-
Notifications
You must be signed in to change notification settings - Fork 183
/
RELEASE_NOTES
8362 lines (7342 loc) · 354 KB
/
RELEASE_NOTES
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
What's new, what's been changed, what's been fixed
--------------------------------------------------
****************************************************************************************
* v2.2.0h (Walaskialf) *
****************************************************************************************
Current working revision.
- v2.2.0h -
-----------
(h) October 26th, 2010.
(g) October 11th, 2010.
(f) October 9th, 2010.
(e) October 6th, 2010.
(d) September 21st, 2010.
(c) September 2nd, 2010.
(b) July 25th, 2010.
(a) July 21st, 2010.
New Features:
(d) = LB_ELECTROHYDRODYNAMICS: charge coupling scheme for Lattice-Boltzmann
simulations. See publication Hickey et. al. (2010)
Added new feature:
LB_ELECTROHYDRODYNAMICS
With this, you can use a coupling scheme to simulate electrostatics and
hydrodynamics
for electrophoresis without long-range interactions, simply in
Lattice-Boltzmann.
For each particle, a new 3D-parameter mu_E can be set and is stored in Variable
p->p.mu_E[3]
This parameter is added to the LB-force routine.
Documentation yet to come.
Changes:
(a) added more reference to original adress papers
Bugfixes:
(h) ADDITIONAL_CHECKS now resets its variables, especially particle
ids
(h) mmm2d now allows again to use the nsquare cellsystem, if no dielectric
contrasts are specified
(g) dpd thermostats will also make particles interact
(f) virtual sites can now be coupled to the NPT integrator
(e) : Virtual sites inconsistent with AdResS
(e) : Added optimization and pressure profile (Todd, Evans and
Davis)
(c) fixed sign of charged plate energy
(b) removed duplicated file in scripts/Makefile.am
- v2.1.5q -
-----------
(q) July 20th, 2010.
(p) June 22nd, 2010.
(o) June 18th, 2010.
(n) June 14th, 2010.
(m) May 30th, 2010.
(l) May 25th, 2010.
(k) May 7th, 2010.
(j) May 4th, 2010.
(i) May 3rd, 2010.
(h) April 30th, 2010.
(g) April 29th, 2010.
(f) April 20th, 2010.
(e) April 1st, 2010.
(d) March 23rd, 2010.
(c) March 16th, 2010.
(b) March 2nd, 2010.
(a) February 25th, 2010.
New Features:
(q) added minimal AdResS documentation to users guide
(o) added the Hertzian interaction.
(o) added a script samples/check_potential.tcl to check that radial potentials
fulfill F(r) = dE(r)/r numerically.
(n) added rudimentary cmake files to support Windows(TM)
(m) Metadynamics added
(l) added automated search for Tcl paths in Ubuntu
(j) added routine copy_particles to make a shifted copy of a set of particles (e.g.
a molecule)
(g) common testsuite infrastructure for testing features and nprocs
etc
(g) rotational particles now also store the director for faster computation of
GB
(g) rotational inertia code by MJW
(e) added detection for Mobile Sempron
Changes:
(p) Metadynamics no longer relies on EXTERNAL forces.
Bugfixes:
(o) fixed documentation on Coulomb interaction, which was missing the Bjerrum
length parameter almost everywhere
(o) added documentation for some particle properties and the copy_particle
proc
(n) removed useless ADOLFO ifdef statement
(m) missing variable definition in virtual_sites.c
(l) detection for some Pentium 4 was broken
(k) fixed runtime errors that potential can cause segfaults when
raised.
(i) fixed a missing GB_sigma and corrected indendation in gb.h
(i) unfolding the coordinates for the DAWAANR dipolar interaction, added missing
prefactor
(h) moved force calculations back from pressure.h to forces.h. This required to
introduce npt.h, so that the holographic pressure.h could be removed from most
headers.
(h) separated Gay-Berne interaction from ROTATION feature
(g) removed temporary static variables from rotation code
(g) removed debug printfs
(f) ljgen now uses the libc-pow function, which also allows for negative exponents,
and is in general faster
(d) fixed wrong DPD formula in Users Guide (C source was correct)
(c) Fixed documentation of LJ-generic potential.
(b) fixed the fix so that compiling without NPT works again
(a) fixed some broken sanity checks connected to npt
(a) repaired broken statistics.c file
- v2.1.4f -
-----------
(f) February 22nd, 2010.
(e) February 16th, 2010.
(d) February 2nd, 2010.
(c) January 28th, 2010.
(b) January 14th, 2010.
(a) January 13th, 2010.
New Features:
(e) writevcf now allows to write arbitrary userdata into a file that can be read
via the VMD plugin VTFTools.
(d) compiler flags for AMD Phenom, use SSE3 if possible
Changes:
(b) Interface correction force is now called adress_tab_ic at Tcl
level.
Bugfixes:
(f) added warning in angle.h that pressure tensor cannot be calculated for
cossquare
(f) fixed a bug in NPT integrator that did check that the domain decomposition
cellsystem is used
(f) fixed a warning in angle.h if the bond potential was not chosen as
harmonic
(f) fixed bug in npt integrator, that didn't check that electrostatics needs to be
P3M or Ewald
(c) added missing guard for bond angles
(c) fixed exported header of rescale_velocities
(b) three body potentials again work with layered decomposition
(a) averaging analyze commands (e.G. <rdf>, <re>, ...) give correct results now
also if called after "integrate" without "analyze append" in
between.
- v2.1.4f -
-----------
(f) February 22nd, 2010.
(e) February 16th, 2010.
(d) February 2nd, 2010.
(c) January 28th, 2010.
(b) January 14th, 2010.
(a) January 13th, 2010.
New Features:
(e) writevcf now allows to write arbitrary userdata into a file that can be read
via the VMD plugin VTFTools.
(d) compiler flags for AMD Phenom, use SSE3 if possible
Changes:
(b) Interface correction force is now called adress_tab_ic at Tcl
level.
Bugfixes:
(f) added warning in angle.h that pressure tensor cannot be calculated for
cossquare
(f) fixed a bug in NPT integrator that did check that the domain decomposition
cellsystem is used
(f) fixed a warning in angle.h if the bond potential was not chosen as
harmonic
(f) fixed bug in npt integrator, that didn't check that electrostatics needs to be
P3M or Ewald
(c) added missing guard for bond angles
(c) fixed exported header of rescale_velocities
(b) three body potentials again work with layered decomposition
(a) averaging analyze commands (e.G. <rdf>, <re>, ...) give correct results now
also if called after "integrate" without "analyze append" in
between.
- v2.1.4f -
-----------
(f) February 22nd, 2010.
(e) February 16th, 2010.
(d) February 2nd, 2010.
(c) January 28th, 2010.
(b) January 14th, 2010.
(a) January 13th, 2010.
New Features:
(e) writevcf now allows to write arbitrary userdata into a file that can be read
via the VMD plugin VTFTools.
(d) compiler flags for AMD Phenom, use SSE3 if possible
Changes:
(b) Interface correction force is now called adress_tab_ic at Tcl
level.
Bugfixes:
(f) added warning in angle.h that pressure tensor cannot be calculated for
cossquare
(f) fixed a bug in NPT integrator that did check that the domain decomposition
cellsystem is used
(f) fixed a warning in angle.h if the bond potential was not chosen as
harmonic
(f) fixed bug in npt integrator, that didn't check that electrostatics needs to be
P3M or Ewald
(c) added missing guard for bond angles
(c) fixed exported header of rescale_velocities
(b) three body potentials again work with layered decomposition
(a) averaging analyze commands (e.G. <rdf>, <re>, ...) give correct results now
also if called after "integrate" without "analyze append" in
between.
- v2.1.3k -
-----------
(k) December 2nd, 2009.
(j) October 28th, 2009.
(i) October 27th, 2009.
(h) October 21st, 2009.
(g) October 16th, 2009.
(f) October 15th, 2009.
(e) October 13th, 2009.
(d) October 9th, 2009.
(c) September 28th, 2009.
(b) September 21st, 2009.
(a) September 17th, 2009.
New Features:
(k) Added gcc support for Core i7
(k) Added correct detection for tcl8.6
(j) added -fastsse flag for tuning using the PGI compiler
(h) AdResS bonded virial implemented
(f) AdResS: Random initialization implemented.
(f) AdResS: Implementation of bond-forces interpolation.
(d) more arguments for LJANGLE
(d) optional 2nd environment with local change in interaction
strength
Changes:
(g) Updated copyright notices. Removed "Responsible" people.
(e) Increased MAX_NUM_CELLS from 216 to 32768. This will make many simulations
faster when using the default settings.
Bugfixes:
(i) Molecular pressure now supports EXCLUSIONS
(g) removed a bug in ljangle (wrong sign in the force calculation).
(f)
(f) AdResS: Initial weight has to be 1.
(e) removed a debug printf command for ljangle.
(c) When MOL_CUT is included, max_cut is well defined independent of the bonded
interactions
(b) virtual sites should not contribute to 'analyze energy kinetic'
(a) make espresso compile on power4
- v2.1.3k -
-----------
(k) December 2nd, 2009.
(j) October 28th, 2009.
(i) October 27th, 2009.
(h) October 21st, 2009.
(g) October 16th, 2009.
(f) October 15th, 2009.
(e) October 13th, 2009.
(d) October 9th, 2009.
(c) September 28th, 2009.
(b) September 21st, 2009.
(a) September 17th, 2009.
New Features:
(k) Added gcc support for Core i7
(k) Added correct detection for tcl8.6
(j) added -fastsse flag for tuning using the PGI compiler
(h) AdResS bonded virial implemented
(f) AdResS: Random initialization implemented.
(f) AdResS: Implementation of bond-forces interpolation.
(d) more arguments for LJANGLE
(d) optional 2nd environment with local change in interaction
strength
Changes:
(g) Updated copyright notices. Removed "Responsible" people.
(e) Increased MAX_NUM_CELLS from 216 to 32768. This will make many simulations
faster when using the default settings.
Bugfixes:
(i) Molecular pressure now supports EXCLUSIONS
(g) removed a bug in ljangle (wrong sign in the force calculation).
(f)
(f) AdResS: Initial weight has to be 1.
(e) removed a debug printf command for ljangle.
(c) When MOL_CUT is included, max_cut is well defined independent of the bonded
interactions
(b) virtual sites should not contribute to 'analyze energy kinetic'
(a) make espresso compile on power4
- v2.1.3k -
-----------
(k) December 2nd, 2009.
(j) October 28th, 2009.
(i) October 27th, 2009.
(h) October 21st, 2009.
(g) October 16th, 2009.
(f) October 15th, 2009.
(e) October 13th, 2009.
(d) October 9th, 2009.
(c) September 28th, 2009.
(b) September 21st, 2009.
(a) September 17th, 2009.
New Features:
(k) Added gcc support for Core i7
(k) Added correct detection for tcl8.6
(j) added -fastsse flag for tuning using the PGI compiler
(h) AdResS bonded virial implemented
(f) AdResS: Random initialization implemented.
(f) AdResS: Implementation of bond-forces interpolation.
(d) more arguments for LJANGLE
(d) optional 2nd environment with local change in interaction
strength
Changes:
(g) Updated copyright notices. Removed "Responsible" people.
(e) Increased MAX_NUM_CELLS from 216 to 32768. This will make many simulations
faster when using the default settings.
Bugfixes:
(i) Molecular pressure now supports EXCLUSIONS
(g) removed a bug in ljangle (wrong sign in the force calculation).
(f)
(f) AdResS: Initial weight has to be 1.
(e) removed a debug printf command for ljangle.
(c) When MOL_CUT is included, max_cut is well defined independent of the bonded
interactions
(b) virtual sites should not contribute to 'analyze energy kinetic'
(a) make espresso compile on power4
- v2.1.2u -
-----------
(u) September 10th, 2009.
(t) September 7th, 2009.
(s) July 27th, 2009.
(r) July 14th, 2009.
(q) June 24th, 2009.
(p) June 8th, 2009.
(o) May 28th, 2009.
(n) May 20th, 2009.
(m) May 6th, 2009.
(l) May 5th, 2009.
(k) April 16th, 2009.
(j) March 31st, 2009.
(i) March 30th, 2009.
(h) March 27th, 2009.
(g) March 26th, 2009.
(f) March 12th, 2009.
(e) March 9th, 2009.
(d) March 5th, 2009.
(c) March 3rd, 2009.
(b) February 20th, 2009.
(a) February 19th, 2009.
New Features:
(s) Implementation of diffusion profiles
(o) added anaylze density profile function
(o) make mol pressure work with adress
(m) added new distance dependent (from wall) angular potential
(k) added ebuild for gentoo and spec file for rpm
(i) added arch-detection for IA-64, in case processor model name is
missing.
(f) added option --with-mpicommand to configure to specify the command used to
invoke a parallel program (typically mpirun, sometimes poe or
dmpirun).
(e) extended the Electrostatics tutorial 2 to cover also constrained electrostatics
with MMM2D
Changes:
(o) address should have a bigger skin
(g) Some changes on the testsuite that make using the testsuite
easier.
(f) all MPI environments respect now the PATH environment variable when looking for
the mpi-command.
(e) In mmm2d, added a warning if particles are out of bounds
(a) Improvement of the documentation.
Bugfixes:
(u) fixed a bug in dihedral angle, when lengths were very small (done by Christine
already years ago!!!)
(t) Diffusion profiles can be calculated in directions x,y and z
(r) compiles again without ADRESS being enabled
(q) initialization of adress vars fixed
(p) Fixed the output of inter coulomb/magnetic in the case that magnetostatics are
switched on.
(o) use folded pos for adress weight
(o) bonded interaction have weight 1
(n) Espresso did not build with VIRTUAL_SITES enabled
(l) Fixed error in bond output to vtf files.
(l) fixed deprecated direct access to interp->result which breaks with Tcl
8.5
(l) uwerr now complains if it cannot allocate its internal
function(s)
(l) Tests that require P3M now also check for FFTW
(l) tabulated now checks relative error to avoid problems with different numerical
precision in Tcl 8.5
(j) fixed broken CPU guessing in config.guess
(h) virtual sites should be ignored by the standard thermostats
(h) VIRTUAL_SITES should have v to calv v of the virtual sites
(f) made maggs-documentation compile again
(e) fixed a bug, that first appeared in CVS version of 2009-02-10. Attention: due
to this bug all simulations that involved Lennard-Jones interactions produced
wrong results.
(d) fixed dlc->mdlc in Makefiles
(c) fixed bug in polymer command - creates correct RW by default
now
[add] added samples/polymer_RW_sphere.tcl to demonstrate correct distribution
of points on sphere surface
(b) fixed some #ifdef's, if MAGNETOSTATICS is on, but FFTW not
(b) fixed some missing feature dependencies like DIPOLES->ROTATION
(b) fixed a warning about fac1 being unused
(b) updated the documentation of features and fixed the documentation of some of
them.
- v2.1.2u -
-----------
(u) September 10th, 2009.
(t) September 7th, 2009.
(s) July 27th, 2009.
(r) July 14th, 2009.
(q) June 24th, 2009.
(p) June 8th, 2009.
(o) May 28th, 2009.
(n) May 20th, 2009.
(m) May 6th, 2009.
(l) May 5th, 2009.
(k) April 16th, 2009.
(j) March 31st, 2009.
(i) March 30th, 2009.
(h) March 27th, 2009.
(g) March 26th, 2009.
(f) March 12th, 2009.
(e) March 9th, 2009.
(d) March 5th, 2009.
(c) March 3rd, 2009.
(b) February 20th, 2009.
(a) February 19th, 2009.
New Features:
(s) Implementation of diffusion profiles
(o) added anaylze density profile function
(o) make mol pressure work with adress
(m) added new distance dependent (from wall) angular potential
(k) added ebuild for gentoo and spec file for rpm
(i) added arch-detection for IA-64, in case processor model name is
missing.
(f) added option --with-mpicommand to configure to specify the command used to
invoke a parallel program (typically mpirun, sometimes poe or
dmpirun).
(e) extended the Electrostatics tutorial 2 to cover also constrained electrostatics
with MMM2D
Changes:
(o) address should have a bigger skin
(g) Some changes on the testsuite that make using the testsuite
easier.
(f) all MPI environments respect now the PATH environment variable when looking for
the mpi-command.
(e) In mmm2d, added a warning if particles are out of bounds
(a) Improvement of the documentation.
Bugfixes:
(u) fixed a bug in dihedral angle, when lengths were very small (done by Christine
already years ago!!!)
(t) Diffusion profiles can be calculated in directions x,y and z
(r) compiles again without ADRESS being enabled
(q) initialization of adress vars fixed
(p) Fixed the output of inter coulomb/magnetic in the case that magnetostatics are
switched on.
(o) use folded pos for adress weight
(o) bonded interaction have weight 1
(n) Espresso did not build with VIRTUAL_SITES enabled
(l) Fixed error in bond output to vtf files.
(l) fixed deprecated direct access to interp->result which breaks with Tcl
8.5
(l) uwerr now complains if it cannot allocate its internal
function(s)
(l) Tests that require P3M now also check for FFTW
(l) tabulated now checks relative error to avoid problems with different numerical
precision in Tcl 8.5
(j) fixed broken CPU guessing in config.guess
(h) virtual sites should be ignored by the standard thermostats
(h) VIRTUAL_SITES should have v to calv v of the virtual sites
(f) made maggs-documentation compile again
(e) fixed a bug, that first appeared in CVS version of 2009-02-10. Attention: due
to this bug all simulations that involved Lennard-Jones interactions produced
wrong results.
(d) fixed dlc->mdlc in Makefiles
(c) fixed bug in polymer command - creates correct RW by default
now
[add] added samples/polymer_RW_sphere.tcl to demonstrate correct distribution
of points on sphere surface
(b) fixed some #ifdef's, if MAGNETOSTATICS is on, but FFTW not
(b) fixed some missing feature dependencies like DIPOLES->ROTATION
(b) fixed a warning about fac1 being unused
(b) updated the documentation of features and fixed the documentation of some of
them.
- v2.1.2u -
-----------
(u) September 10th, 2009.
(t) September 7th, 2009.
(s) July 27th, 2009.
(r) July 14th, 2009.
(q) June 24th, 2009.
(p) June 8th, 2009.
(o) May 28th, 2009.
(n) May 20th, 2009.
(m) May 6th, 2009.
(l) May 5th, 2009.
(k) April 16th, 2009.
(j) March 31st, 2009.
(i) March 30th, 2009.
(h) March 27th, 2009.
(g) March 26th, 2009.
(f) March 12th, 2009.
(e) March 9th, 2009.
(d) March 5th, 2009.
(c) March 3rd, 2009.
(b) February 20th, 2009.
(a) February 19th, 2009.
New Features:
(s) Implementation of diffusion profiles
(o) added anaylze density profile function
(o) make mol pressure work with adress
(m) added new distance dependent (from wall) angular potential
(k) added ebuild for gentoo and spec file for rpm
(i) added arch-detection for IA-64, in case processor model name is
missing.
(f) added option --with-mpicommand to configure to specify the command used to
invoke a parallel program (typically mpirun, sometimes poe or
dmpirun).
(e) extended the Electrostatics tutorial 2 to cover also constrained electrostatics
with MMM2D
Changes:
(o) address should have a bigger skin
(g) Some changes on the testsuite that make using the testsuite
easier.
(f) all MPI environments respect now the PATH environment variable when looking for
the mpi-command.
(e) In mmm2d, added a warning if particles are out of bounds
(a) Improvement of the documentation.
Bugfixes:
(u) fixed a bug in dihedral angle, when lengths were very small (done by Christine
already years ago!!!)
(t) Diffusion profiles can be calculated in directions x,y and z
(r) compiles again without ADRESS being enabled
(q) initialization of adress vars fixed
(p) Fixed the output of inter coulomb/magnetic in the case that magnetostatics are
switched on.
(o) use folded pos for adress weight
(o) bonded interaction have weight 1
(n) Espresso did not build with VIRTUAL_SITES enabled
(l) Fixed error in bond output to vtf files.
(l) fixed deprecated direct access to interp->result which breaks with Tcl
8.5
(l) uwerr now complains if it cannot allocate its internal
function(s)
(l) Tests that require P3M now also check for FFTW
(l) tabulated now checks relative error to avoid problems with different numerical
precision in Tcl 8.5
(j) fixed broken CPU guessing in config.guess
(h) virtual sites should be ignored by the standard thermostats
(h) VIRTUAL_SITES should have v to calv v of the virtual sites
(f) made maggs-documentation compile again
(e) fixed a bug, that first appeared in CVS version of 2009-02-10. Attention: due
to this bug all simulations that involved Lennard-Jones interactions produced
wrong results.
(d) fixed dlc->mdlc in Makefiles
(c) fixed bug in polymer command - creates correct RW by default
now
[add] added samples/polymer_RW_sphere.tcl to demonstrate correct distribution
of points on sphere surface
(b) fixed some #ifdef's, if MAGNETOSTATICS is on, but FFTW not
(b) fixed some missing feature dependencies like DIPOLES->ROTATION
(b) fixed a warning about fac1 being unused
(b) updated the documentation of features and fixed the documentation of some of
them.
- v2.1.1v -
-----------
(v) February 16th, 2009.
(u) February 9th, 2009.
(t) January 31st, 2009.
(s) January 23rd, 2009.
(r) January 19th, 2009.
(q) January 12th, 2009.
(p) December 1st, 2008.
(o) November 11th, 2008.
(n) November 5th, 2008.
(m) October 31st, 2008.
(l) October 24th, 2008.
(k) October 23rd, 2008.
(j) October 22nd, 2008.
(i) October 20th, 2008.
(h) October 14th, 2008.
(g) October 10th, 2008.
(f) October 9th, 2008.
(e) September 23rd, 2008.
(d) September 22nd, 2008.
(c) September 5th, 2008.
(b) August 29th, 2008.
(a) August 28th, 2008.
New Features:
(u) r_min for lennard-jones
(t) separated electro- and magnetostatics. Instead of configuring for either
electrostatics or magnetostatics using the DIPOLES switch, there is now a
switch MAGNETOSTATICS to activate magnetic dipolar interactions. Using both
ELECTROSTATICS and MAGNETOSTATICS, it is now possible to run systems with
charges and magnetic dipoles simulataneously.
(l) started a new documentation section "tutorials"
(l) added detection and compiler flags for Intel Atom CPU.
(j) harmonic spring now has a cutoff
(e) added tabulated adress force, tabulated correction function
(e) mmm2d with dielectric contrast now uses internally dielectric contrasts, which
allows to specify metallic boundary conditions also. To set the contrasts
directly, use the dielectric-contrasts option.
(c) included extended LJGEN potential in main cvs trunk
(c) updated generic lennard-jones interaction in users guide
(a) The tunable slip boundary module has been included into the main ESPResSo
branch
Changes:
(k) harmonic cutoff is by default off, but still possible to set
(g) ELC with dielectric contrast now also prints out the space layer, and the out
output can actually be fed back into inter coulomb as intended
Bugfixes:
(v) Fixed some documentation errors in the Lennard-Jones description. Thanks to
Ahmad A. J. Agung!
(s) fixed a bug in "analyze energy coulomb" which would report a random
energy/pressure if no electrostatics method is switched on.
(r) Re-added configure-ac and Makefile-am.in after dead revision
(r) Re-added acconfig.h.in to CVS
(r) included Makefile.in files again into CVS (this matter is still discussed and
may change again in future)
(r) Resurrecting and re-adding several Makefile.in after dead
revision
(r) Re-added scripts/Makefile.in after dead revision
(q) Configure can handle the situation when configure-ac is not
executable.
(q) Fix in the LJ documenatation (thanks to David Sean and Antoine)
(p) Fixed a bug in writevsf related to the bond information.
(o) added a security warning for image charge correction, which requires the far
formula to work
(n) Another bugfix on aggregation routine
(n) fixed a bug in aggregation routine
(m) fixed the distribution to also contain the sources for the
tutorial
(m) fixed error message in case the hash line is missing
(i) fixed the harmonic-testcase to set a skin of 1 so that the bonding partners are
always on the same node.
(h) dpd and adress global parameters have not been broadcasted correctly, when
lattice was not defined.
(h) - fixed default weight for init_particle in particle_data.c
(g) ELC tuning now also works for ELC with dielectric contrast, and an stray
constant force proportional to the charge sum was removed.
(g) Adjusted lj-generic test to new format of the lj-generic
command
(f) calc_eigenvector_3x3 was accessing out-of-bounds stack memory for singular
matrizes
(f) fixed several (justified) warnings of gcc-4.3
(f) fixed two bugs in mmm2d with dielectric interfaces. Calculations in the top
layer were wrong so far
(e) the documentation now points out the dielectric features.
(d) forgotten adress flag
(b) In order to satisfy the dissipation-fluctuation theorem, DPD is not applied to
fixed particles or particles that interact with fixed particles any
more.
- v2.1.1v -
-----------
(v) February 16th, 2009.
(u) February 9th, 2009.
(t) January 31st, 2009.
(s) January 23rd, 2009.
(r) January 19th, 2009.
(q) January 12th, 2009.
(p) December 1st, 2008.
(o) November 11th, 2008.
(n) November 5th, 2008.
(m) October 31st, 2008.
(l) October 24th, 2008.
(k) October 23rd, 2008.
(j) October 22nd, 2008.
(i) October 20th, 2008.
(h) October 14th, 2008.
(g) October 10th, 2008.
(f) October 9th, 2008.
(e) September 23rd, 2008.
(d) September 22nd, 2008.
(c) September 5th, 2008.
(b) August 29th, 2008.
(a) August 28th, 2008.
New Features:
(u) r_min for lennard-jones
(t) separated electro- and magnetostatics. Instead of configuring for either
electrostatics or magnetostatics using the DIPOLES switch, there is now a
switch MAGNETOSTATICS to activate magnetic dipolar interactions. Using both
ELECTROSTATICS and MAGNETOSTATICS, it is now possible to run systems with
charges and magnetic dipoles simulataneously.
(l) started a new documentation section "tutorials"
(l) added detection and compiler flags for Intel Atom CPU.
(j) harmonic spring now has a cutoff
(e) added tabulated adress force, tabulated correction function
(e) mmm2d with dielectric contrast now uses internally dielectric contrasts, which
allows to specify metallic boundary conditions also. To set the contrasts
directly, use the dielectric-contrasts option.
(c) included extended LJGEN potential in main cvs trunk
(c) updated generic lennard-jones interaction in users guide
(a) The tunable slip boundary module has been included into the main ESPResSo
branch
Changes:
(k) harmonic cutoff is by default off, but still possible to set
(g) ELC with dielectric contrast now also prints out the space layer, and the out
output can actually be fed back into inter coulomb as intended
Bugfixes:
(v) Fixed some documentation errors in the Lennard-Jones description. Thanks to
Ahmad A. J. Agung!
(s) fixed a bug in "analyze energy coulomb" which would report a random
energy/pressure if no electrostatics method is switched on.
(r) Re-added configure-ac and Makefile-am.in after dead revision
(r) Re-added acconfig.h.in to CVS
(r) included Makefile.in files again into CVS (this matter is still discussed and
may change again in future)
(r) Resurrecting and re-adding several Makefile.in after dead
revision
(r) Re-added scripts/Makefile.in after dead revision
(q) Configure can handle the situation when configure-ac is not
executable.
(q) Fix in the LJ documenatation (thanks to David Sean and Antoine)
(p) Fixed a bug in writevsf related to the bond information.
(o) added a security warning for image charge correction, which requires the far
formula to work
(n) Another bugfix on aggregation routine
(n) fixed a bug in aggregation routine
(m) fixed the distribution to also contain the sources for the
tutorial
(m) fixed error message in case the hash line is missing
(i) fixed the harmonic-testcase to set a skin of 1 so that the bonding partners are
always on the same node.
(h) dpd and adress global parameters have not been broadcasted correctly, when
lattice was not defined.
(h) - fixed default weight for init_particle in particle_data.c
(g) ELC tuning now also works for ELC with dielectric contrast, and an stray
constant force proportional to the charge sum was removed.
(g) Adjusted lj-generic test to new format of the lj-generic
command
(f) calc_eigenvector_3x3 was accessing out-of-bounds stack memory for singular
matrizes
(f) fixed several (justified) warnings of gcc-4.3
(f) fixed two bugs in mmm2d with dielectric interfaces. Calculations in the top
layer were wrong so far
(e) the documentation now points out the dielectric features.
(d) forgotten adress flag
(b) In order to satisfy the dissipation-fluctuation theorem, DPD is not applied to
fixed particles or particles that interact with fixed particles any
more.
- v2.1.1v -
-----------
(v) February 16th, 2009.
(u) February 9th, 2009.
(t) January 31st, 2009.
(s) January 23rd, 2009.
(r) January 19th, 2009.
(q) January 12th, 2009.
(p) December 1st, 2008.
(o) November 11th, 2008.
(n) November 5th, 2008.
(m) October 31st, 2008.
(l) October 24th, 2008.
(k) October 23rd, 2008.
(j) October 22nd, 2008.
(i) October 20th, 2008.
(h) October 14th, 2008.
(g) October 10th, 2008.
(f) October 9th, 2008.
(e) September 23rd, 2008.
(d) September 22nd, 2008.
(c) September 5th, 2008.
(b) August 29th, 2008.
(a) August 28th, 2008.
New Features:
(u) r_min for lennard-jones
(t) separated electro- and magnetostatics. Instead of configuring for either
electrostatics or magnetostatics using the DIPOLES switch, there is now a
switch MAGNETOSTATICS to activate magnetic dipolar interactions. Using both
ELECTROSTATICS and MAGNETOSTATICS, it is now possible to run systems with
charges and magnetic dipoles simulataneously.
(l) started a new documentation section "tutorials"
(l) added detection and compiler flags for Intel Atom CPU.
(j) harmonic spring now has a cutoff
(e) added tabulated adress force, tabulated correction function
(e) mmm2d with dielectric contrast now uses internally dielectric contrasts, which
allows to specify metallic boundary conditions also. To set the contrasts
directly, use the dielectric-contrasts option.
(c) included extended LJGEN potential in main cvs trunk
(c) updated generic lennard-jones interaction in users guide
(a) The tunable slip boundary module has been included into the main ESPResSo
branch
Changes:
(k) harmonic cutoff is by default off, but still possible to set
(g) ELC with dielectric contrast now also prints out the space layer, and the out
output can actually be fed back into inter coulomb as intended
Bugfixes:
(v) Fixed some documentation errors in the Lennard-Jones description. Thanks to
Ahmad A. J. Agung!
(s) fixed a bug in "analyze energy coulomb" which would report a random
energy/pressure if no electrostatics method is switched on.
(r) Re-added configure-ac and Makefile-am.in after dead revision
(r) Re-added acconfig.h.in to CVS
(r) included Makefile.in files again into CVS (this matter is still discussed and
may change again in future)
(r) Resurrecting and re-adding several Makefile.in after dead
revision
(r) Re-added scripts/Makefile.in after dead revision
(q) Configure can handle the situation when configure-ac is not
executable.
(q) Fix in the LJ documenatation (thanks to David Sean and Antoine)
(p) Fixed a bug in writevsf related to the bond information.
(o) added a security warning for image charge correction, which requires the far
formula to work
(n) Another bugfix on aggregation routine
(n) fixed a bug in aggregation routine
(m) fixed the distribution to also contain the sources for the
tutorial
(m) fixed error message in case the hash line is missing
(i) fixed the harmonic-testcase to set a skin of 1 so that the bonding partners are
always on the same node.
(h) dpd and adress global parameters have not been broadcasted correctly, when
lattice was not defined.
(h) - fixed default weight for init_particle in particle_data.c
(g) ELC tuning now also works for ELC with dielectric contrast, and an stray
constant force proportional to the charge sum was removed.
(g) Adjusted lj-generic test to new format of the lj-generic
command
(f) calc_eigenvector_3x3 was accessing out-of-bounds stack memory for singular
matrizes
(f) fixed several (justified) warnings of gcc-4.3
(f) fixed two bugs in mmm2d with dielectric interfaces. Calculations in the top
layer were wrong so far
(e) the documentation now points out the dielectric features.
(d) forgotten adress flag
(b) In order to satisfy the dissipation-fluctuation theorem, DPD is not applied to
fixed particles or particles that interact with fixed particles any
more.
- v2.1.0d -
-----------
(d) August 19th, 2008.
(c) August 10th, 2008.
(b) August 6th, 2008.
(a) August 5th, 2008.
New Features:
(c) The interactions of constraints can now be any non-bonded
potential, not just Lennard-Jones
(a) added a command line option -quiet that switches off the startup
message. Alternatively, it is possible to specify "set quiet 1"
in the .espressorc to permanently get rid of the output.
Changes:
(a) analyze centermass works for all particle types with -1 option
Bugfixes:
(d) ran autogen to fix version number in make dist
(c) added a testcase for generic Lennard-Jones, and fixed a bug
that generic LJ forces/pressure were ignored.
(b) fixed compiling problem with gcc on IBM machines
- v2.1.0d -
-----------
(d) August 19th, 2008.
(c) August 10th, 2008.
(b) August 6th, 2008.
(a) August 5th, 2008.
New Features:
(c) The interactions of constraints can now be any non-bonded
potential, not just Lennard-Jones
(a) added a command line option -quiet that switches off the startup
message. Alternatively, it is possible to specify "set quiet 1"
in the .espressorc to permanently get rid of the output.
Changes:
(a) analyze centermass works for all particle types with -1 option
Bugfixes:
(d) ran autogen to fix version number in make dist
(c) added a testcase for generic Lennard-Jones, and fixed a bug
that generic LJ forces/pressure were ignored.
(b) fixed compiling problem with gcc on IBM machines
- v2.1.0d -
-----------
(d) August 19th, 2008.
(c) August 10th, 2008.
(b) August 6th, 2008.
(a) August 5th, 2008.
New Features:
(c) The interactions of constraints can now be any non-bonded
potential, not just Lennard-Jones
(a) added a command line option -quiet that switches off the startup
message. Alternatively, it is possible to specify "set quiet 1"
in the .espressorc to permanently get rid of the output.
Changes:
(a) analyze centermass works for all particle types with -1 option
Bugfixes:
(d) ran autogen to fix version number in make dist
(c) added a testcase for generic Lennard-Jones, and fixed a bug
that generic LJ forces/pressure were ignored.
(b) fixed compiling problem with gcc on IBM machines
****************************************************************************************
* v2.0.6w (Ydalir) *
****************************************************************************************
version jump due to new release
****************************************************************************************
* v2.0.6w (Ydalir) *
****************************************************************************************
version jump due to new release
****************************************************************************************
* v2.0.6w (Ydalir) *
****************************************************************************************
version jump due to new release
- v2.0.6w -
-----------
(w) August 4th, 2008.
(v) August 1st, 2008.