534 thassine 184 2006-03-14 08:45 thassine
535 thassine 177
536 thassine 184 * 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 thassine 177 missing srand() calls added.
539    
540 thassine 184 2006-03-10 12:12 thassine
541 thassine 177
542 thassine 184 * src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h,
543 thassine 245 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 thassine 177
547 thassine 184 2006-03-08 10:33 thassine
548 thassine 177
549 thassine 184 * ., .cvsignore, aclocal.m4, src/eng1_mm.cpp, src/engine.cpp:
550 thassine 177 aclocal.m4 removed ; some mol.dyn. related changes added.
551    
552 thassine 184 2006-03-07 13:42 thassine
553 thassine 177
554     * aclocal.m4, src/engine.cpp: a bugfix for CheckLocations().
555    
556 thassine 184 2006-03-07 13:22 thassine
557 thassine 177
558     * aclocal.m4, src/eng1_mm.cpp, src/engine.cpp, src/engine.h:
559     CheckLocations() changed.
560    
561 thassine 184 2006-03-07 10:49 thassine
562 thassine 177
563     * aclocal.m4, autogen.sh, config.guess, config.sub, ltmain.sh:
564     updated autogen.sh
565    
566 thassine 184 2006-03-07 08:44 thassine
567 thassine 177
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 thassine 184 2006-03-06 08:53 thassine
573 thassine 177
574     * aclocal.m4, src/engine.h, src/model.cpp: added a method
575     RequestUpdateTerms().
576    
577 thassine 184 2006-03-06 07:46 thassine
578 thassine 177
579     * aclocal.m4, src/moldyn.cpp: a minor fix in mol.dyn.
580    
581 thassine 184 2006-03-03 12:56 thassine
582 thassine 177
583 thassine 245 * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed atom
584     changes.
585 thassine 177
586 thassine 184 2006-03-03 12:24 thassine
587 thassine 177
588 thassine 184 * ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, bin,
589 thassine 245 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 thassine 184 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 thassine 245 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 thassine 177
606 thassine 184 2006-03-01 12:15 thassine
607 thassine 177
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 thassine 184 2006-02-28 12:14 thassine
615 thassine 177
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 thassine 184 2006-02-27 11:25 thassine
625 thassine 177
626 thassine 245 * 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 thassine 177
631 thassine 184 2006-02-27 08:29 thassine
632 thassine 177
633     * aclocal.m4, src/eng1_sf.h: a bugfix added...
634    
635 thassine 184 2006-02-24 13:50 thassine
636 thassine 177
637     * aclocal.m4, src/model.cpp: fixed a bug in box solvation.
638    
639 thassine 184 2006-02-20 12:34 thassine
640 thassine 177
641 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
645     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
646 thassine 184 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 thassine 177
655 thassine 184 2006-02-17 19:14 hutchisn
656 thassine 177
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 thassine 245 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 thassine 184 fixes backwards-compatibility warnings using GCC.
666 thassine 177
667 thassine 184 2006-02-17 16:18 hutchisn
668 thassine 177
669 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
673     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
674 thassine 184 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 thassine 245 */Makefile.in: Update with latest automake (1.9.6), libtool
682     (1.5.22).
683 thassine 177
684 thassine 184 2006-02-16 09:20 thassine
685 thassine 177
686     * aclocal.m4, config.guess, config.sub, ltmain.sh: configure
687     updates.
688    
689 thassine 184 2006-02-10 14:22 thassine
690 thassine 177
691 thassine 184 * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in,
692 thassine 177 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 thassine 184 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 thassine 177 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 thassine 245 src/seqbuild.cpp, src/seqbuild.h, src/typedef.h, src/utility.cpp,
702     src/utility.h, src/v3d.h: many changes...
703 thassine 177
704 thassine 184 2006-02-07 12:44 thassine
705 thassine 177
706 thassine 184 * 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 thassine 177
711 thassine 184 2006-02-06 14:02 thassine
712 thassine 177
713 thassine 184 * 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 thassine 177
717 thassine 184 2006-02-06 09:40 thassine
718 thassine 177
719     * src/utility.cpp: some comments added.
720    
721 thassine 184 2006-02-06 08:29 thassine
722 thassine 177
723 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h, src/model.h: minor changes.
724 thassine 177
725 thassine 184 2006-01-19 13:38 thassine
726 thassine 177
727 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h: removed some unnecessary changes.
728 thassine 177
729 thassine 184 2006-01-19 07:41 thassine
730 thassine 177
731 thassine 184 * 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 thassine 245 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h:
738     libdefine.h was renamed to libghemicaldefine.h
739 thassine 177
740 thassine 184 2005-12-14 14:10 thassine
741 thassine 177
742 thassine 184 * src, src/.cvsignore: minor changes.
743 thassine 177
744 thassine 184 2005-11-29 10:54 thassine
745 thassine 177
746     * src/geomopt.cpp: oops ; geomopt.cpp pathed wrong way.
747    
748 thassine 184 2005-11-29 10:39 thassine
749 thassine 177
750 thassine 184 * src/atom.h, src/geomopt.cpp, src/model.cpp, src/moldyn.cpp,
751     src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp,
752 thassine 245 src/tab_mm_tripos52.cpp: some changes in the atom flags ; need to
753     separate the user/system level hidden atoms.
754 thassine 177
755 thassine 184 2005-11-17 12:31 thassine
756 thassine 177
757     * src/eng1_sf.h: added an another table.
758    
759 thassine 184 2005-11-17 11:56 thassine
760 thassine 177
761     * src/eng1_sf.h: a new table was added for visualization params.
762    
763 thassine 184 2005-11-10 10:00 thassine
764 thassine 177
765 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
769     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
770 thassine 184 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 thassine 177
774 thassine 184 2005-11-02 12:24 thassine
775 thassine 177
776     * configure, src/model.h: minor changes ; needed for the app.
777    
778 thassine 184 2005-10-26 21:44 hutchisn
779 thassine 177
780 thassine 184 * ., .cvsignore, ChangeLog, Makefile.in, aclocal.m4,
781     bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in,
782 thassine 177 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 thassine 184 bin/param_sf/default/Makefile.in, config.guess, config.sub,
786     configure, configure.ac, ltmain.sh, src, src/.cvsignore,
787 thassine 245 src/Makefile.in: * configure.ac, configure: Update to use
788     openbabel-2.0 check,
789 thassine 184 rather than openbabel.
790    
791 thassine 245 * ltmain.sh, aclocal.m4, */Makefile.in: Update with latest
792 thassine 184 autoconf, libtool (1.5.20).
793 thassine 177
794 thassine 184 2005-10-08 15:12 thassine
795 thassine 177
796 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
800     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
801 thassine 184 bin/param_sf/default/Makefile.in, configure, configure.ac,
802     src/Makefile.in, src/atom.cpp, src/atom.h, src/libdefine.h,
803 thassine 245 src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms ;
804     just a new value stored in atom objects
805 thassine 177
806 thassine 184 2005-09-26 08:46 thassine
807 thassine 177
808 thassine 184 * 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 thassine 177
811 thassine 184 2005-09-19 09:21 thassine
812 thassine 177
813 thassine 184 * src/eng1_qm_mopac.cpp, src/search.cpp: minor tweaks ; now should
814 thassine 177 compile with the FC4 compiler.
815    
816 thassine 184 2005-08-24 09:55 thassine
817 thassine 177
818 thassine 184 * 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 thassine 177
821 thassine 184 2005-08-23 11:27 thassine
822 thassine 177
823 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
828     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
829 thassine 184 bin/param_sf/default/Makefile.in, configure, configure.ac,
830 thassine 245 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 thassine 177
834 thassine 184 2005-07-06 08:59 thassine
835 thassine 177
836 thassine 184 * 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 thassine 177 bin/param_mm/prmfit/Makefile.in,
840     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
841 thassine 184 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 thassine 177
855 thassine 184 2005-07-05 08:01 thassine
856 thassine 177
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 thassine 184 2005-07-01 12:48 thassine
863 thassine 177
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 thassine 245 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 thassine 177
875 thassine 184 2005-07-01 10:49 thassine
876 thassine 177
877     * ChangeLog, INSTALL, aclocal.m4, configure, configure.ac: did the
878     final changes for a release 1.90.
879    
880 thassine 184 2005-06-30 13:01 thassine
881 thassine 123
882 thassine 184 * Makefile.in, acconfig.h, acinclude.m4, aclocal.m4,
883     bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in,
884 thassine 123 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 thassine 184 bin/param_sf/default/Makefile.in, configure, configure.ac,
888     configure.in, libghemical.pc.in, src/Makefile.in,
889 thassine 123 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 thassine 184 2005-06-23 13:19 thassine
895 thassine 123
896 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/model.cpp,
897     src/model.h: the lib/app interface changed.
898 thassine 123
899 thassine 184 2005-06-21 08:14 thassine
900 thassine 123
901 thassine 184 * 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 thassine 123
905 thassine 184 2005-06-20 13:07 thassine
906 thassine 123
907 thassine 184 * 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 thassine 123
910 thassine 184 2005-06-20 10:57 thassine
911 thassine 123
912 thassine 184 * 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 thassine 123
915 thassine 184 2005-06-20 09:29 thassine
916 thassine 123
917 thassine 184 * src/geomopt.h, src/model.cpp, src/model.h: minor changes related
918     to app multithreading.
919 thassine 123
920 thassine 184 2005-06-14 10:23 thassine
921 thassine 123
922 thassine 184 * src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: started
923     converting GO and MD into multithreaded versions.
924 thassine 123
925 thassine 184 2005-06-13 10:17 thassine
926 thassine 123
927 thassine 184 * src/model.cpp, src/model.h: a complete multi-threaded Random
928     Search added ; others will follow.
929 thassine 123
930 thassine 184 2005-06-13 07:13 thassine
931 thassine 123
932 thassine 184 * config.guess, config.sub, ltmain.sh, src, src/.cvsignore,
933 thassine 123 src/model.cpp, src/model.h, src/search.cpp, src/search.h: added
934     an initial framework for multithreading.
935    
936 thassine 184 2005-06-08 08:40 thassine
937 thassine 123
938 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h, src/search.cpp: some formatting
939     changes and a macro changed in eng1_sf.h
940 thassine 123
941 thassine 184 2005-05-11 15:14 thassine
942 thassine 123
943 thassine 184 * 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 thassine 123
947 thassine 184 2005-05-09 06:50 thassine
948 thassine 123
949 thassine 184 * src/atom.h, src/moldyn.cpp, src/moldyn.h: an initial
950     implementation for a LOCKED atom flag.
951 thassine 123
952 thassine 184 2005-05-06 10:05 thassine
953 thassine 123
954 thassine 184 * 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 thassine 123
958 thassine 184 2005-05-03 12:12 thassine
959 thassine 123
960 thassine 184 * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp,
961 thassine 245 src/eng1_sf.cpp, src/model.cpp: some bugfixes added for solvation
962     functions.
963 thassine 123
964 thassine 184 2005-04-28 10:17 thassine
965 thassine 123
966 thassine 184 * 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 thassine 123
971 thassine 184 2005-04-26 07:20 thassine
972 thassine 123
973 thassine 184 * 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 thassine 123
977 thassine 184 2005-04-22 13:41 thassine
978 thassine 123
979 thassine 245 * Makefile.in, aclocal.m4, src/model.h: some class names changed in
980     the app ; sync here.
981 thassine 123
982 thassine 184 2005-04-21 12:24 thassine
983 thassine 123
984 thassine 184 * 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 thassine 123 bin/param_mm/prmfit/Makefile.in,
988     bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in,
989 thassine 184 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 thassine 123 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 thassine 184 2005-04-19 12:23 thassine
997 thassine 123
998 thassine 184 * 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 thassine 123
1003 thassine 184 2005-04-19 12:20 thassine
1004 thassine 123
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 thassine 184 src/simple_test/example3.h, src/simple_test/example3_extra,
1009 thassine 123 src/simple_test/example3_extra/TestForm.html,
1010     src/simple_test/example3_extra/dumpdata.sh,
1011     src/simple_test/example3_extra/input_example,
1012 thassine 184 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 thassine 123
1017 thassine 184 2005-04-19 08:48 thassine
1018 thassine 123
1019 thassine 184 * Makefile.in, aclocal.m4, bin/README, bin/param_mm/Makefile.am,
1020 thassine 123 bin/param_mm/Makefile.in, bin/param_mm/prmfit/Makefile.in,
1021 thassine 184 bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore,
1022 thassine 123 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 thassine 184 bin/param_mm/tripos52/parameters5.txt, config.guess, config.sub,
1030     configure, configure.in, ltmain.sh, src/Makefile.am,
1031 thassine 123 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 thassine 245 src/libconfig.h.in, src/model.h: ported the tripos5.2 force field
1034     implementation from ghemical-1.01 into libghemical.
1035 thassine 123
1036 thassine 184 2005-04-08 14:59 thassine
1037 thassine 123
1038 thassine 184 * src/model.cpp, src/model.h: added an utility function.
1039 thassine 123
1040 thassine 184 2005-03-21 12:52 thassine
1041 thassine 123
1042     * src/Makefile.SIMPLE: added an alternative simple makefile in
1043     src/.
1044    
1045 thassine 184 2005-02-08 07:12 thassine
1046 thassine 123
1047     * src/conjgrad.cpp: some updates in conjgrad.cpp Simple linesearch.
1048    
1049 thassine 184 2005-02-03 11:44 thassine
1050 thassine 123
1051 thassine 184 * 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 thassine 123
1054 thassine 184 2005-01-19 11:29 thassine
1055 thassine 123
1056     * Makefile.in, src/model.cpp, src/model.h: some minor changes for
1057     new stuff of my own ; not yet functional.
1058    
1059 thassine 184 2005-01-04 11:28 thassine
1060 thassine 123
1061 thassine 245 * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added a
1062     new virtual method DoSHAKE() in engine class.
1063 thassine 123
1064 thassine 184 2004-12-10 15:14 thassine
1065 thassine 123
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 thassine 184 2004-09-13 09:17 thassine
1071 thassine 123
1072     * Makefile.in, src/atom.cpp, src/atom.h, src/eng1_sf.h,
1073 thassine 245 src/model.cpp: the atom objects now are aware of the model object
1074     ; added some stuff to make everything compile.
1075 thassine 123
1076 thassine 184 2004-08-30 09:28 thassine
1077 thassine 123
1078 thassine 184 * Makefile.in, aclocal.m4, bin/Makefile.in, configure,
1079     configure.in: the include dir is changed into
1080 thassine 123 <prefix>/include/ghemical.
1081    
1082 thassine 184 2004-08-27 12:07 thassine
1083 thassine 123
1084     * Makefile.am, Makefile.in, aclocal.m4, libghemical.pc.in,
1085 thassine 245 src/Makefile.am, src/Makefile.in: changed includedir to /ghemical
1086     and some other changes ; .pc file not updated?
1087 thassine 123
1088 thassine 184 2004-08-26 12:34 thassine
1089 thassine 123
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 thassine 184 2004-08-25 11:13 thassine
1095 thassine 123
1096 thassine 184 * 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 thassine 123 bin/param_mm/default/Makefile.am,
1103 thassine 184 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 thassine 123 bin/param_sf/default/Makefile.am,
1109 thassine 184 bin/param_sf/default/Makefile.in, config.guess, config.sub,
1110     configure, configure.in, ltmain.sh, src/Makefile.am,
1111 thassine 123 src/Makefile.in, src/Makefile.include, src/model.cpp: added
1112     automake-based configuration scripts (M. Banck and J. Brefort).
1113    
1114 thassine 184 2004-08-13 12:14 thassine
1115 thassine 123
1116     * CHANGES, ChangeLog, Makefile.am, Makefile.in, NEWS, README,
1117 thassine 184 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 thassine 123 bin/param_mm/default/Makefile.in, bin/param_sf/Makefile.am,
1123     bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.am,
1124 thassine 184 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 thassine 123
1129 thassine 184 2004-06-07 19:54 hutchisn
1130 thassine 123
1131     * src/atom.cpp: Updated with standardized element colors.
1132    
1133 thassine 184 2004-05-28 15:10 thassine
1134 thassine 123
1135     * src/typerule.cpp: some checks added to typerule class.
1136    
1137 thassine 184 2004-05-13 11:45 thassine
1138 thassine 123
1139     * acinclude.m4, aclocal.m4, configure, configure.in,
1140     libghemical.pc.in: some improvements in configure.in
1141    
1142 thassine 184 2004-04-16 09:24 thassine
1143 thassine 123
1144     * src/seqbuild.cpp: added a fix for TRP-residues in
1145     sequencebuilder::Identify().
1146    
1147 thassine 184 2004-04-08 10:13 thassine
1148 thassine 123
1149 thassine 184 * 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 thassine 123
1153 thassine 184 2004-03-26 09:05 thassine
1154 thassine 123
1155 thassine 245 * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a new
1156     GetRange() method for bonds in model class.
1157 thassine 123
1158 thassine 184 2004-03-18 12:04 thassine
1159 thassine 123
1160 thassine 184 * src/model.cpp, src/resonance.h: minor changes in
1161 thassine 123 resonance_structures class (just a framework, under
1162     construction).
1163    
1164 thassine 184 2004-03-15 13:01 thassine
1165 thassine 123
1166     * src/typerule.cpp: implemented the fc=? test in the typerule
1167     class.
1168    
1169 thassine 184 2004-03-09 08:44 thassine
1170 thassine 123
1171 thassine 184 * src/model.cpp, src/model.h: added model::GetRS().
1172 thassine 123
1173 thassine 184 2004-03-03 13:13 thassine
1174 thassine 123
1175 thassine 184 * 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 thassine 123
1179 thassine 184 2004-02-18 11:47 thassine
1180 thassine 123
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 thassine 184 2004-01-28 08:56 thassine
1186 thassine 123
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 thassine 184 2004-01-28 08:53 thassine
1193 thassine 123
1194 thassine 184 * Makefile.in, bin/param_mm/default/atomtypes.txt,
1195 thassine 123 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 thassine 184 bin/param_mm/prmfit/parameters4.txt, configure, configure.in,
1204 thassine 245 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 thassine 123
1208 thassine 184 2003-11-06 11:59 thassine
1209 thassine 123
1210 thassine 184 * 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 thassine 123
1213 thassine 184 2003-09-24 06:47 thassine
1214 thassine 123
1215     * src/conjgrad.cpp: minor improvements in conjgrad search.
1216    
1217 thassine 184 2003-09-11 11:56 thassine
1218 thassine 123
1219 thassine 184 * src/typerule.cpp, src/typerule.h: some changes in typerules.
1220 thassine 123
1221 thassine 184 2003-09-01 09:25 thassine
1222 thassine 123
1223 thassine 245 * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp: some
1224     bugfixes added.
1225 thassine 123
1226 thassine 184 2003-08-29 07:39 thassine
1227 thassine 123
1228 thassine 184 * 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 thassine 245 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 thassine 123
1241 thassine 184 2003-08-21 09:09 thassine
1242 thassine 123
1243 thassine 184 * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/engine.cpp,
1244     src/engine.h: some changes in bp (boundary potential) details.
1245 thassine 123
1246 thassine 184 2003-08-21 05:35 thassine
1247 thassine 123
1248     * src/tab_mm_default.cpp: a bug related to out-of-plane terms is
1249     fixed.
1250    
1251 thassine 184 2003-08-19 13:12 thassine
1252 thassine 123
1253 thassine 184 * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp,
1254     src/tab_mm_default.cpp: removed some type checks ; (temporarily).
1255 thassine 123
1256 thassine 184 2003-08-19 11:20 thassine
1257 thassine 123
1258 thassine 184 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: the langevin switch
1259     works now better in GUI.
1260 thassine 123
1261 thassine 184 2003-08-18 12:58 thassine
1262 thassine 123
1263 thassine 184 * 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 thassine 123
1266 thassine 184 2003-08-14 09:51 thassine
1267 thassine 123
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 thassine 184 2003-08-08 06:33 thassine
1274 thassine 123
1275 thassine 184 * 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 thassine 123
1279 thassine 184 2003-08-04 06:45 thassine
1280 thassine 123
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 thassine 184 2003-07-29 13:41 thassine
1299 thassine 123
1300     * src/model.h: some small changes due to changes in app.
1301    
1302 thassine 184 2003-07-24 08:37 thassine
1303 thassine 123
1304     * src/model.h: some changes added due to changes in the app.
1305    
1306 thassine 184 2003-07-15 12:13 thassine
1307 thassine 123
1308 thassine 184 * src/model.cpp, src/model.h: some changes added to model class
1309 thassine 123 (required by the app).
1310    
1311 thassine 184 2003-07-11 11:56 thassine
1312 thassine 123
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 thassine 184 src/seqbuild.h, src/simple_test/fileio.cpp,
1324     src/tab_mm_default.cpp, src/tab_mm_default.h,
1325 thassine 123 src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp,
1326 thassine 184 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 thassine 123
1330 thassine 184 2003-06-17 12:53 thassine
1331 thassine 89
1332 thassine 245 * src/typerule.cpp: bugfixes added to the typerule class ; the next
1333     rule was not checked in many cases earlier.
1334 thassine 89
1335 thassine 184 2003-06-13 10:15 thassine
1336 thassine 89
1337     * AUTHORS, acconfig.h, src/Doxyfile, src/eng1_sf.h, src/geomopt.h,
1338 thassine 245 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 thassine 89
1343 thassine 184 2003-06-12 12:53 thassine
1344 thassine 89
1345 thassine 184 * 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 thassine 89
1349 thassine 184 2003-06-11 10:40 thassine
1350 thassine 89
1351 thassine 245 * 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 thassine 184 stationary_state_search + many related changes here and there.
1356     still need to do some testing, and after that add docs in
1357 thassine 123 user-docs and some example molecules.
1358 thassine 89
1359 thassine 184 2003-06-05 03:08 thassine
1360 thassine 89
1361 thassine 184 * bin/param_mm/prmfit, bin/param_mm/prmfit/atomtypes.txt,
1362 thassine 123 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 thassine 89
1369 thassine 184 2003-06-02 15:20 thassine
1370 thassine 89
1371 thassine 184 * src/eng1_mm.cpp, src/eng1_mm_prmfit.h, src/tab_mm_default.cpp,
1372 thassine 245 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 thassine 89
1375 thassine 184 2003-06-02 14:29 thassine
1376 thassine 89
1377     * bin/builder/amino.txt, bin/builder/nucleic.txt,
1378 thassine 123 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 thassine 89
1382 thassine 184 2003-05-21 14:32 thassine
1383 thassine 89
1384 thassine 184 * src/eng1_mm_prmfit.cpp, src/tab_mm_prmfit.cpp,
1385     src/tab_mm_prmfit.h: added misc changes in mol mech stuff.
1386 thassine 89
1387 thassine 184 2003-05-19 07:05 thassine
1388 thassine 89
1389 thassine 184 * 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 thassine 89
1395 thassine 184 2003-05-16 10:20 thassine
1396 thassine 89
1397 thassine 245 * bin/param_mm/default/parameters6.txt: changes to MM force field ;
1398     added one input file.
1399 thassine 89
1400 thassine 184 2003-05-16 10:19 thassine
1401 thassine 89
1402     * bin/param_mm/default/parameters4.txt,
1403 thassine 123 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 thassine 245 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 thassine 89
1409 thassine 184 2003-05-12 09:11 thassine
1410 thassine 89
1411     * src/eng1_sf.h: minor changes to ribbon, etc.
1412    
1413 thassine 184 2003-04-29 10:14 thassine
1414 thassine 89
1415 thassine 184 * 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 thassine 89
1420 thassine 184 2003-04-25 10:20 thassine
1421 thassine 89
1422     * bin/param_mm/default/parameters5.txt, src/atom.cpp, src/atom.h,
1423 thassine 123 src/eng1_mm.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h:
1424 thassine 245 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 thassine 123 later.
1429 thassine 89
1430 thassine 184 2003-04-17 07:34 thassine
1431 thassine 89
1432 thassine 184 * src/model.cpp, src/seqbuild.cpp: setup objects were not deleted,
1433 thassine 245 causing MOPAC to leave some files around and also memory leaking;
1434     fixed now.
1435 thassine 89
1436 thassine 184 2003-04-16 13:43 thassine
1437 thassine 89
1438 thassine 184 * 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 thassine 89
1443 thassine 184 2003-04-10 13:49 thassine
1444 thassine 89
1445     * src/libconfig.h.in: only whitespace changed.
1446    
1447 thassine 184 2003-04-10 12:50 thassine
1448 thassine 89
1449 thassine 184 * 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 thassine 89
1455 thassine 184 2003-04-10 12:48 thassine
1456 thassine 89
1457     * Makefile.in, configure, configure.in, src/libconfig.h.in:
1458 thassine 123 configuration files updated.
1459 thassine 89
1460 thassine 184 2003-04-10 12:46 thassine
1461 thassine 89
1462 thassine 184 * 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 thassine 245 bin/builder/amino.txt, bin/builder/nucleic.txt: changes/additions
1466     in data files.
1467 thassine 89
1468 thassine 184 2003-04-02 06:12 thassine
1469 thassine 89
1470 thassine 184 * 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 thassine 89
1473 thassine 184 2003-03-18 10:08 thassine
1474 thassine 89
1475 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h: just minor rearrangements.
1476 thassine 89
1477 thassine 184 2003-03-17 10:13 thassine
1478 thassine 89
1479     * src/eng1_sf.cpp: added a notice about solvation model (not yet
1480 thassine 123 automatically set).
1481 thassine 89
1482 thassine 184 2003-03-17 10:11 thassine
1483 thassine 89
1484 thassine 245 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for ribbons
1485     added, and some changes in moldyn.
1486 thassine 89
1487 thassine 184 2003-03-12 07:19 thassine
1488 thassine 89
1489     * src/eng1_sf.cpp: just some cleanups in comments etc.
1490    
1491 thassine 184 2003-03-11 14:22 thassine
1492 thassine 89
1493     * src/model.cpp: added the frame_save_frq variable to
1494 thassine 123 model::DoMoldyn()
1495 thassine 89
1496 thassine 184 2003-03-11 07:58 thassine
1497 thassine 89
1498     * src/model.h: ooops; a function was missing.
1499    
1500 thassine 184 2003-03-07 10:39 thassine
1501 thassine 89
1502 thassine 184 * 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 thassine 89
1507 thassine 184 2003-02-14 10:56 thassine
1508 thassine 89
1509     * src/eng1_sf.cpp: slight changes in output.
1510    
1511 thassine 184 2003-02-14 07:59 thassine
1512 thassine 89
1513 thassine 184 * src/model.cpp, src/moldyn.cpp, src/moldyn.h: many
1514 thassine 123 molecular-dynamics-related changes.
1515 thassine 89
1516 thassine 184 2003-02-11 14:44 thassine
1517 thassine 89
1518 thassine 184 * 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 thassine 89
1523 thassine 184 2003-02-08 07:35 thassine
1524 thassine 89
1525 thassine 184 * 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 thassine 245 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 thassine 89
1533 thassine 184 2003-02-06 14:50 thassine
1534 thassine 89
1535     * bin/param_mm/default/parameters1.txt,
1536 thassine 123 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 thassine 89
1544 thassine 184 2003-02-03 09:50 thassine
1545 thassine 89
1546     * bin/param_mm/default/parameters5.txt, src/eng1_mm.cpp,
1547 thassine 123 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 thassine 245 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 thassine 89
1553 thassine 184 2003-01-31 12:24 thassine
1554 thassine 89
1555 thassine 184 * 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 thassine 245 important to note that model::GetAtomCount() may now be different
1558     from engine::GetAtomCount().
1559 thassine 89
1560 thassine 184 2003-01-31 09:25 thassine
1561 thassine 89
1562 thassine 184 * 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 thassine 89
1566 thassine 184 2003-01-30 16:31 thassine
1567 thassine 89
1568 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h: several fixes to SF; should now
1569 thassine 123 work more or less again.
1570 thassine 89
1571 thassine 184 2003-01-30 14:14 thassine
1572 thassine 89
1573 thassine 184 * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp: many changes in
1574     SF.
1575 thassine 89
1576 thassine 184 2003-01-30 08:29 thassine
1577 thassine 89
1578 thassine 184 * 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 thassine 245 different models; compiles but SF-stuff does not work yet; QM and
1585     MM should work.
1586 thassine 89
1587 thassine 184 2003-01-27 13:43 thassine
1588 thassine 89
1589 thassine 184 * 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 thassine 89
1597 thassine 184 2003-01-24 08:01 thassine
1598 thassine 89
1599     * src/seqbuild.cpp: a fix to sequence-builder: identify now also
1600 thassine 123 includes H atoms to residues that it detects, so that selecting
1601     by chain/residue now works as expected.
1602 thassine 89
1603 thassine 184 2003-01-23 12:55 thassine
1604 thassine 89
1605 thassine 184 * src/atom.h, src/model.cpp, src/model.h, src/seqbuild.cpp,
1606     src/seqbuild.h: some improvements to seqbuilder.
1607 thassine 89
1608 thassine 184 2003-01-22 11:09 thassine
1609 thassine 89
1610 thassine 184 * src, src/.cvsignore: minor cleanups.
1611 thassine 89
1612 thassine 184 2003-01-22 09:25 thassine
1613 thassine 89
1614     * src/eng1_mm_prmfit.h: minor cleanups.
1615    
1616 thassine 184 2003-01-22 09:11 thassine
1617 thassine 89
1618 thassine 184 * src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some cleanups, again.
1619 thassine 89
1620 thassine 184 2003-01-22 08:28 thassine
1621 thassine 89
1622     * src/typedef.h: added a missing file
1623    
1624 thassine 184 2003-01-22 08:28 thassine
1625 thassine 89
1626 thassine 184 * src/model.cpp, src/model.h: minor cleanups.
1627 thassine 89
1628 thassine 184 2003-01-22 07:18 thassine
1629 thassine 89
1630     * Makefile.in, src/Makefile.in, src/eng1_sf.cpp, src/libdefine.h,
1631 thassine 123 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 thassine 89
1635 thassine 184 2003-01-21 11:42 thassine
1636 thassine 89
1637 thassine 184 * src/eng2_qm_mm.h, src/errutil.cpp, src/errutil.h,
1638     src/libdefine.h: various improvements...
1639 thassine 89
1640 thassine 184 2003-01-21 11:19 thassine
1641 thassine 89
1642     * Makefile.in, configure, configure.in, src/Makefile.in,
1643 thassine 123 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 thassine 89
1655 thassine 184 2003-01-20 14:05 thassine
1656 thassine 89
1657     * configure, src/engine.h: minor fixes; not ready yet...
1658    
1659 thassine 184 2003-01-20 08:38 thassine
1660 thassine 89
1661 thassine 184 * ., .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 thassine 123 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 thassine 184 bin/param_mm/default/parameters5.txt, bin/param_sf,
1670     bin/param_sf/default, bin/param_sf/default/loopdip.txt,
1671 thassine 123 bin/param_sf/default/looptor.txt,
1672 thassine 184 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 thassine 123 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 thassine 184 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 thassine 245 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 thassine 184 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 thassine 123 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 thassine 245 src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h,
1853     src/v3d.h: Initial revision
1854 thassine 89
1855 thassine 184 2003-01-20 08:38
1856 thassine 89
1857 thassine 245 * .: New repository initialized by cvs2svn.

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