Author: tlinnet
Date: Thu May 29 11:52:37 2014
New Revision: 23583
URL: http://svn.gna.org/viewcvs/relax?rev=23583&view=rev
Log:
Converting back to having back_calc as a function argument to model MMQ CR72:
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/mmq_cr72.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
Modified: branches/disp_speed/lib/dispersion/mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/mmq_cr72.py?rev=23583&r1=23582&r2=23583&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/mmq_cr72.py (original)
+++ branches/disp_speed/lib/dispersion/mmq_cr72.py Thu May 29 11:52:37
2014
@@ -50,7 +50,7 @@
from numpy import arccosh, array, cos, cosh, isfinite, log, max, sin, sqrt,
sum
-def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None,
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None,
num_points=None, power=None):
+def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None,
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
"""The CR72 model extended to MMQ CPMG data.
This function calculates and stores the R2eff values.
@@ -78,7 +78,9 @@
@type inv_tcpmg: 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 power: The matrix exponential power array.
@type power: numpy int16, rank-1 array
@@ -86,7 +88,8 @@
# 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 and dwH == 0.0) or pA == 1.0 or k_AB == 0.0:
- return array([r20]*num_points)
+ back_calc[:] = array([r20]*num_points)
+ return
# Repetitive calculations (to speed up calculations).
dw2 = dw**2
@@ -130,7 +133,8 @@
# Catch math domain error of cosh(val > 710).
# This is when etapos > 710.
if max(etapos) > 700:
- return array([r20]*num_points)
+ back_calc[:] = array([r20]*num_points)
+ return
# The full eta - values.
etaneg = etaneg_part / cpmg_frqs
@@ -156,4 +160,4 @@
if not isfinite(sum(R2eff)):
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=23583&r1=23582&r2=23583&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Thu May 29 11:52:37
2014
@@ -1335,7 +1335,7 @@
aliased_dwH = dw_frq
# Back calculate the R2eff values.
- self.back_calc[ei][si][mi][0] =
r2eff_mmq_cr72(r20=R20[r20_index], pA=pA, pB=pB, dw=aliased_dw,
dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA,
cpmg_frqs=self.cpmg_frqs[ei][mi][0], inv_tcpmg=self.inv_relax_times[ei][mi],
tcp=self.tau_cpmg[ei][mi], num_points=self.num_disp_points[ei][si][mi][0],
power=self.power[ei][mi])
+ r2eff_mmq_cr72(r20=R20[r20_index], pA=pA, pB=pB,
dw=aliased_dw, dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA,
cpmg_frqs=self.cpmg_frqs[ei][mi][0], inv_tcpmg=self.inv_relax_times[ei][mi],
tcp=self.tau_cpmg[ei][mi], back_calc=self.back_calc[ei][si][mi][0],
num_points=self.num_disp_points[ei][si][mi][0], power=self.power[ei][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[ei][si][mi][0]):
Modified:
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=23583&r1=23582&r2=23583&view=diff
==============================================================================
---
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
(original)
+++
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
Thu May 29 11:52:37 2014
@@ -47,6 +47,7 @@
self.cpmg_frqs = self.ncyc / relax_times
self.inv_relax_times = 1.0 / relax_times
self.tau_cpmg = 0.25 / self.cpmg_frqs
+ self.R2eff = zeros(self.num_points, float64)
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
@@ -59,11 +60,11 @@
k_AB, k_BA, pB, dw_frq, dwH_frq = self.param_conversion(pA=self.pA,
kex=self.kex, dw=self.dw, dwH=self.dwH, sfrq=self.sfrq)
# Calculate the R2eff values.
- R2eff = r2eff_mmq_cr72(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq,
dwH=dwH_frq, kex=self.kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs,
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg,
num_points=self.num_points, power=self.ncyc)
+ r2eff_mmq_cr72(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq,
dwH=dwH_frq, kex=self.kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs,
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff,
num_points=self.num_points, power=self.ncyc)
# Check all R2eff values.
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, dwH=None,
sfrq=None):
r23583 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/