Re: r23839 - /branches/disp_spin_speed/lib/dispersion/cr72.py -- June 11, 2014 - 15:31

Hi,

Where you have used the numpy.subtract() function, you should just
before it use the numpy.multiply() function.  In the line:

+    subtract(r20_kex, cpmg_frqs * arccosh( fact ), out=back_calc)

You actually create a data structure "cpmg_frqs * arccosh( fact )"
which is later destroyed.  See
http://thread.gmane.org/gmane.science.nmr.relax.devel/6159/focus=6171
for how to do this.

Regards,

Edward

On 11 June 2014 15:25,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Wed Jun 11 15:25:32 2014
> New Revision: 23839
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23839&view=rev
> Log:
> Replaced the temporary variable R2eff with back_calc, and used numpy 
> subtract to speed up.
>
> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
> models for Clustered analysis.
>
> Modified:
>     branches/disp_spin_speed/lib/dispersion/cr72.py
>
> Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=23839&r1=23838&r2=23839&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/cr72.py     (original)
> +++ branches/disp_spin_speed/lib/dispersion/cr72.py     Wed Jun 11 15:25:32 
> 2014
> @@ -92,7 +92,7 @@
>  """
>
>  # Python module imports.
> -from numpy import arccosh, array, cos, cosh, isfinite, fabs, min, max, 
> sqrt, sum
> +from numpy import arccosh, array, cos, cosh, isfinite, fabs, min, max, 
> sqrt, subtract, sum
>  from numpy.ma import fix_invalid, masked_greater_equal, masked_less, 
> masked_where
>
>  # Repetitive calculations (to speed up calculations).
> @@ -181,8 +181,8 @@
>          back_calc[:] = r20_kex
>          return
>
> -    # Calculate R2eff.
> -    R2eff = r20_kex - cpmg_frqs * arccosh( fact )
> +    # Calculate R2eff. This uses the temporary buffer and fill directly to 
> back_calc.
> +    subtract(r20_kex, cpmg_frqs * arccosh( fact ), out=back_calc)
>
>      # Replace data in array.
>      # If dw is zero.
> @@ -191,7 +191,7 @@
>              back_calc[:] = array([r20a]*num_points)
>              return
>          else:
> -            R2eff[mask_dw_zero.mask] = r20a[mask_dw_zero.mask]
> +            back_calc[mask_dw_zero.mask] = r20a[mask_dw_zero.mask]
>
>      # If eta_pos above 700.
>      if t_max_etapos:
> @@ -199,12 +199,10 @@
>              back_calc[:] = array([r20a]*num_points)
>              return
>          else:
> -            R2eff[mask_max_etapos.mask] = r20a[mask_max_etapos.mask]
> +            back_calc[mask_max_etapos.mask] = r20a[mask_max_etapos.mask]
>
>      # 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)):
> +    if not isfinite(sum(back_calc)):
>          # Replaces nan, inf, etc. with fill value.
> -        fix_invalid(R2eff, copy=False, fill_value=1e100)
> -
> -    back_calc[:] = R2eff
> +        fix_invalid(back_calc, copy=False, fill_value=1e100)
>
>
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