Author: tlinnet
Date: Tue Jul 22 17:53:43 2014
New Revision: 24644
URL: http://svn.gna.org/viewcvs/relax?rev=24644&view=rev
Log:
For model ns mmq 3site, moved the parameter conversion of dw_AB from target
function to 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_mmq_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py
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=24644&r1=24643&r2=24644&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Tue Jul 22
17:53:43 2014
@@ -210,7 +210,7 @@
return matrix
-def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64),
R20A=None, R20B=None, R20C=None, pA=None, pB=None, dw_AB=None, dw_AC=None,
dwH_AB=None, dwH_AC=None, kex_AB=None, kex_BC=None, kex_AC=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
+def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64),
R20A=None, R20B=None, R20C=None, pA=None, pB=None, dw_AB=None, dw_BC=None,
dwH_AB=None, dwH_BC=None, kex_AB=None, kex_BC=None, kex_AC=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for MQ
data.
The notation used here comes from:
@@ -240,12 +240,12 @@
@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 dwH_AB: The proton chemical exchange difference between
states A and B in rad/s.
@type dwH_AB: numpy float array of rank [NS][NM][NO][ND]
- @keyword dwH_AC: The proton chemical exchange difference between
states A and C in rad/s.
- @type dwH_AC: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dwH_BC: The proton chemical exchange difference between
states B and C in rad/s.
+ @type dwH_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)
@@ -265,6 +265,8 @@
"""
# Once off parameter conversions.
+ dw_AC = dw_AB + dw_BC
+ dwH_AC = dwH_AB + dwH_BC
pC = 1.0 - pA - pB
pA_pB = pA + pB
pA_pC = pA + pC
@@ -397,7 +399,7 @@
back_calc[si, mi, oi, i]= -inv_tcpmg[si, mi, oi, i]
* log(Mx / pA)
-def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], float64),
R20A=None, R20B=None, R20C=None, pA=None, pB=None, dw_AB=None, dw_AC=None,
dwH_AB=None, dwH_AC=None, kex_AB=None, kex_BC=None, kex_AC=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
+def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], float64),
R20A=None, R20B=None, R20C=None, pA=None, pB=None, dw_AB=None, dw_BC=None,
dwH_AB=None, dwH_BC=None, kex_AB=None, kex_BC=None, kex_AC=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for SQ,
ZQ, and DQ data.
The notation used here comes from:
@@ -423,12 +425,12 @@
@type pB: float
@keyword dw_AB: The combined chemical exchange difference
between states A and B in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
@type dw_AB: numpy float array of rank [NS][NM][NO][ND]
- @keyword dw_AC: The combined chemical exchange difference
between states A and C in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
- @type dw_AC: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dw_BC: The combined chemical exchange difference
between states B and C in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
+ @type dw_BC: numpy float array of rank [NS][NM][NO][ND]
@keyword dwH_AB: Unused - this is simply to match the
r2eff_mmq_3site_mq() function arguments.
@type dwH_AB: numpy float array of rank [NS][NM][NO][ND]
- @keyword dwH_AC: Unused - this is simply to match the
r2eff_mmq_3site_mq() function arguments.
- @type dwH_AC: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dwH_BC: Unused - this is simply to match the
r2eff_mmq_3site_mq() function arguments.
+ @type dwH_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)
@@ -448,6 +450,7 @@
"""
# 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=24644&r1=24643&r2=24644&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jul 22
17:53:43 2014
@@ -244,10 +244,9 @@
self.dw_struct = deepcopy(numpy_array_zeros)
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.dwH_BC_struct = deepcopy(numpy_array_zeros)
self.phi_ex_struct = deepcopy(numpy_array_zeros)
self.phi_ex_B_struct = deepcopy(numpy_array_zeros)
self.phi_ex_C_struct = deepcopy(numpy_array_zeros)
@@ -693,15 +692,11 @@
@rtype: float
"""
- # Once off parameter conversions.
- dw_AC = dw_AB + dw_BC
- dwH_AC = dwH_AB + dwH_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 )
multiply( multiply.outer( dwH_AB.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_AB_struct )
- multiply( multiply.outer( dwH_AC.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_AC_struct )
+ multiply( multiply.outer( dwH_BC.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_BC_struct )
# Reshape R20A and R20B to per experiment, spin and frequency.
self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS,
self.NM), self.no_nd_ones )
@@ -714,38 +709,38 @@
r20b = self.r20b_struct[ei]
r20c = self.r20b_struct[ei]
dw_AB_frq = self.dw_AB_struct[ei]
- dw_AC_frq = self.dw_AC_struct[ei]
+ dw_BC_frq = self.dw_BC_struct[ei]
dwH_AB_frq = self.dwH_AB_struct[ei]
- dwH_AC_frq = self.dwH_AC_struct[ei]
+ dwH_BC_frq = self.dwH_BC_struct[ei]
# Alias the dw frequency combinations.
aliased_dwH_AB = 0.0 * self.dwH_AB_struct[ei]
- aliased_dwH_AC = 0.0 * self.dwH_AC_struct[ei]
+ aliased_dwH_BC = 0.0 * self.dwH_BC_struct[ei]
if self.exp_types[ei] == EXP_TYPE_CPMG_SQ:
aliased_dw_AB = dw_AB_frq
- aliased_dw_AC = dw_AC_frq
+ aliased_dw_BC = dw_BC_frq
elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ:
aliased_dw_AB = dwH_AB_frq
- aliased_dw_AC = dwH_AC_frq
+ aliased_dw_BC = dwH_BC_frq
elif self.exp_types[ei] == EXP_TYPE_CPMG_DQ:
aliased_dw_AB = dw_AB_frq + dwH_AB_frq
- aliased_dw_AC = dw_AC_frq + dwH_AC_frq
+ aliased_dw_BC = dw_BC_frq + dwH_BC_frq
elif self.exp_types[ei] == EXP_TYPE_CPMG_ZQ:
aliased_dw_AB = dw_AB_frq - dwH_AB_frq
- aliased_dw_AC = dw_AC_frq - dwH_AC_frq
+ aliased_dw_BC = dw_BC_frq - dwH_BC_frq
elif self.exp_types[ei] == EXP_TYPE_CPMG_MQ:
aliased_dw_AB = dw_AB_frq
- aliased_dw_AC = dw_AC_frq
+ aliased_dw_BC = dw_BC_frq
aliased_dwH_AB = dwH_AB_frq
- aliased_dwH_AC = dwH_AC_frq
+ aliased_dwH_BC = dwH_BC_frq
elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_MQ:
aliased_dw_AB = dwH_AB_frq
- aliased_dw_AC = dwH_AC_frq
+ aliased_dw_BC = dwH_BC_frq
aliased_dwH_AB = dw_AB_frq
- aliased_dwH_AC = dw_AC_frq
+ aliased_dwH_BC = dw_BC_frq
# Back calculate the R2eff values for each experiment type.
- self.r2eff_ns_mmq[ei](M0=self.M0, R20A=r20a, R20B=r20b,
R20C=r20c, pA=pA, pB=pB, dw_AB=aliased_dw_AB, dw_AC=aliased_dw_AC,
dwH_AB=aliased_dwH_AB, dwH_AC=aliased_dwH_AC, kex_AB=kex_AB, kex_BC=kex_BC,
kex_AC=kex_AC, inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
+ self.r2eff_ns_mmq[ei](M0=self.M0, R20A=r20a, R20B=r20b,
R20C=r20c, pA=pA, pB=pB, dw_AB=aliased_dw_AB, dw_BC=aliased_dw_BC,
dwH_AB=aliased_dwH_AB, dwH_BC=aliased_dwH_BC, kex_AB=kex_AB, kex_BC=kex_BC,
kex_AC=kex_AC, inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24644 - in /branches/disp_spin_speed: lib/dispersion/ns_mmq_3site.py target_functions/relax_disp.py