Author: tlinnet
Date: Tue May 6 17:27:12 2014
New Revision: 23018
URL: http://svn.gna.org/viewcvs/relax?rev=23018&view=rev
Log:
Added B14_FULL to the the target function.
The systemtest Relax_disp.test_baldwin_synthetic_full is now back and running.
sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014)
B14 model - 2-site exact solution model for all time scales.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
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=23018&r1=23017&r2=23018&view=diff
==============================================================================
--- trunk/target_functions/relax_disp.py (original)
+++ trunk/target_functions/relax_disp.py Tue May 6 17:27:12 2014
@@ -54,7 +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_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
+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_B14_FULL, 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:
@@ -73,7 +73,8 @@
- '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).
- 'TSMFK01': The Tollinger et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.
- - 'B14': The Baldwin (2014) 2-site exact solution model for all
time scales.
+ - 'B14': The Baldwin (2014) 2-site exact solution model for all
time scales with R20A = R20B..
+ - 'B14 full': The Baldwin (2014) 2-site exact solution model
for all time scales.
- 'M61': The Meiboom (1961) 2-site fast exchange model for
R1rho-type experiments.
- 'DPL94': The Davis, Perlman and London (1994) 2-site fast
exchange model for R1rho-type experiments.
- 'M61 skew': The Meiboom (1961) on-resonance 2-site model with
skewed populations (pA >> pB) for R1rho-type experiments.
@@ -228,7 +229,7 @@
# The spin and frequency dependent R2 parameters.
self.end_index.append(self.num_exp * self.num_spins * self.num_frq)
- if model in [MODEL_B14, MODEL_CR72_FULL,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
+ if model in [MODEL_B14, MODEL_B14_FULL, 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).
@@ -275,7 +276,7 @@
self.M0 = zeros(9, float64)
# Special CPMG-type data structures.
- if model in [MODEL_B14, MODEL_MMQ_CR72, 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_TSMFK01]:
+ if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72,
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_TSMFK01]:
# The number of CPMG blocks.
self.power = []
for ei in range(self.num_exp):
@@ -321,7 +322,7 @@
self.spin_lock_omega1_squared[ei][mi][oi] =
self.spin_lock_omega1[ei][mi][oi] ** 2
# The inverted relaxation delay.
- if model in [MODEL_B14, MODEL_MMQ_CR72, 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]:
+ if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72,
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]:
self.inv_relax_times = 1.0 / relax_times
# Special storage matrices for the multi-quantum CPMG N-site
numerical models.
@@ -352,6 +353,8 @@
if model == MODEL_TSMFK01:
self.func = self.func_TSMFK01
if model == MODEL_B14:
+ self.func = self.func_B14
+ if model == MODEL_B14_FULL:
self.func = self.func_B14_full
if model == MODEL_NS_CPMG_2SITE_3D_FULL:
self.func = self.func_ns_cpmg_2site_3D_full
r23018 - /trunk/target_functions/relax_disp.py