Author: tlinnet
Date: Tue Jun 24 10:43:06 2014
New Revision: 24265
URL: http://svn.gna.org/viewcvs/relax?rev=24265&view=rev
Log:
Modified profiling script for NS R1rho 3site, to be functional.
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_ns_r1rho_3site.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py?rev=24265&r1=24264&r2=24265&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
Tue Jun 24 10:43:06 2014
@@ -54,7 +54,7 @@
# relax module imports.
from lib.physical_constants import g1H, g15N
from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO,
MODEL_NS_R1RHO_3SITE
+from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO,
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR
# Alter setup.
@@ -109,7 +109,7 @@
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, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None,
kex_AB=None, pB=None, kex_BC=None, kex_AC=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.
@@ -172,7 +172,7 @@
self.chemical_shift = 1.0
# 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, dw=dw, dw_AB=dw_AB, dw_BC=dw_BC, pA=pA, kex=kex,
kex_AB=kex_AB, pB=pB, kex_BC=kex_BC, kex_AC=kex_AC,
spins_params=spins_params)
# Make nested list arrays of data. And return them.
values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times,
offsets, spin_lock_nu1 = self.return_r2eff_arrays()
@@ -402,7 +402,7 @@
return values, errors, None, missing, frqs, exp_types,
relax_times, offsets, asarray(spin_lock_nu1)
- 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, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None,
kex_AB=None, pB=None, kex_BC=None, kex_AC=None, spins_params=None):
"""Assemble the dispersion relaxation dispersion curve fitting
parameter vector.
@keyword r2: The transversal relaxation rate.
@@ -443,10 +443,22 @@
value = phi_ex + spin_index
elif param_name == 'dw':
value = dw + spin_index
+ elif param_name == 'dw_AB':
+ value = dw_AB + spin_index
+ elif param_name == 'dw_BC':
+ value = dw_BC + spin_index
elif param_name == 'pA':
value = pA
elif param_name == 'kex':
value = kex
+ elif param_name == 'kex_AB':
+ value = kex_AB
+ elif param_name == 'pB':
+ value = pB
+ elif param_name == 'kex_BC':
+ value = kex_BC
+ elif param_name == 'kex_AC':
+ value = kex_AC
# Add to the vector.
param_vector.append(value)
@@ -502,15 +514,31 @@
yield 'padw2', pspin_index, 0
if 'dw' in spins_params:
yield 'dw', spin_index, 0
+ if 'dw_AB' in spins_params:
+ yield 'dw_AB', spin_index, 0
+ if 'dw_BC' in spins_params:
+ yield 'dw_BC', spin_index, 0
# All other parameters (one per spin cluster).
for param in spins_params:
if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B',
'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB',
'dwH_BC', 'dwH_AB']:
if param == 'pA':
yield 'pA', 0, 0
+
elif param == 'kex':
yield 'kex', 0, 0
+ elif param == 'kex_AB':
+ yield 'kex_AB', 0, 0
+
+ elif param == 'pB':
+ yield 'pB', 0, 0
+
+ elif param == 'kex_BC':
+ yield 'kex_BC', 0, 0
+
+ elif param == 'kex_AC':
+ yield 'kex_AC', 0, 0
def calc(self, params):
"""Calculate chi2 values.
@@ -522,11 +550,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_ns_r1rho_2site(params)
+ chi2 = self.model.func_ns_r1rho_3site(params)
return chi2
-def single(num_spins=1, model=MODEL_NS_R1RHO_2SITE, iter=None):
+def single(num_spins=1, model=MODEL_NS_R1RHO_3SITE, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -540,7 +568,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9,
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0,
spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC',
'kex_AC'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -550,7 +578,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_NS_R1RHO_2SITE, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_R1RHO_3SITE, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -564,7 +592,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9,
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0,
spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC',
'kex_AC'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
Re: r24265 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py