Author: bugman
Date: Sun Mar 23 01:18:50 2008
New Revision: 5169
URL: http://svn.gna.org/viewcvs/relax?rev=5169&view=rev
Log:
Started the break up of the insanely complex model-free minimisation methods
in specific_fns.
The configuration of the spin specific part of the grid search has been
shifted into its own
function.
Modified:
1.3/specific_fns/model_free/mf_minimise.py
Modified: 1.3/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/mf_minimise.py?rev=5169&r1=5168&r2=5169&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/mf_minimise.py (original)
+++ 1.3/specific_fns/model_free/mf_minimise.py Sun Mar 23 01:18:50 2008
@@ -531,38 +531,8 @@
if index != None and i != index:
continue
- # Loop over the model-free parameters.
- for j in xrange(len(spin.params)):
- # Local tm.
- if spin.params[j] == 'local_tm':
- min_options.append([inc[m], 1.0 * 1e-9, 12.0 * 1e-9])
-
- # {S2, S2f, S2s}.
- elif match('S2', spin.params[j]):
- min_options.append([inc[m], 0.0, 1.0])
-
- # {te, tf, ts}.
- elif match('t', spin.params[j]):
- min_options.append([inc[m], 0.0, 500.0 * 1e-12])
-
- # Rex.
- elif spin.params[j] == 'Rex':
- min_options.append([inc[m], 0.0, 5.0 / (2.0 * pi *
spin.frq[0])**2])
-
- # Bond length.
- elif spin.params[j] == 'r':
- min_options.append([inc[m], 1.0 * 1e-10, 1.05 *
1e-10])
-
- # CSA.
- elif spin.params[j] == 'CSA':
- min_options.append([inc[m], -120 * 1e-6, -200 *
1e-6])
-
- # Unknown option.
- else:
- raise RelaxError, "Unknown model-free parameter."
-
- # Increment m.
- m = m + 1
+ # Get the spin specific configuration.
+ m = self.grid_search_config_spin(min_options, spin, inc, m)
# Set the lower and upper bounds if these are supplied.
if lower != None:
@@ -588,6 +558,65 @@
# Minimisation.
self.minimise(min_algor='grid', min_options=min_options,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+
+
+ def grid_search_config_spin(min_options, spin, inc, m):
+ """Set up of the grid search for a single spin.
+
+ This method appends the grid search configuration details to
min_options list. These
+ details are in the form of a list consisting of the number of
increments, lower bound, and
+ upper bound for the corresponding residue. The ordering of the
lists in min_options matches
+ that of the params list in the spin container.
+
+ @param min_options: An array to append the grid search configuration
details to.
+ @type min_options: list
+ @param spin: A SpinContainer object.
+ @type spin: class instance
+ @param inc: The increments for each dimension of the space
for the grid search. The
+ number of elements in the array must equal to
the number of parameters
+ in the model.
+ @type inc: array of int
+ @param m: The parameter index for the complete model.
+ @type m: int
+ @return: The index of the last parameter encountered (m).
+ @rtype: int
+ """
+
+ # Loop over the model-free parameters.
+ for i in xrange(len(spin.params)):
+ # Local tm.
+ if spin.params[i] == 'local_tm':
+ min_options.append([inc[m], 1.0 * 1e-9, 12.0 * 1e-9])
+
+ # {S2, S2f, S2s}.
+ elif match('S2', spin.params[i]):
+ min_options.append([inc[m], 0.0, 1.0])
+
+ # {te, tf, ts}.
+ elif match('t', spin.params[i]):
+ min_options.append([inc[m], 0.0, 500.0 * 1e-12])
+
+ # Rex.
+ elif spin.params[i] == 'Rex':
+ min_options.append([inc[m], 0.0, 5.0 / (2.0 * pi *
spin.frq[0])**2])
+
+ # Bond length.
+ elif spin.params[i] == 'r':
+ min_options.append([inc[m], 1.0 * 1e-10, 1.05 * 1e-10])
+
+ # CSA.
+ elif spin.params[i] == 'CSA':
+ min_options.append([inc[m], -120 * 1e-6, -200 * 1e-6])
+
+ # Unknown option.
+ else:
+ raise RelaxError, "Unknown model-free parameter."
+
+ # Increment m.
+ m = m + 1
+
+ # Return the parameter index.
+ return m
def minimise(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, constraints=0, scaling=1, verbosity=0,
sim_index=None):
r5169 - /1.3/specific_fns/model_free/mf_minimise.py