Author: bugman
Date: Mon Jan 21 20:16:20 2013
New Revision: 18243
URL: http://svn.gna.org/viewcvs/relax?rev=18243&view=rev
Log:
Merged revisions 18242 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18242 | bugman | 2013-01-21 20:01:52 +0100 (Mon, 21 Jan 2013) | 6 lines
Added Monte Carlo simulation support for the paramagnetic centre for PCSs
in the N-state model.
As the paramagnetic centre position can be optimised, including in Monte
Carlo simulations, then it
makes sense to add this support.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/specific_fns/n_state_model.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Jan 21 20:16:20 2013
@@ -1,1 +1,1 @@
-/trunk:1-18239
+/trunk:1-18242
Modified: branches/frame_order_testing/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/n_state_model.py?rev=18243&r1=18242&r2=18243&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/n_state_model.py (original)
+++ branches/frame_order_testing/specific_fns/n_state_model.py Mon Jan 21
20:16:20 2013
@@ -82,8 +82,7 @@
def _assemble_param_vector(self, sim_index=None):
"""Assemble all the parameters of the model into a single array.
- @param sim_index: The index of the simulation to optimise.
This should be None if
- normal optimisation is desired.
+ @param sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
@type sim_index: None or int
@return: The parameter vector used for optimisation.
@rtype: numpy array
@@ -155,6 +154,11 @@
param_vector.append(0.0)
param_vector.append(0.0)
param_vector.append(0.0)
+
+ elif sim_index != None:
+
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][0])
+
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][1])
+
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][2])
else:
param_vector.append(cdp.paramagnetic_centre[0])
@@ -632,9 +636,16 @@
cdp.paramagnetic_centre = zeros(3, float64)
# The position.
- cdp.paramagnetic_centre[0] = param_vector[-3]
- cdp.paramagnetic_centre[1] = param_vector[-2]
- cdp.paramagnetic_centre[2] = param_vector[-1]
+ if sim_index == None:
+ cdp.paramagnetic_centre[0] = param_vector[-3]
+ cdp.paramagnetic_centre[1] = param_vector[-2]
+ cdp.paramagnetic_centre[2] = param_vector[-1]
+
+ # Monte Carlo simulated positions.
+ else:
+ cdp.paramagnetic_centre_sim[sim_index][0] = param_vector[-3]
+ cdp.paramagnetic_centre_sim[sim_index][1] = param_vector[-2]
+ cdp.paramagnetic_centre_sim[sim_index][2] = param_vector[-1]
def _elim_no_prob(self):
@@ -852,11 +863,13 @@
rdc_index = rdc_index + 1
- def _minimise_setup_atomic_pos(self):
+ def _minimise_setup_atomic_pos(self, sim_index=None):
"""Set up the atomic position data structures for optimisation using
PCSs and PREs as base data sets.
- @return: The atomic positions (the first index is the spins, the
second is the structures, and the third is the atomic coordinates) and the
paramagnetic centre.
- @rtype: numpy rank-3 array, numpy rank-1 array.
+ @keyword sim_index: The index of the simulation to optimise. This
should be None if normal optimisation is desired.
+ @type sim_index: None or int
+ @return: The atomic positions (the first index is the
spins, the second is the structures, and the third is the atomic coordinates)
and the paramagnetic centre.
+ @rtype: numpy rank-3 array, numpy rank-1 array.
"""
# Initialise.
@@ -883,7 +896,10 @@
# The paramagnetic centre.
if hasattr(cdp, 'paramagnetic_centre'):
- paramag_centre = array(cdp.paramagnetic_centre)
+ if sim_index != None and hasattr(cdp, 'paramag_centre_fixed')
and not cdp.paramag_centre_fixed:
+ paramag_centre =
array(cdp.paramagnetic_centre_sim[sim_index])
+ else:
+ paramag_centre = array(cdp.paramagnetic_centre)
else:
paramag_centre = zeros(3, float64)
@@ -1529,7 +1545,7 @@
# Get the atomic_positions.
atomic_pos, paramag_centre, centre_fixed = None, None, True
if 'pcs' in data_types or 'pre' in data_types:
- atomic_pos, paramag_centre = self._minimise_setup_atomic_pos()
+ atomic_pos, paramag_centre =
self._minimise_setup_atomic_pos(sim_index=sim_index)
# Optimisation of the centre.
if hasattr(cdp, 'paramag_centre_fixed'):
@@ -2447,7 +2463,11 @@
"""Initialise the Monte Carlo parameter values."""
# Get the minimisation statistic object names.
- min_names = self.data_names(set='min')
+ sim_names = self.data_names(set='min')
+
+ # Add the paramagnetic centre, if optimised.
+ if hasattr(cdp, 'paramag_centre_fixed') and not
cdp.paramag_centre_fixed:
+ sim_names += ['paramagnetic_centre']
# Alignments.
if hasattr(cdp, 'align_tensors'):
@@ -2468,8 +2488,8 @@
for j in range(cdp.sim_number):
cdp.align_tensors[i].set(param=object_name,
value=deepcopy(getattr(cdp.align_tensors[i], object_name)), category='sim',
sim_index=j)
- # Loop over all the minimisation object names.
- for object_name in min_names:
+ # Create all other simulation objects.
+ for object_name in sim_names:
# Name for the simulation object.
sim_object_name = object_name + '_sim'
r18243 - in /branches/frame_order_testing: ./ specific_fns/n_state_model.py