Author: tlinnet
Date: Thu May 1 09:18:41 2014
New Revision: 22901
URL: http://svn.gna.org/viewcvs/relax?rev=22901&view=rev
Log:
Added model B14 to be found as target function.
sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014)
B14 model - 2-site exact solution model for all time scales.
Modified:
trunk/target_functions/relax_disp.py
Modified: trunk/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=22901&r1=22900&r2=22901&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Thu May 1 09:18:41 2014
@@ -2,6 +2,7 @@
#
#
# Copyright (C) 2013-2014 Edward d'Auvergne
#
# Copyright (C) 2009 Sebastien Morin
#
+# Copyright (C) 2014 Troels E. Linnet
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -29,6 +30,7 @@
from numpy import complex64, dot, float64, int16, zeros
# relax module imports.
+from lib.dispersion.b14 import r2eff_B14
from lib.dispersion.cr72 import r2eff_CR72
from lib.dispersion.dpl94 import r1rho_DPL94
from lib.dispersion.it99 import r2eff_IT99
@@ -52,7 +54,7 @@
from lib.errors import RelaxError
from lib.float import isNaN
from target_functions.chi2 import chi2
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL,
MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72,
MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_B14, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL,
MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LM63,
MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72,
MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE,
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
class Dispersion:
@@ -67,6 +69,7 @@
- 'No Rex': The model for no chemical exchange relaxation.
- 'LM63': The Luz and Meiboom (1963) 2-site fast exchange
model.
- 'LM63 3-site': The Luz and Meiboom (1963) 3-site fast
exchange model.
+ - 'B14': The Baldwin (2014) 2-site exact solution model for
all time scales.
- 'CR72': The reduced Carver and Richards (1972) 2-site model
for all time scales with R20A = R20B.
- 'CR72 full': The full Carver and Richards (1972) 2-site
model for all time scales.
- 'IT99': The Ishima and Torchia (1999) 2-site model for all
time scales with skewed populations (pA >> pB).
@@ -225,7 +228,7 @@
# The spin and frequency dependent R2 parameters.
self.end_index.append(self.num_exp * self.num_spins * self.num_frq)
- if model in [MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR_FULL]:
+ if model in [MODEL_B14, MODEL_CR72_FULL,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
self.end_index.append(2 * self.num_exp * self.num_spins *
self.num_frq)
# The spin and dependent parameters (phi_ex, dw, padw2).
@@ -340,6 +343,8 @@
self.func = self.func_LM63
if model == MODEL_LM63_3SITE:
self.func = self.func_LM63_3site
+ if model == MODEL_B14:
+ self.func = self.func_B14
if model == MODEL_CR72_FULL:
self.func = self.func_CR72_full
if model == MODEL_CR72:
@@ -758,6 +763,33 @@
raise RelaxError("The '%s' CPMG model is not compatible
with the '%s' experiment type." % (self.model, self.exp_types[0]))
+ def func_B14(self, params):
+ """Target function for the Baldwin (2014) 2-site exact solution
model for all time scales.
+
+ This assumes that pA > pB, and hence this must be implemented as a
constraint.
+
+
+ @param params: The vector of parameter values.
+ @type params: numpy rank-1 float array
+ @return: The chi-squared value.
+ @rtype: float
+ """
+
+ # Scaling.
+ if self.scaling_flag:
+ params = dot(params, self.scaling_matrix)
+
+ # Unpack the parameter values.
+ R20A = params[:self.end_index[0]]
+ R20B = params[self.end_index[0]:self.end_index[1]]
+ dw = params[self.end_index[1]:self.end_index[2]]
+ pA = params[self.end_index[2]]
+ kex = params[self.end_index[2]+1]
+
+ # Calculate and return the chi-squared value.
+ return self.calc_CR72_chi2(R20A=R20A, R20B=R20B, dw=dw, pA=pA,
kex=kex)
+
+
def func_CR72(self, params):
"""Target function for the reduced Carver and Richards (1972)
2-site exchange model on all time scales.
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Re: r22901 - /trunk/target_functions/relax_disp.py