Hi Ed. The original was indeed [ei][si][mi][oi]. This gives much more sense.
The number of dispersion points is only used in the numerical models. They are only needed for looping over power, to evolve the matrix. They should have been removed from all analytical models. Best Troels 2014-06-17 9:26 GMT+02:00 Edward d'Auvergne <[email protected]>: > 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
