Author: tlinnet
Date: Wed Jun 18 20:17:29 2014
New Revision: 24141
URL: http://svn.gna.org/viewcvs/relax?rev=24141&view=rev
Log:
Implemented profiling script for LM63.
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.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py?rev=24141&r1=24140&r2=24141&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
Wed Jun 18 20:17:29 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_LM63,
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,
phi_ex=None, dw=None, pA=None, kex=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.
@@ -130,6 +130,8 @@
@type r2a: float
@keyword r2b: The transversal relaxation rate for state B
in the absence of exchange.
@type r2b: float
+ @keyword phi_ex: The phi_ex = pA.pB.dw**2 value (ppm^2)
+ @type phi_ex: float
@keyword dw: The chemical exchange difference between
states A and B in ppm.
@type dw: float
@keyword pA: The population of state A.
@@ -168,7 +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,
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, dw=dw, pA=pA, kex=kex, 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 +294,7 @@
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,
phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
"""Assemble the dispersion relaxation dispersion curve fitting
parameter vector.
@keyword r2: The transversal relaxation rate.
@@ -301,6 +303,8 @@
@type r2a: float
@keyword r2b: The transversal relaxation rate for state B
in the absence of exchange.
@type r2b: float
+ @keyword phi_ex: The phi_ex = pA.pB.dw**2 value (ppm^2)
+ @type phi_ex: float
@keyword dw: The chemical exchange difference between
states A and B in ppm.
@type dw: float
@keyword pA: The population of state A.
@@ -327,6 +331,8 @@
elif param_name == 'r2b':
value = r2b
value = value + mi + spin_index*0.1
+ elif param_name == 'phi_ex':
+ value = phi_ex + spin_index
elif param_name == 'dw':
value = dw + spin_index
elif param_name == 'pA':
@@ -377,6 +383,15 @@
# Then the chemical shift difference parameters 'phi_ex',
'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per
spin).
for spin_index in range(self.num_spins):
+ # Yield the data.
+ if 'phi_ex' in spins_params:
+ yield 'phi_ex', spin_index, 0
+ if 'phi_ex_B' in spins_params:
+ yield 'phi_ex_B', spin_index, 0
+ if 'phi_ex_C' in spins_params:
+ yield 'phi_ex_C', spin_index, 0
+ if 'padw2' in spins_params:
+ yield 'padw2', pspin_index, 0
if 'dw' in spins_params:
yield 'dw', spin_index, 0
@@ -399,11 +414,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_CR72(params)
+ chi2 = self.model.func_LM63(params)
return chi2
-def single(num_spins=1, model=MODEL_CR72, iter=None):
+def single(num_spins=1, model=MODEL_LM63, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -417,7 +432,7 @@
"""
# 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, phi_ex=3.0,
kex=1000.0, spins_params=['r2', 'phi_ex', 'kex'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -427,7 +442,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_CR72, iter=None):
+def cluster(num_spins=100, model=MODEL_LM63, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -441,7 +456,7 @@
"""
# 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, phi_ex=3.0,
kex=1000.0, spins_params=['r2', 'phi_ex', 'kex'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
r24141 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py