Re: r23227 - /branches/disp_speed/lib/dispersion/it99.py -- May 19, 2014 - 10:54

Hi Troels,

Awesome work with all these speed ups!!  If you are feeling really
adventurous, I'll soon place a hint about an ultimate solution for
speed in the thread at
http://thread.gmane.org/gmane.science.nmr.relax.devel/5726.  The
chi2_5D() function and missing data ideas there should already give
you some great speed ups as well.

Cheers,

Edward


On 19 May 2014 03:20,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Mon May 19 03:20:53 2014
> New Revision: 23227
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23227&view=rev
> Log:
> Speed-up of model IT99.
>
> task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
>
> Change in speed is:
> test_hansen_cpmg_data_auto_analysis
> 9.74s -> 8.330s
>
> test_hansen_cpmg_data_to_it99
> 4.928s ->  3.138s
>
> Modified:
>     branches/disp_speed/lib/dispersion/it99.py
>
> Modified: branches/disp_speed/lib/dispersion/it99.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/it99.py?rev=23227&r1=23226&r2=23227&view=diff
> ==============================================================================
> --- branches/disp_speed/lib/dispersion/it99.py  (original)
> +++ branches/disp_speed/lib/dispersion/it99.py  Mon May 19 03:20:53 2014
> @@ -73,7 +73,7 @@
>  """
>
>  # Python module imports.
> -from math import sqrt
> +from numpy import array, isfinite, sqrt, sum
>
>
>  def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None, 
> cpmg_frqs=None, back_calc=None, num_points=None):
> @@ -109,24 +109,21 @@
>      # The numerator.
>      numer = padw2 * pB * tex
>
> -    # Loop over the time points, back calculating the R2eff values.
> +    # The effective rotating frame field.
> +    omega_1eff4 = 2304.0 * cpmg_frqs**4
> +
> +    # Denominator.
> +    omega_a2 = sqrt(omega_1eff4 + pa2dw4)
> +    denom = 1.0 + omega_a2 * tex2
> +
> +    # R2eff calculation.
> +    R2eff = r20 + numer / denom
> +
> +    # 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 (to avoid pointless mathematical operations).
> -        if numer == 0.0:
> -            back_calc[i] = r20
> -            continue
> -
> -        # The effective rotating frame field.
> -        omega_1eff4 = 2304.0 * cpmg_frqs[i]**4
> -
> -        # Denominator.
> -        omega_a2 = sqrt(omega_1eff4 + pa2dw4)
> -        denom = 1.0 + omega_a2 * tex2
> -
> -        # Avoid divide by zero.
> -        if denom == 0.0:
> -            back_calc[i] = 1e100
> -            continue
> -
> -        # R2eff calculation.
> -        back_calc[i] = r20 + numer / denom
> +        back_calc[i] = R2eff[i]
>
>
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