Hi Troels,
I have a suggestion for this change too, specifically:
@@ -123,6 +129,8 @@
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
Mx = fabs(Mint[1] / pA)
if Mx <= 0.0 or isNaN(Mx):
- back_calc[i] = 1e99
+ for i in range(num_points):
+ back_calc[i] = r20a
+ return
else:
back_calc[i]= -inv_tcpmg * log(Mx)
Here you have introduced a second loop over the index i inside an
index i loop. This is not the best idea, instead try:
# The next lines calculate the R2eff using a two-point
approximation, i.e. assuming that the decay is mono-exponential.
Mx = fabs(Mint[1] / pA)
if Mx <= 0.0 or isNaN(Mx):
back_calc[i] = r20a
else:
back_calc[i]= -inv_tcpmg * log(Mx)
There is no need to return at this point, just let the loop continue
harmlessly. Also, one hint for the commit message would be to explain
why you changed the 1e99 value to r20a. I.e. that when kex is very
large, Mx will be zero, and although the log of zero is not defined,
this is in the 'no Rex' region so it should return r20a rather than
the -1/tcpmg*log(0.0) value of -1/tcpmg*-infinity (which is positive
infinity). This makes me wonder if this numeric model is any good for
large kex values which actually do cause exchange!
Cheers,
Edward
On 27 May 2014 00:08, <[email protected]> wrote:
> Author: tlinnet
> Date: Tue May 27 00:08:08 2014
> New Revision: 23451
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23451&view=rev
> Log:
> Critical fix for the math domain catching of model NS CPMG 2site 3D.
>
> This was discovered with the added 8 unit tests demonstrating edge case 'no
> Rex' failures.
>
> This follows from the ideas in the post
> http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
> This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
> dispersion models.
>
> This is to implement catching of math domain errors, before they occur.
>
> Modified:
> branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py
>
> Modified: branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py
> URL:
> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=23451&r1=23450&r2=23451&view=diff
> ==============================================================================
> --- branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
> +++ branches/disp_speed/lib/dispersion/ns_cpmg_2site_3d.py Tue May 27
> 00:08:08 2014
> @@ -103,6 +103,12 @@
> @type power: numpy int16, rank-1 array
> """
>
> + # Catch parameter values that will result in no exchange, returning flat
> R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
> + if dw == 0.0 or pA == 1.0 or k_AB == 0.0:
> + for i in range(num_points):
> + back_calc[i] = r20a
> + return
> +
> # The matrix R that contains all the contributions to the evolution,
> i.e. relaxation, exchange and chemical shift evolution.
> R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=r20a, R2B=r20b, pA=pA, pB=pB,
> dw=dw, k_AB=k_AB, k_BA=k_BA)
>
> @@ -123,6 +129,8 @@
> # The next lines calculate the R2eff using a two-point
> approximation, i.e. assuming that the decay is mono-exponential.
> Mx = fabs(Mint[1] / pA)
> if Mx <= 0.0 or isNaN(Mx):
> - back_calc[i] = 1e99
> + for i in range(num_points):
> + back_calc[i] = r20a
> + return
> else:
> back_calc[i]= -inv_tcpmg * log(Mx)
>
>
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