Author: tlinnet
Date: Mon Jun 23 16:23:31 2014
New Revision: 24250
URL: http://svn.gna.org/viewcvs/relax?rev=24250&view=rev
Log:
Implemented profiling script for LM63, 3 site.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py?rev=24250&r1=24249&r2=24250&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py
Mon Jun 23 16:23:31 2014
@@ -55,7 +55,7 @@
from lib.physical_constants import g1H, g15N
from target_functions.chi2 import chi2
from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_LM63,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_LM63, MODEL_LM63_3SITE,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
# Alter setup.
@@ -110,7 +110,7 @@
Class Profile inherits the Dispersion container class object.
"""
- def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None,
phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
+ def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None,
phi_ex=None, phi_ex_B=None, phi_ex_C=None, dw=None, pA=None, kex=None,
kB=None, kC=None, spins_params=None):
"""
Special method __init__() is called first (acts as Constructor).
It brings in data from outside the class like the variable num_spins.
@@ -170,7 +170,7 @@
self.error.append([1.0]*len(cpmg_point))
# Assemble param vector.
- self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b,
phi_ex=phi_ex, dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+ self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b,
phi_ex=phi_ex, phi_ex_B=phi_ex_B, phi_ex_C=phi_ex_C, dw=dw, pA=pA, kex=kex,
kB=kB, kC=kC, spins_params=spins_params)
# Make nested list arrays of data. And return them.
values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times,
offsets = self.return_r2eff_arrays()
@@ -295,7 +295,7 @@
return values, errors, cpmg_frqs, missing, frqs, exp_types,
relax_times, offsets
- def assemble_param_vector(self, r2=None, r2a=None, r2b=None,
phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
+ def assemble_param_vector(self, r2=None, r2a=None, r2b=None,
phi_ex=None, phi_ex_B=None, phi_ex_C=None, dw=None, pA=None, kex=None,
kB=None, kC=None, spins_params=None):
"""Assemble the dispersion relaxation dispersion curve fitting
parameter vector.
@keyword r2: The transversal relaxation rate.
@@ -306,12 +306,20 @@
@type r2b: float
@keyword phi_ex: The phi_ex = pA.pB.dw**2 value (ppm^2)
@type phi_ex: float
+ @keyword phi_ex_B: The fast exchange factor between sites A and
B (ppm^2)
+ @type phi_ex_B: float
+ @keyword phi_ex_C: The fast exchange factor between sites A and
C (ppm^2)
+ @type phi_ex_C: float
@keyword dw: The chemical exchange difference between
states A and B in ppm.
@type dw: float
@keyword pA: The population of state A.
@type pA: float
@keyword kex: The rate of exchange.
@type kex: float
+ @keyword kB : The rate of exchange.
+ @type kB: float
+ @keyword kC: The rate of exchange.
+ @type kC: float
@keyword spins_params: List of parameter strings used in dispersion
model.
@type spins_params: array of strings
@return: An array of the parameter values of the
dispersion relaxation model.
@@ -334,12 +342,20 @@
value = value + mi + spin_index*0.1
elif param_name == 'phi_ex':
value = phi_ex + spin_index
+ elif param_name == 'phi_ex_B':
+ value = phi_ex_B + spin_index
+ elif param_name == 'phi_ex_C':
+ value = phi_ex_C + spin_index
elif param_name == 'dw':
value = dw + spin_index
elif param_name == 'pA':
value = pA
elif param_name == 'kex':
value = kex
+ elif param_name == 'kB':
+ value = kB
+ elif param_name == 'kC':
+ value = kC
# Add to the vector.
param_vector.append(value)
@@ -392,7 +408,7 @@
if 'phi_ex_C' in spins_params:
yield 'phi_ex_C', spin_index, 0
if 'padw2' in spins_params:
- yield 'padw2', pspin_index, 0
+ yield 'padw2', spin_index, 0
if 'dw' in spins_params:
yield 'dw', spin_index, 0
@@ -403,6 +419,10 @@
yield 'pA', 0, 0
elif param == 'kex':
yield 'kex', 0, 0
+ elif param == 'kB':
+ yield 'kB', 0, 0
+ elif param == 'kC':
+ yield 'kC', 0, 0
def calc(self, params):
@@ -415,11 +435,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_LM63(params)
+ chi2 = self.model.func_LM63_3site(params)
return chi2
-def single(num_spins=1, model=MODEL_LM63, iter=None):
+def single(num_spins=1, model=MODEL_LM63_3SITE, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -433,7 +453,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=3.0,
kex=1000.0, spins_params=['r2', 'phi_ex', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex_B=3.0,
phi_ex_C=4.0, kB=2000.0, kC=1000.0, spins_params=['r2', 'phi_ex_B',
'phi_ex_C', 'kB', 'kC'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -443,7 +463,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_LM63, iter=None):
+def cluster(num_spins=100, model=MODEL_LM63_3SITE, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -457,7 +477,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=3.0,
kex=1000.0, spins_params=['r2', 'phi_ex', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex_B=3.0,
phi_ex_C=4.0, kB=2000.0, kC=1000.0, spins_params=['r2', 'phi_ex_B',
'phi_ex_C', 'kB', 'kC'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
@@ -467,4 +487,4 @@
# Execute main function.
if __name__ == "__main__":
- main()
+ main()
r24250 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63_3site.py