Author: tlinnet
Date: Fri Jun 20 19:44:05 2014
New Revision: 24223
URL: http://svn.gna.org/viewcvs/relax?rev=24223&view=rev
Log:
Moved parameter conversion for ns r1rho 3site inside lib 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/ns_r1rho_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py
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=24223&r1=24222&r2=24223&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py Fri Jun 20
19:44:05 2014
@@ -65,7 +65,7 @@
from lib.linear_algebra.matrix_exponential import matrix_exponential,
matrix_exponential_rankN
-def ns_r1rho_3site(M0=None, r1rho_prime=None, omega=None, offset=None,
r1=0.0, pA=None, pB=None, dw_AB=None, dw_AC=None, kex_AB=None, kex_BC=None,
kex_AC=None, spin_lock_fields=None, relax_time=None, inv_relax_time=None,
back_calc=None, num_points=None):
+def ns_r1rho_3site(M0=None, r1rho_prime=None, omega=None, offset=None,
r1=0.0, pA=None, pB=None, dw_AB=None, dw_BC=None, kex_AB=None, kex_BC=None,
kex_AC=None, spin_lock_fields=None, relax_time=None, inv_relax_time=None,
back_calc=None, num_points=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for
R1rho data.
This function calculates and stores the R1rho values.
@@ -87,8 +87,8 @@
@type pB: float
@keyword dw_AB: The chemical exchange difference between
states A and B in rad/s.
@type dw_AB: numpy float array of rank [NS][NM][NO][ND]
- @keyword dw_AC: The chemical exchange difference between
states A and C in rad/s.
- @type dw_AC: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dw_BC: The chemical exchange difference between
states B and C in rad/s.
+ @type dw_BC: numpy float array of rank [NS][NM][NO][ND]
@keyword kex_AB: The exchange rate between sites A and B for
3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)
@type kex_AB: float
@keyword kex_BC: The exchange rate between sites A and C for
3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)
@@ -108,6 +108,7 @@
"""
# Once off parameter conversions.
+ dw_AC = dw_AB + dw_BC
pC = 1.0 - pA - pB
pA_pB = pA + pB
pA_pC = pA + pC
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=24223&r1=24222&r2=24223&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun 20
19:44:05 2014
@@ -234,6 +234,7 @@
self.dwH_struct = deepcopy(numpy_array_zeros)
self.dw_AB_struct = deepcopy(numpy_array_zeros)
self.dw_AC_struct = deepcopy(numpy_array_zeros)
+ self.dw_BC_struct = deepcopy(numpy_array_zeros)
self.dwH_AB_struct = deepcopy(numpy_array_zeros)
self.dwH_AC_struct = deepcopy(numpy_array_zeros)
self.phi_ex_struct = deepcopy(numpy_array_zeros)
@@ -764,18 +765,15 @@
@rtype: float
"""
- # Once off parameter conversions.
- dw_AC = dw_AB + dw_BC
-
# Convert dw from ppm to rad/s. Use the out argument, to pass
directly to structure.
multiply( multiply.outer( dw_AB.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs, out=self.dw_AB_struct )
- multiply( multiply.outer( dw_AC.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs, out=self.dw_AC_struct )
+ multiply( multiply.outer( dw_BC.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs, out=self.dw_BC_struct )
# Reshape R20 to per experiment, spin and frequency.
self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE,
self.NS, self.NM), self.no_nd_ones )
# Back calculate the R2eff values for each experiment type.
- ns_r1rho_3site(M0=self.M0, r1rho_prime=self.r20_struct,
omega=self.chemical_shifts, offset=self.offset, r1=self.r1, pA=pA, pB=pB,
dw_AB=self.dw_AB_struct, dw_AC=self.dw_AC_struct, kex_AB=kex_AB,
kex_BC=kex_BC, kex_AC=kex_AC, spin_lock_fields=self.spin_lock_omega1,
relax_time=self.relax_times, inv_relax_time=self.inv_relax_times,
back_calc=self.back_calc, num_points=self.num_disp_points)
+ ns_r1rho_3site(M0=self.M0, r1rho_prime=self.r20_struct,
omega=self.chemical_shifts, offset=self.offset, r1=self.r1, pA=pA, pB=pB,
dw_AB=self.dw_AB_struct, dw_BC=self.dw_BC_struct, kex_AB=kex_AB,
kex_BC=kex_BC, kex_AC=kex_AC, spin_lock_fields=self.spin_lock_omega1,
relax_time=self.relax_times, inv_relax_time=self.inv_relax_times,
back_calc=self.back_calc, num_points=self.num_disp_points)
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24223 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_3site.py target_functions/relax_disp.py