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 <edward@xxxxxxxxxxxxx>:
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, <tlinnet@xxxxxxxxxxxxx> 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)
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Re: r23989 - /branches/disp_spin_speed/lib/dispersion/