Author: tlinnet
Date: Wed Jun 18 17:11:24 2014
New Revision: 24103
URL: http://svn.gna.org/viewcvs/relax?rev=24103&view=rev
Log:
Moved the Ãparter conversion in LM63 3site into the lib function.
This cleans up the target api function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/lm63_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py
Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63_3site.py?rev=24103&r1=24102&r2=24103&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/lm63_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63_3site.py Wed Jun 18
17:11:24 2014
@@ -69,7 +69,7 @@
from numpy.ma import fix_invalid, masked_where
-def r2eff_LM63_3site(r20=None, rex_B=None, rex_C=None, quart_kB=None,
quart_kC=None, cpmg_frqs=None, back_calc=None):
+def r2eff_LM63_3site(r20=None, phi_ex_B=None, phi_ex_C=None, kB=None,
kC=None, cpmg_frqs=None, back_calc=None):
"""Calculate the R2eff values for the LM63 3-site model.
See the module docstring for details.
@@ -77,19 +77,29 @@
@keyword r20: The R20 parameter value (R2 with no exchange).
@type r20: numpy float array of rank [NS][NM][NO][ND]
- @keyword rex_B: The phi_ex_B / kB parameter value.
- @type rex_B: numpy float array of rank [NS][NM][NO][ND]
- @keyword rex_C: The phi_ex_C / kC parameter value.
- @type rex_C: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword quart_kB: Approximate chemical exchange rate constant
between sites A and B (the exchange rate in rad/s) divided by 4.
- @type quart_kB: float
- @keyword quart_kC: Approximate chemical exchange rate constant
between sites A and C (the exchange rate in rad/s) divided by 4.
- @type quart_kC: float
+ @keyword phi_ex_B: The fast exchange factor between sites A and B
(ppm^2)
+ @type phi_ex_B: numpy float array of rank [NS][NM][NO][ND]
+ @keyword phi_ex_C: The fast exchange factor between sites A and C
(ppm^2)
+ @type phi_ex_C: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword kB: Approximate chemical exchange rate constant
between sites A and B (the exchange rate in rad/s).
+ @type kB: float
+ @keyword kC: Approximate chemical exchange rate constant
between sites A and C (the exchange rate in rad/s).
+ @type kC: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: numpy float array of rank [NE][NS][NM][NO][ND]
@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 float array of rank [NE][NS][NM][NO][ND]
"""
+
+ # Once off parameter conversions.
+ # The phi_ex_B / kB parameter value.
+ rex_B = phi_ex_B / kB
+ # The phi_ex_C / kC parameter value.
+ rex_C = phi_ex_C / kC
+ # Approximate chemical exchange rate constant between sites A and B (the
exchange rate in rad/s) divided by 4.
+ quart_kB = kB / 4.0
+ # Approximate chemical exchange rate constant between sites A and C (the
exchange rate in rad/s) divided by 4.
+ quart_kC = kC / 4.0
# Flag to tell if values should be replaced.
t_rex_zero = False
Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24103&r1=24102&r2=24103&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18
17:11:24 2014
@@ -1062,21 +1062,15 @@
kB = params[self.end_index[2]]
kC = params[self.end_index[2]+1]
- # Once off parameter conversions.
- rex_B = phi_ex_B / kB
- rex_C = phi_ex_C / kC
- quart_kB = kB / 4.0
- quart_kC = kC / 4.0
-
# Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
- multiply( multiply.outer( rex_B.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_B_struct )
- multiply( multiply.outer( rex_C.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_C_struct )
+ multiply( multiply.outer( phi_ex_B.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_B_struct )
+ multiply( multiply.outer( phi_ex_C.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_C_struct )
# Reshape R20 to per experiment, spin and frequency.
self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
# Back calculate the R2eff values.
- r2eff_LM63_3site(r20=self.r20_struct, rex_B=self.phi_ex_B_struct,
rex_C=self.phi_ex_C_struct, quart_kB=quart_kB, quart_kC=quart_kC,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc)
+ r2eff_LM63_3site(r20=self.r20_struct, phi_ex_B=self.phi_ex_B_struct,
phi_ex_C=self.phi_ex_C_struct, kB=kB, kC=kC, cpmg_frqs=self.cpmg_frqs,
back_calc=self.back_calc)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24103 - in /branches/disp_spin_speed: lib/dispersion/lm63_3site.py target_functions/relax_disp.py