Hi Troels,
The test for 'no Rex' is still wrong:
if kex == 1.0 or pA == 1:
This needs to be:
if kex == 0.0 or pA == 1.0:
Regards,
Edward
On 11 June 2014 13:12, <[email protected]> wrote:
> Author: tlinnet
> Date: Wed Jun 11 13:12:21 2014
> New Revision: 23831
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23831&view=rev
> Log:
> Made the lib/cr72.py to a numpy multi dimensional numpy array calculation.
>
> 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=23831&r1=23830&r2=23831&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/cr72.py (original)
> +++ branches/disp_spin_speed/lib/dispersion/cr72.py Wed Jun 11 13:12:21
> 2014
> @@ -105,19 +105,19 @@
>
>
> @keyword r20a: The R20 parameter value of state A (R2 with no
> exchange).
> - @type r20a: float
> + @type r20a: numpy float array of rank [NE][NS][[NM][NO][ND]
> @keyword r20b: The R20 parameter value of state B (R2 with no
> exchange).
> - @type r20b: float
> + @type r20b: numpy float array of rank [NE][NS][[NM][NO][ND]
> @keyword pA: The population of state A.
> @type pA: float
> @keyword dw: The chemical exchange difference between states
> A and B in rad/s.
> - @type dw: float
> + @type dw: numpy array of rank [NE][NS][[NM][NO][ND]
> @keyword kex: The kex parameter value (the exchange rate in
> rad/s).
> @type kex: float
> @keyword cpmg_frqs: The CPMG nu1 frequencies.
> - @type cpmg_frqs: numpy rank-1 float array
> + @type cpmg_frqs: numpy float array of rank [NE][NS][[NM][NO][ND]
> @keyword back_calc: The array for holding the back calculated R2eff
> values. Each element corresponds to one of the CPMG nu1 frequencies.
> - @type back_calc: numpy rank-1 float array
> + @type back_calc: numpy float array of rank [NE][NS][[NM][NO][ND]
> @keyword num_points: The number of points on the dispersion curve,
> equal to the length of the cpmg_frqs and back_calc arguments.
> @type num_points: int
> """
> @@ -125,34 +125,16 @@
> # Flag to tell if values should be replaced if max_etapos in cosh
> function is violated.
> t_max_etapos = False
>
> - # Determine if calculating in numpy rank-1 float array, of higher
> dimensions.
> - rank_1 = True
> - if isinstance(num_points, ndarray):
> - rank_1 = False
> -
> # Catch parameter values that will result in no exchange, returning flat
> R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
> - # For rank-1 float array.
> - if rank_1:
> - if dw == 0.0 or pA == 1.0 or kex == 0.0:
> - back_calc[:] = array([r20a]*num_points)
> - return
> -
> - # For higher dimensions, return same structure.
> - else:
> - # Test if kex is zero.
> - if kex == 1.0:
> + # Test if pA or kex is zero.
> + if kex == 1.0 or pA == 1:
> back_calc[:] = r20a
> return
>
> - # Test if pA is 1.
> - if pA == 1.0:
> - back_calc[:] = r20a
> - return
> -
> - # Test if dw is zero.
> - if allclose(dw, zeros(dw.shape)):
> - back_calc[:] = r20a
> - return
> + # Test if dw is zero.
> + if allclose(dw, zeros(dw.shape)):
> + back_calc[:] = r20a
> + return
>
> # The B population.
> pB = 1.0 - pA
> @@ -187,28 +169,20 @@
> # Catch math domain error of cosh(val > 710).
> # This is when etapos > 710.
> if max(etapos) > 700:
> - if rank_1:
> - back_calc[:] = array([r20a]*num_points)
> - return
> # For higher dimensions, find the mask to replace values.
> # Reset to 1.0 and wait for replacement to later.
> - else:
> - # Set the flag to tell to replace values.
> - t_max_etapos = True
> - # Find the mask, where to replace values.
> - mask_max_etapos = masked_greater_equal(etapos, 700.0)
> - # To prevent math errors, set etapos to 1.
> - etapos[mask_max_etapos.mask] = 1.0
> + # Set the flag to tell to replace values.
> + t_max_etapos = True
> + # Find the mask, where to replace values.
> + mask_max_etapos = masked_greater_equal(etapos, 700.0)
> + # To prevent math errors, set etapos to 1.
> + etapos[mask_max_etapos.mask] = 1.0
>
> # The arccosh argument - catch invalid values.
> fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
> if min(fact) < 1.0:
> - if rank_1:
> - back_calc[:] = array([r20_kex]*num_points)
> - return
> - else:
> - back_calc[:] = r20_kex
> - return
> + back_calc[:] = r20_kex
> + return
>
> # Calculate R2eff.
> R2eff = r20_kex - cpmg_frqs * arccosh( fact )
> @@ -224,4 +198,4 @@
> mask = isnan(R2eff)
> R2eff[mask] = 1e100
>
> - back_calc[:] = R2eff
> + back_calc[:] = R2eff
>
>
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