Author: tlinnet
Date: Thu May 29 12:24:23 2014
New Revision: 23585
URL: http://svn.gna.org/viewcvs/relax?rev=23585&view=rev
Log:
Converting back to having back_calc as a function argument to model NS CPMG
2site expanded.
This is to clean up the API.
There can be bo no partial measures/implementations in the relax trunk.
The problem is, that many numerical models can't be optimised further, since
they
evolve the spin-magnetisation in a matrix. That spin evolvement can't be put
into
a larger numpy array.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Modified:
branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
Modified: branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=23585&r1=23584&r2=23585&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py
(original)
+++ branches/disp_speed/lib/dispersion/ns_cpmg_2site_expanded.py Thu
May 29 12:24:23 2014
@@ -241,7 +241,7 @@
from lib.float import isNaN
-def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None,
k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, num_points=None,
num_cpmg=None):
+def r2eff_ns_cpmg_2site_expanded(r20=None, pA=None, dw=None, k_AB=None,
k_BA=None, relax_time=None, inv_relax_time=None, tcp=None, back_calc=None,
num_points=None, num_cpmg=None):
"""The 2-site numerical solution to the Bloch-McConnell equation using
complex conjugate matrices.
This function calculates and stores the R2eff values.
@@ -263,7 +263,9 @@
@type inv_relax_time: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@type tcp: numpy rank-1 float array
- @keyword num_points: The number of points on the dispersion
curve, equal to the length of the tcp .
+ @keyword back_calc: The array for holding the back calculated
R2eff values. Each element corresponds to one of the CPMG nu1 frequencies.
+ @type back_calc: numpy rank-1 float array
+ @keyword num_points: The number of points on the dispersion
curve, equal to the length of the tcp and back_calc arguments.
@type num_points: int
@keyword num_cpmg: The array of numbers of CPMG blocks.
@type num_cpmg: numpy int16, rank-1 array
@@ -271,7 +273,8 @@
# Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
if dw == 0.0 or pA == 1.0 or k_AB == 0.0:
- return array([r20]*num_points)
+ back_calc[:] = array([r20]*num_points)
+ return
# Repeditive calculations.
half_tcp = 0.5 * tcp
@@ -363,4 +366,4 @@
if not isfinite(sum(R2eff)) or min(Mx) <= 0.0 or not isfinite(sum(Mx)):
R2eff = array([1e100]*num_points)
- return R2eff
+ back_calc[:] = R2eff
Modified: branches/disp_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/target_functions/relax_disp.py?rev=23585&r1=23584&r2=23585&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Thu May 29 12:24:23
2014
@@ -1480,7 +1480,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- self.back_calc[0][si][mi][0] =
r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA, dw=dw_frq, k_AB=k_AB,
k_BA=k_BA, relax_time=self.relax_times[0][mi],
inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi])
+ r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA,
dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_times[0][mi],
inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
back_calc=self.back_calc[0][si][mi][0],
num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi])
# For all missing data points, set the back-calculated value
to the measured values so that it has no effect on the chi-squared value.
for di in range(self.num_disp_points[0][si][mi][0]):
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py?rev=23585&r1=23584&r2=23585&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
Thu May 29 12:24:23 2014
@@ -43,6 +43,7 @@
self.num_points = 3
self.tcp = array([0.1, 0.2, 0.3], float64)
self.num_cpmg = array([1, 2, 3], int16)
+ self.R2eff = zeros(self.num_points, float64)
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
@@ -55,14 +56,14 @@
k_AB, k_BA, dw_frq = self.param_conversion(pA=self.pA, kex=self.kex,
dw=self.dw, sfrq=self.sfrq)
# Calculate the R2eff values.
- R2eff = r2eff_ns_cpmg_2site_expanded(r20=self.r20, pA=self.pA,
dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=0.3, inv_relax_time=1/0.3,
tcp=self.tcp, num_points=self.num_points, num_cpmg=self.num_cpmg)
+ r2eff_ns_cpmg_2site_expanded(r20=self.r20, pA=self.pA, dw=dw_frq,
k_AB=k_AB, k_BA=k_BA, relax_time=0.3, inv_relax_time=1/0.3, tcp=self.tcp,
back_calc=self.R2eff, num_points=self.num_points, num_cpmg=self.num_cpmg)
if self.kex >= 1.e5:
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20, 5)
+ self.assertAlmostEqual(self.R2eff[i], self.r20, 5)
else:
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20)
+ self.assertAlmostEqual(self.R2eff[i], self.r20)
def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
r23585 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/