tlinnet@linmac:dispersion$ grep -r "@keyword num_points" . | grep -v ".pyc"
./lm63_3site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the cpmg_frqs and back_calc arguments. ./ns_cpmg_2site_3d.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_cpmg_2site_star.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_mmq_2site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_mmq_2site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_mmq_3site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_mmq_3site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_r1rho_2site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. ./ns_r1rho_3site.py: @keyword num_points: The number of points on the dispersion curve, equal to the length of the tcp and back_calc arguments. 2014-06-17 9:39 GMT+02:00 Troels Emtekær Linnet <[email protected]>: > 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
