Author: tlinnet
Date: Tue Jun 24 14:17:59 2014
New Revision: 24273
URL: http://svn.gna.org/viewcvs/relax?rev=24273&view=rev
Log:
Added profiling script for model mmq cr72,
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_mmq_cr72.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py?rev=24273&r1=24272&r2=24273&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py
Tue Jun 24 14:17:59 2014
@@ -53,7 +53,7 @@
# 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_CPMG_SQ,
MODEL_CR72
+from specific_analyses.relax_disp.variables import MODEL_MMQ_CR72,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ
# Alter setup.
@@ -108,7 +108,7 @@
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, dw_AB=None, dw_BC=None, dwH=None, dwH_AB=None, dwH_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.
@@ -144,7 +144,8 @@
#self.fields = array([800. * 1E6])
#self.fields = array([600. * 1E6, 800. * 1E6])
self.fields = array([600. * 1E6, 800. * 1E6, 900. * 1E6])
- self.exp_type = [EXP_TYPE_CPMG_SQ]
+ # EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ
+ self.exp_type = [EXP_TYPE_CPMG_MQ]
self.offset = [0]
# Required data structures.
@@ -166,13 +167,13 @@
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, dw_AB=dw_AB, dw_BC=dw_BC, dwH=dwH, dwH_AB=dwH_AB, dwH_BC=dwH_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 = self.return_r2eff_arrays()
+ values, errors, cpmg_frqs, missing, frqs, frqs_H, exp_types,
relax_times, offsets = self.return_r2eff_arrays()
# Init the Dispersion Class.
- self.model = Dispersion(model=self.model, num_params=None,
num_spins=self.num_spins, num_frq=len(self.fields), exp_types=exp_types,
values=values, errors=errors, missing=missing, frqs=frqs, frqs_H=None,
cpmg_frqs=cpmg_frqs, spin_lock_nu1=None, chemical_shifts=None,
offset=offsets, tilt_angles=None, r1=None, relax_times=relax_times,
scaling_matrix=None)
+ self.model = Dispersion(model=self.model, num_params=None,
num_spins=self.num_spins, num_frq=len(self.fields), exp_types=exp_types,
values=values, errors=errors, missing=missing, frqs=frqs, frqs_H=frqs_H,
cpmg_frqs=cpmg_frqs, spin_lock_nu1=None, chemical_shifts=None,
offset=offsets, tilt_angles=None, r1=None, relax_times=relax_times,
scaling_matrix=None)
def return_r2eff_arrays(self):
@@ -248,6 +249,7 @@
# The Larmor frequency for this spin (and that of an
attached proton for the MMQ models) and field strength (in MHz*2pi to speed
up the ppm to rad/s conversion).
frqs[ei][si][mi] = 2.0 * pi * frq / g1H * g15N * 1e-6
+ frqs_H[ei][si][mi] = 2.0 * pi * frq * 1e-6
# Get the cpmg frq.
cpmg_frqs[ei][mi][oi] = self.points[mi]
@@ -288,10 +290,10 @@
missing[ei][si][mi][oi] =
array(missing[ei][si][mi][oi], int32)
# Return the structures.
- 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):
+ return values, errors, cpmg_frqs, missing, frqs, frqs_H, exp_types,
relax_times, offsets
+
+
+ def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None,
dw_AB=None, dw_BC=None, dwH=None, dwH_AB=None, dwH_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.
@@ -328,10 +330,28 @@
value = value + mi + spin_index*0.1
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 == 'dwH':
+ value = dwH + spin_index
+ elif param_name == 'dwH_AB':
+ value = dw_AB + spin_index
+ elif param_name == 'dwH_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)
@@ -378,6 +398,20 @@
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
+
+ # Then a separate block for the proton chemical shift difference
parameters for the MQ models (one per spin).
+ for spin_index in range(self.num_spins):
+
+ if 'dwH' in spins_params:
+ yield 'dwH', spin_index, 0
+ if 'dwH_AB' in spins_params:
+ yield 'dwH_AB', spin_index, 0
+ if 'dwH_BC' in spins_params:
+ yield 'dwH_BC', spin_index, 0
# All other parameters (one per spin cluster).
for param in spins_params:
@@ -386,7 +420,14 @@
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.
@@ -398,11 +439,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_CR72(params)
+ chi2 = self.model.func_mmq_CR72(params)
return chi2
-def single(num_spins=1, model=MODEL_CR72, iter=None):
+def single(num_spins=1, model=MODEL_MMQ_CR72, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -416,7 +457,7 @@
"""
# 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, dwH=0.03,
pA=0.9, kex=1000.0, spins_params=['r2', 'dw', 'dwH', 'pA', 'kex'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -426,7 +467,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_CR72, iter=None):
+def cluster(num_spins=100, model=MODEL_MMQ_CR72, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -440,7 +481,7 @@
"""
# 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, dwH=0.03,
pA=0.9, kex=1000.0, spins_params=['r2', 'dw', 'dwH', 'pA', 'kex'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
r24273 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mmq_cr72.py