Hi, Cheers, I'll release relax 3.2.1 with the perfect "B14" and "B14 full" model implementations (http://wiki.nmr-relax.com/B14 and http://wiki.nmr-relax.com/B14_full) probably tomorrow. Andy, if you missed it, I released relax 3.2.0 yesterday with your CPMG analytic models being the major feature of this new version:
http://www.nmr-relax.com/download.html, https://mail.gna.org/public/relax-announce/2014-05/msg00000.html, https://freecode.com/projects/nmr-relax/releases/363882, https://gna.org/forum/forum.php?forum_id=2461. You can see the new code at: http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html, http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-pysrc.html These links will be updated with the corrections once relax 3.2.1 is released. Regards, Edward On 22 May 2014 10:22, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > Hi Andrew, I have added you to this mail, since this relates to your work. > > -- > > Before the fix Andrew sent, B14 would not be able to do it. > I tried, and the results was miserable. > > Hence the statement: > "The model B14 was previously in a state of non-functioning." > > The problem was, that I could fit Andrews original result from the > paper just fine. > https://gna.org/bugs/index.php?22021#comment7 > > But when I gave the challenging try, it would fail. > https://gna.org/bugs/index.php?22021#comment5 > > I did try my self to implement the trigometric functions: > https://gna.org/bugs/index.php?22021#comment6 > > But I did that wrong. > > I was first when Andrew corrected me, that I got it right: > https://gna.org/bugs/index.php?22021#comment10 > > I tested it a little yesterday, and the results are as good as the numerical. > > This is indeed a very interesting and promising model! > > And I am sure it will get some attention. > > Best > Troels > > > > 2014-05-22 9:50 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Hi Troels, >> >> For reference, do you have the B14 optimisation results for this >> parameter set prior to the fix? This is just to see the difference >> the change makes. >> >> Cheers, >> >> Edward >> >> >> >> On 21 May 2014 20:36, <[email protected]> wrote: >>> Author: tlinnet >>> Date: Wed May 21 20:36:36 2014 >>> New Revision: 23316 >>> >>> URL: http://svn.gna.org/viewcvs/relax?rev=23316&view=rev >>> Log: >>> Extremely important fix to the model B14. >>> >>> This was discovered by author Andrew Baldwin of the inspection of his code >>> in relax. >>> >>> bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to >>> data. >>> >>> The implementation was performed wrong for calculation of g3 and g4. >>> The implementations should be performed by trigonometric functions. >>> >>> The model B14 was previously in a state of non-functioning. >>> >>> The B14 model now shows excellent performance. >>> >>> For the challenging case of data created with numerical model NS CPMG >>> 2-site 3D: >>> >>> sfrq_1 = 599.8908617*1E6 >>> time_T2_1 = 0.06 >>> ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60] >>> sfrq_2 = 499.8908617*1E6 >>> time_T2_2 = 0.05 >>> ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50] >>> >>> r2 = 10. rad/s. >>> kex: 1000 rad/s >>> pA: 0.99 >>> dw: 2. ppm >>> >>> CR72 would fit: >>> ---------- >>> CR72 Ala :1@N r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000 >>> CR72 Ala :1@N r2 499.9 GRID=10.080 MIN=9.999 SET=10.000 RELC=0.000 >>> CR72 Ala :1@N pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000 >>> CR72 Ala :1@N dw GRID=1.429 MIN=1.925 SET=2.000 RELC=0.039 >>> CR72 Ala :1@N kex GRID=5714.714 MIN=1034.721 SET=1000.000 RELC=0.034 >>> >>> B14 fits: >>> ----------- >>> B14 Ala :1@N r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000 >>> B14 Ala :1@N r2 499.9 GRID=10.080 MIN=10.000 SET=10.000 RELC=0.000 >>> B14 Ala :1@N pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000 >>> B14 Ala :1@N dw GRID=1.429 MIN=2.000 SET=2.000 RELC=0.000 >>> B14 Ala :1@N kex GRID=10000.000 MIN=1000.001 SET=1000.000 RELC=0.000 >>> >>> Modified: >>> trunk/lib/dispersion/b14.py >>> >>> Modified: trunk/lib/dispersion/b14.py >>> URL: >>> http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/b14.py?rev=23316&r1=23315&r2=23316&view=diff >>> ============================================================================== >>> --- trunk/lib/dispersion/b14.py (original) >>> +++ trunk/lib/dispersion/b14.py Wed May 21 20:36:36 2014 >>> @@ -111,7 +111,7 @@ >>> >>> # Python module imports. >>> import numpy >>> -from numpy import arccosh, array, cos, cosh, in1d, log, nonzero, sin, >>> sinh, sqrt, power >>> +from numpy import arccosh, arctan2, array, cos, cosh, in1d, log, nonzero, >>> sin, sinh, sqrt, power >>> >>> # Repetitive calculations (to speed up calculations). >>> g_fact = 1/sqrt(2) >>> @@ -161,11 +161,12 @@ >>> # Repetitive calculations (to speed up calculations). >>> dw2 = dw**2 >>> two_tcp = 2.0 * tcp >>> - sqrt_zeta2_Psi2 = sqrt(zeta**2 + Psi**2) >>> >>> # Get the real and imaginary components of the exchange induced shift. >>> - g3 = g_fact * sqrt( Psi + sqrt_zeta2_Psi2) >>> - g4 = g_fact * sqrt(-Psi + sqrt_zeta2_Psi2) >>> + # Trigonometric functions faster than square roots. >>> + quad_zeta2_Psi2 = (zeta**2 + Psi**2)**0.25 >>> + g3 = cos(0.5 * arctan2(-zeta, Psi)) * quad_zeta2_Psi2 >>> + g4 = sin(0.5 * arctan2(-zeta, Psi)) * quad_zeta2_Psi2 >>> >>> # Repetitive calculations (to speed up calculations). >>> g32 = g3**2 >>> >>> >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-commits mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
