Re: r23219 - /branches/disp_speed/lib/dispersion/tsmfk01.py -- May 19, 2014 - 10:13

Hi Troels,

For even faster code , have a look at:

https://stackoverflow.com/questions/6431973/how-to-copy-data-from-a-numpy-array-to-another

Regards,

Edward


On 19 May 2014 00:51,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Mon May 19 00:51:18 2014
> New Revision: 23219
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23219&view=rev
> Log:
> Speed-up of model TSMFK01.
>
> task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
>
> This is won by not checking single values in the R2eff array for math domain
> errors, but calculating all steps, and in one single round check for finite 
> values.
> If just one non-finite value is found, the whole array is returned with a 
> large
> penalty of 1e100.
>
> This makes all calculations be the fastest numpy array way.
>
> Modified:
>     branches/disp_speed/lib/dispersion/tsmfk01.py
>
> Modified: branches/disp_speed/lib/dispersion/tsmfk01.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/tsmfk01.py?rev=23219&r1=23218&r2=23219&view=diff
> ==============================================================================
> --- branches/disp_speed/lib/dispersion/tsmfk01.py       (original)
> +++ branches/disp_speed/lib/dispersion/tsmfk01.py       Mon May 19 00:51:18 
> 2014
> @@ -67,7 +67,7 @@
>  """
>
>  # Python module imports.
> -from math import sin
> +from numpy import sin, isfinite, sum
>
>
>  def r2eff_TSMFK01(r20a=None, dw=None, k_AB=None, tcp=None, back_calc=None, 
> num_points=None):
> @@ -90,24 +90,20 @@
>      @type num_points:       int
>      """
>
> -    # Loop over the time points, back calculating the R2eff values.
> +    # Denominator.
> +    denom = dw * tcp
> +
> +    # The numerator.
> +    numer = sin(denom)
> +
> +    # Calculate R2eff.
> +    R2eff = r20a + k_AB - k_AB * 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):
> -        # Denominator.
> -        denom = dw * tcp[i]
> -
> -        # The numerator.
> -        numer = sin(denom)
> -
> -        # Catch zeros (to avoid pointless mathematical operations).
> -        if numer == 0.0:
> -            back_calc[i] = r20a + k_AB
> -            continue
> -
> -        # Avoid divide by zero.
> -        if denom == 0.0:
> -            back_calc[i] = 1e100
> -            continue
> -
> -        # The full formula.
> -        else:
> -            back_calc[i] = r20a + k_AB - k_AB * numer / denom
> +        back_calc[i] = R2eff[i]
>
>
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