Hi Ed. 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
