Hi, What were the original indices in "num_points[0][si][mi][0][0]"? Were they [ei][si][mi][oi][di]? I guess the di index is dropped as the dimensionality of that index is now stored in the oi index. It might be worth updating the lib.dispersion docstrings to remove the [ND] part in describing the num_points argument. The structure is now rank-4 rather than rank-5.
Cheers, Edward > The number of offsets and cpmg points has been lowered 2 and 1 dimension. > This one actually tells the number of dispersion point at offset dimension > 0. > That 0 can be changed to oi later. > > Best > Troels > > > > 2014-06-16 19:21 GMT+02:00 Edward d'Auvergne <[email protected]>: >> >> 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, <[email protected]> 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) >> > >> > >> > _______________________________________________ >> > relax (http://www.nmr-relax.com) >> > >> > This is the relax-commits mailing list >> > [email protected] >> > >> > To unsubscribe from this list, get a password >> > reminder, or change your subscription options, >> > visit the list information page at >> > https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
