Author: tlinnet
Date: Wed Jun 18 20:17:26 2014
New Revision: 24140
URL: http://svn.gna.org/viewcvs/relax?rev=24140&view=rev
Log:
Added profiling script for IT99.
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_it99.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py?rev=24140&r1=24139&r2=24140&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
Wed Jun 18 20:17:26 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_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_IT99,
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,
dw=None, pA=None, kex=None, spins_params=None):
+ def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None,
dw=None, pA=None, kex=None, tex=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.
@@ -168,7 +168,7 @@
self.error.append([1.0]*len(cpmg_point))
# Assemble param vector.
- self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b,
dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+ self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b,
dw=dw, pA=pA, kex=kex, tex=tex, 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()
@@ -292,7 +292,7 @@
return values, errors, cpmg_frqs, missing, frqs, exp_types,
relax_times, offsets
- def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None,
pA=None, kex=None, spins_params=None):
+ def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None,
pA=None, kex=None, tex=None, spins_params=None):
"""Assemble the dispersion relaxation dispersion curve fitting
parameter vector.
@keyword r2: The transversal relaxation rate.
@@ -333,6 +333,8 @@
value = pA
elif param_name == 'kex':
value = kex
+ elif param_name == 'tex':
+ value = tex
# Add to the vector.
param_vector.append(value)
@@ -387,6 +389,8 @@
yield 'pA', 0, 0
elif param == 'kex':
yield 'kex', 0, 0
+ elif param == 'tex':
+ yield 'tex', 0, 0
def calc(self, params):
@@ -399,11 +403,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_CR72(params)
+ chi2 = self.model.func_IT99(params)
return chi2
-def single(num_spins=1, model=MODEL_CR72, iter=None):
+def single(num_spins=1, model=MODEL_IT99, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -417,7 +421,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9,
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9,
tex=1/1000.0, spins_params=['r2', 'dw', 'pA', 'tex'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -427,7 +431,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_CR72, iter=None):
+def cluster(num_spins=2, model=MODEL_IT99, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -441,7 +445,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9,
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9,
tex=1/1000.0, spins_params=['r2', 'dw', 'pA', 'tex'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
r24140 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py