Author: bugman
Date: Mon Oct 14 15:31:50 2013
New Revision: 21093
URL: http://svn.gna.org/viewcvs/relax?rev=21093&view=rev
Log:
Updated the dispersion grid search function to user the loop_parameters()
function.
This is an important fix as the
specific_analyses.relax_disp.optimisation.grid_search_setup()
function was not matching the rest of the dispersion code, hence the
parameters of the grid
increments and bounds were not matching the parameter vector, scaling matrix,
target function
parameter depacking, etc.
Modified:
branches/relax_disp/specific_analyses/relax_disp/optimisation.py
Modified: branches/relax_disp/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/optimisation.py?rev=21093&r1=21092&r2=21093&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Mon Oct
14 15:31:50 2013
@@ -91,85 +91,80 @@
# The R2eff model.
if cdp.model_type == 'R2eff':
- for spin_index in range(len(spins)):
- # Alias the spin.
- spin = spins[spin_index]
-
- # Loop over each spectrometer frequency and dispersion point.
- for exp_type, frq, point in loop_exp_frq_point():
- # Loop over the parameters.
- for i in range(len(spin.params)):
- # R2eff relaxation rate (from 1 to 40 s^-1).
- if spin.params[i] == 'r2eff':
- lower.append(1.0)
- upper.append(40.0)
-
- # Intensity.
- elif spin.params[i] == 'i0':
- lower.append(0.0001)
- upper.append(max(spin.intensities.values()))
+ # Loop over each spectrometer frequency and dispersion point.
+ for exp_type, frq, point in loop_exp_frq_point():
+ # Loop over the parameters.
+ for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
+ # R2eff relaxation rate (from 1 to 40 s^-1).
+ if param_name == 'r2eff':
+ lower.append(1.0)
+ upper.append(40.0)
+
+ # Intensity.
+ elif param_name == 'i0':
+ lower.append(0.0001)
+
upper.append(max(spins[spin_index].intensities.values()))
# All other models.
else:
- # The spin specific parameters.
- for spin in spins:
- for i in range(len(spin.params)):
- # R2 relaxation rates (from 1 to 40 s^-1).
- if spin.params[i] in ['r2', 'r2a', 'r2b']:
- lower.append(1.0)
- upper.append(40.0)
-
- # The pA.pB.dw**2 and pA.dw**2 parameters.
- elif spin.params[i] in ['phi_ex', 'phi_ex_B',
'phi_ex_C', 'padw2']:
- lower.append(0.0)
- upper.append(10.0)
-
- # Chemical shift difference between states A and B.
- elif spin.params[i] in ['dw', 'dwH']:
- lower.append(0.0)
- upper.append(10.0)
-
- # The cluster specific parameters (only use the values from the
first spin of the cluster).
- spin = spins[0]
- for i in range(len(spin.params)):
+ # Loop over the parameters.
+ for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
+ # Cluster specific parameter.
+ if spin_index == None:
+ spin_index = 0
+
+ # R2 relaxation rates (from 1 to 40 s^-1).
+ if param_name in ['r2', 'r2a', 'r2b']:
+ lower.append(1.0)
+ upper.append(40.0)
+
+ # The pA.pB.dw**2 and pA.dw**2 parameters.
+ elif param_name in ['phi_ex', 'phi_ex_B', 'phi_ex_C',
'padw2']:
+ lower.append(0.0)
+ upper.append(10.0)
+
+ # Chemical shift difference between states A and B.
+ elif param_name in ['dw', 'dwH']:
+ lower.append(0.0)
+ upper.append(10.0)
+
# The population of state A.
- if spin.params[i] == 'pA':
- if spin.model == MODEL_M61B:
+ elif param_name == 'pA':
+ if spins[spin_index].model == MODEL_M61B:
lower.append(0.85)
else:
lower.append(0.5)
upper.append(1.0)
# Exchange rates.
- elif spin.params[i] in ['kex', 'k_AB', 'kB', 'kC']:
+ elif param_name in ['kex', 'k_AB', 'kB', 'kC']:
lower.append(1.0)
upper.append(100000.0)
# Time of exchange.
- elif spin.params[i] in ['tex']:
+ elif param_name in ['tex']:
lower.append(1/200000.0)
upper.append(0.5)
# Pre-set parameters.
- index = 0
- for spin_index in range(len(spins)):
- for param in spins[spin_index].params:
- # Get the parameter.
- if hasattr(spins[spin_index], param):
- val = getattr(spins[spin_index], param)
-
- # Value already set.
- if is_float(val) and val != 0.0:
- # Printout.
- print("The spin '%s' parameter '%s' is pre-set to %s,
skipping it in the grid search." % (spin_ids[spin_index], param, val))
-
- # Turn of the grid search for this parameter.
- inc[index] = 1
- lower[index] = val
- upper[index] = val
-
- # Increment the parameter index.
- index += 1
+ for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins):
+ # Cluster specific parameter.
+ if spin_index == None:
+ spin_index = 0
+
+ # Get the parameter.
+ if hasattr(spins[spin_index], param_name):
+ val = getattr(spins[spin_index], param_name)
+
+ # Value already set.
+ if is_float(val) and val != 0.0:
+ # Printout.
+ print("The spin '%s' parameter '%s' is pre-set to %s,
skipping it in the grid search." % (spin_ids[spin_index], param_name, val))
+
+ # Turn of the grid search for this parameter.
+ inc[param_index] = 1
+ lower[param_index] = val
+ upper[param_index] = val
# The full grid size.
grid_size = 1
r21093 - /branches/relax_disp/specific_analyses/relax_disp/optimisation.py