Re: r23989 - /branches/disp_spin_speed/lib/dispersion/ -- June 16, 2014 - 19:21

Hi Troels,

There is something that worries me in this change, specifically:

-            num_points_si_mi = int(num_points[0][si][mi][0][0])
+            num_points_si_mi = int(num_points[0][si][mi][0])

This is in the numeric models for CPMG-type data.  Have you dropped
the offset dimension?  Note that the offset dimension will be
essential when the first point in the TODO list in the dispersion
chapter is implemented - the handling of offsets in the CPMG
experiments 
(http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html).

Regards,

Edward



On 16 June 2014 19:01,  <tlinnet@xxxxxxxxxxxxx> wrote:
> Author: tlinnet
> Date: Mon Jun 16 19:01:36 2014
> New Revision: 23989
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23989&view=rev
> Log:
> Various index fixes, after the data structures have been reordered.
>
> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
> models for Clustered analysis.
>
> Modified:
>     branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
>     branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
>     branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
>     branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
>     branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
>     branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Mon Jun 16 
> 19:01:36 2014
> @@ -136,7 +136,7 @@
>              R2A_si_mi=r20a[0][si][mi][0][0]
>              R2B_si_mi=r20b[0][si][mi][0][0]
>              dw_si_mi = dw[0][si][mi][0][0]
> -            num_points_si_mi = int(num_points[0][si][mi][0][0])
> +            num_points_si_mi = int(num_points[0][si][mi][0])
>
>              # The matrix R that contains all the contributions to the 
> evolution, i.e. relaxation, exchange and chemical shift evolution.
>              R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, R2B=R2B_si_mi, 
> pA=pA, pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA)
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py       
> (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py       Mon 
> Jun 16 19:01:36 2014
> @@ -145,7 +145,7 @@
>              R2A_si_mi=r20a[0][si][mi][0][0]
>              R2B_si_mi=r20b[0][si][mi][0][0]
>              dw_si_mi = dw[0][si][mi][0][0]
> -            num_points_si_mi = int(num_points[0][si][mi][0][0])
> +            num_points_si_mi = int(num_points[0][si][mi][0])
>
>              # The matrix that contains only the R2 relaxation terms 
> ("Redfield relaxation", i.e. non-exchange broadening).
>              Rr[0, 0] = -R2A_si_mi
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py     (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py     Mon Jun 16 
> 19:01:36 2014
> @@ -216,7 +216,7 @@
>          if Mx <= 0.0 or isNaN(Mx):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i]= -inv_tcpmg * log(Mx / pA)
> +            back_calc[i]= -inv_tcpmg[i] * log(Mx / pA)
>
>
>  def r2eff_ns_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64), 
> m1=None, m2=None, R20A=None, R20B=None, pA=None, pB=None, dw=None, 
> dwH=None, k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None, back_calc=None, 
> num_points=None, power=None):
> @@ -287,4 +287,4 @@
>          if Mx <= 0.0 or isNaN(Mx):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i] = -inv_tcpmg * log(Mx / pA)
> +            back_calc[i] = -inv_tcpmg[i] * log(Mx / pA)
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py     (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py     Mon Jun 16 
> 19:01:36 2014
> @@ -259,7 +259,7 @@
>          if Mx <= 0.0 or isNaN(Mx):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i]= -inv_tcpmg * log(Mx / pA)
> +            back_calc[i]= -inv_tcpmg[i] * log(Mx / pA)
>
>
>  def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], 
> float64), m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, 
> pB=None, pC=None, dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, 
> k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None, 
> inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
> @@ -338,4 +338,4 @@
>          if Mx <= 0.0 or isNaN(Mx):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i] = -inv_tcpmg * log(Mx / pA)
> +            back_calc[i] = -inv_tcpmg[i] * log(Mx / pA)
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Mon Jun 16 
> 19:01:36 2014
> @@ -117,7 +117,7 @@
>          M0[2] = cos(theta)    # The A state initial Z magnetisation.
>
>          # This matrix is a propagator that will evolve the magnetization 
> with the matrix R.
> -        Rexpo = matrix_exponential(matrix*relax_time)
> +        Rexpo = matrix_exponential(matrix*relax_time[i])
>
>          # Magnetization evolution.
>          MA = dot(M0, dot(Rexpo, M0))
> @@ -126,6 +126,6 @@
>          if MA <= 0.0 or isNaN(MA):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i]= -inv_relax_time * log(MA)
> +            back_calc[i]= -inv_relax_time[i] * log(MA)
>
>
>
> Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
> URL: 
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py?rev=23989&r1=23988&r2=23989&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   (original)
> +++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   Mon Jun 16 
> 19:01:36 2014
> @@ -146,4 +146,4 @@
>          if MA <= 0.0 or isNaN(MA):
>              back_calc[i] = 1e99
>          else:
> -            back_calc[i]= -inv_relax_time * log(MA)
> +            back_calc[i]= -inv_relax_time[i] * log(MA)
>
>
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