tlinnet@linmac:dispersion$ grep -r "@keyword num_points" . | grep -v ".pyc"
| awk '{print $1}'
./lm63_3site.py:
./ns_cpmg_2site_3d.py:
./ns_cpmg_2site_star.py:
./ns_mmq_2site.py:
./ns_mmq_2site.py:
./ns_mmq_3site.py:
./ns_mmq_3site.py:
./ns_r1rho_2site.py:
./ns_r1rho_3site.py:2014-06-17 9:40 GMT+02:00 Troels Emtekær Linnet <[email protected]>: > tlinnet@linmac:dispersion$ 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
