Hi Troels,
In this case, do we even need the isfinite() check? Can this equation
ever calculate R2eff to be Inf? The only case I can think of is when
kex is 0.0, as rex = phi_ex/kex. Therefore you could replace this
check with:
if kex == 0.0:
back_calc[:] = array([1e100]*num_points)
return
This can go at the very start of the function too. This was the
reason for the original kex check deleted in this commit.
Regards,
Edward
On 19 May 2014 03:20, <[email protected]> wrote:
> Author: tlinnet
> Date: Mon May 19 03:20:51 2014
> New Revision: 23226
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23226&view=rev
> Log:
> Speed-up of model LM63.
>
> task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
>
> Change in systemtest was:
> test_hansen_cpmg_data_auto_analysis
> 13.731s -> 9.971s
>
> test_hansen_cpmg_data_auto_analysis_r2eff
> 13.370s -> 9.510s
>
> test_hansen_cpmg_data_to_lm63
> 3.254s -> 2.080s
>
> Modified:
> branches/disp_speed/lib/dispersion/lm63.py
>
> Modified: branches/disp_speed/lib/dispersion/lm63.py
> URL:
> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/lm63.py?rev=23226&r1=23225&r2=23226&view=diff
> ==============================================================================
> --- branches/disp_speed/lib/dispersion/lm63.py (original)
> +++ branches/disp_speed/lib/dispersion/lm63.py Mon May 19 03:20:51 2014
> @@ -64,7 +64,7 @@
> """
>
> # Python module imports.
> -from math import tanh
> +from numpy import isfinite, sum, tanh
>
>
> def r2eff_LM63(r20=None, phi_ex=None, kex=None, cpmg_frqs=None,
> back_calc=None, num_points=None):
> @@ -91,16 +91,14 @@
> rex = phi_ex / kex
> kex_4 = 4.0 / kex
>
> - # Loop over the time points, back calculating the R2eff values.
> + # Calculate R2eff.
> + R2eff = r20 + rex * (1.0 - kex_4 * cpmg_frqs * tanh(kex / (4.0 *
> cpmg_frqs)))
> +
> + # Catch errors, taking a sum over array is the fastest way to check for
> + # +/- inf (infinity) and nan (not a number).
> + if not isfinite(sum(R2eff)):
> + R2eff = array([1e100]*num_points)
> +
> + # Parse back the value to update the back_calc class object.
> for i in range(num_points):
> - # Catch zeros.
> - if phi_ex == 0.0:
> - back_calc[i] = r20
> -
> - # Avoid divide by zero.
> - elif kex == 0.0:
> - back_calc[i] = 1e100
> -
> - # The full formula.
> - else:
> - back_calc[i] = r20 + rex * (1.0 - kex_4 * cpmg_frqs[i] *
> tanh(kex / (4.0 * cpmg_frqs[i])))
> + back_calc[i] = R2eff[i]
>
>
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