Author: tlinnet
Date: Tue Jun 24 14:46:29 2014
New Revision: 24278
URL: http://svn.gna.org/viewcvs/relax?rev=24278&view=rev
Log:
Implemented profiling script for ns mmq 3site and 3site linear.
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_mmq_3site.py
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py?rev=24278&r1=24277&r2=24278&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site.py
Tue Jun 24 14:46:29 2014
@@ -53,14 +53,14 @@
# relax module imports.
from lib.physical_constants import g1H, g15N
from target_functions.relax_disp import Dispersion
-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
+from specific_analyses.relax_disp.variables import MODEL_NS_MMQ_3SITE,
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.
def main():
if True:
# Nr of iterations.
- nr_iter = 100
+ nr_iter = 10
# Print statistics.
verbose = True
@@ -337,9 +337,9 @@
elif param_name == 'dwH':
value = dwH + spin_index
elif param_name == 'dwH_AB':
- value = dw_AB + spin_index
+ value = dwH_AB + spin_index
elif param_name == 'dwH_BC':
- value = dw_BC + spin_index
+ value = dwH_BC + spin_index
elif param_name == 'pA':
value = pA
elif param_name == 'kex':
@@ -439,11 +439,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_mmq_CR72(params)
+ chi2 = self.model.func_ns_mmq_3site(params)
return chi2
-def single(num_spins=1, model=MODEL_MMQ_CR72, iter=None):
+def single(num_spins=1, model=MODEL_NS_MMQ_3SITE, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -457,7 +457,7 @@
"""
# Instantiate class
- 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'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, dwH_AB=0.01, dwH_BC=0.02, 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', 'dwH_AB',
'dwH_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):
@@ -467,7 +467,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_MMQ_CR72, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_MMQ_3SITE, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -481,7 +481,7 @@
"""
# Instantiate class
- 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'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, dwH_AB=0.01, dwH_BC=0.02, 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', 'dwH_AB',
'dwH_BC', 'pA', 'kex_AB', 'pB', 'kex_BC', 'kex_AC'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py?rev=24278&r1=24277&r2=24278&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_mmq_3site_linear.py
Tue Jun 24 14:46:29 2014
@@ -53,14 +53,14 @@
# relax module imports.
from lib.physical_constants import g1H, g15N
from target_functions.relax_disp import Dispersion
-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
+from specific_analyses.relax_disp.variables import
MODEL_NS_MMQ_3SITE_LINEAR, 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.
def main():
if True:
# Nr of iterations.
- nr_iter = 100
+ nr_iter = 10
# Print statistics.
verbose = True
@@ -337,9 +337,9 @@
elif param_name == 'dwH':
value = dwH + spin_index
elif param_name == 'dwH_AB':
- value = dw_AB + spin_index
+ value = dwH_AB + spin_index
elif param_name == 'dwH_BC':
- value = dw_BC + spin_index
+ value = dwH_BC + spin_index
elif param_name == 'pA':
value = pA
elif param_name == 'kex':
@@ -439,11 +439,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_mmq_CR72(params)
+ chi2 = self.model.func_ns_mmq_3site_linear(params)
return chi2
-def single(num_spins=1, model=MODEL_MMQ_CR72, iter=None):
+def single(num_spins=1, model=MODEL_NS_MMQ_3SITE_LINEAR, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -457,7 +457,7 @@
"""
# Instantiate class
- 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'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, dwH_AB=0.01, dwH_BC=0.02, pA=0.8, kex_AB=5000.0, pB=0.1,
kex_BC=3000.0, spins_params=['r2', 'dw_AB', 'dw_BC', 'dwH_AB', 'dwH_BC',
'pA', 'kex_AB', 'pB', 'kex_BC'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -467,7 +467,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_MMQ_CR72, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_MMQ_3SITE_LINEAR, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -481,7 +481,7 @@
"""
# Instantiate class
- 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'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0,
dw_BC=2.0, dwH_AB=0.01, dwH_BC=0.02, 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', 'dwH_AB',
'dwH_BC', 'pA', 'kex_AB', 'pB', 'kex_BC'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
r24278 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/