Author: michaelbieri
Date: Tue Jul 13 01:35:11 2010
New Revision: 11297
URL: http://svn.gna.org/viewcvs/relax?rev=11297&view=rev
Log:
Merged revisions 11291-11296 via svnmerge from
svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/1.3
........
r11291 | bugman | 2010-07-08 19:45:21 +1000 (Thu, 08 Jul 2010) | 3 lines
Docstring improvements - the geometric info should be in Angstroms.
........
r11292 | bugman | 2010-07-08 19:49:35 +1000 (Thu, 08 Jul 2010) | 9 lines
Better support for the optimisation and mapping of the Ln3+ position.
The position is now treated in Angstrom, and is properly scaled. A few
additional API methods have
been added for the mapping of the optimisation space, and a few modified to
support the Ln3+
position.
........
r11293 | bugman | 2010-07-08 19:56:42 +1000 (Thu, 08 Jul 2010) | 3 lines
Fix for the Ln3+ position optimisation with no populations, the target
function was overwritten.
........
r11294 | bugman | 2010-07-08 21:03:13 +1000 (Thu, 08 Jul 2010) | 5 lines
Fix for the N-state model _assemble_scaling_matrix() method for the
2-domain model.
This is a recently introduced bug. For the 2-domain model, no alignment
parameters are optimised.
........
r11295 | bugman | 2010-07-08 21:49:04 +1000 (Thu, 08 Jul 2010) | 3 lines
Changed the alignment tensor parameter scaling back to 1 as this was
slowing down the optimisation.
........
r11296 | bugman | 2010-07-08 23:26:24 +1000 (Thu, 08 Jul 2010) | 3 lines
Created the n_state_model.elim_no_prob() to remove structures with zero
probability.
........
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/maths_fns/n_state_model.py
branches/bieri_gui/maths_fns/paramag_centre.py
branches/bieri_gui/prompt/n_state_model.py
branches/bieri_gui/specific_fns/n_state_model.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jul 13 01:35:11 2010
@@ -1,1 +1,1 @@
-/1.3:1-11289
+/1.3:1-11296
Modified: branches/bieri_gui/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/n_state_model.py?rev=11297&r1=11296&r2=11297&view=diff
==============================================================================
--- branches/bieri_gui/maths_fns/n_state_model.py (original)
+++ branches/bieri_gui/maths_fns/n_state_model.py Tue Jul 13 01:35:11 2010
@@ -375,7 +375,7 @@
self.d2Dij_theta = zeros((self.total_num_params,
self.total_num_params, self.num_align, self.num_spins), float64)
# Set the target function, gradient, and Hessian (paramagnetic
centre optimisation).
- if not centre_fixed:
+ if not self.centre_fixed:
self.func = self.func_population
self.dfunc = None
self.d2func = None
@@ -387,7 +387,7 @@
self.d2func = self.d2func_population
# Pure tensor optimisation overrides.
- if model == 'fixed':
+ if model == 'fixed' and self.centre_fixed:
# The probs are unpacked by self.func in the population model,
so just override that function.
self.func = self.func_tensor_opt
self.dfunc = self.dfunc_tensor_opt
Modified: branches/bieri_gui/maths_fns/paramag_centre.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/paramag_centre.py?rev=11297&r1=11296&r2=11297&view=diff
==============================================================================
--- branches/bieri_gui/maths_fns/paramag_centre.py (original)
+++ branches/bieri_gui/maths_fns/paramag_centre.py Tue Jul 13 01:35:11 2010
@@ -30,9 +30,9 @@
def paramag_data(atomic_pos, paramag_centre, unit_vector, r):
"""Calculate the electron spin to nuclear spin unit vectors and
distances.
- @param atomic_pos: The atomic positions. The first index is the
spins, the second is the structures, and the third is the atomic coordinates.
+ @param atomic_pos: The atomic positions in Angstrom. The first
index is the spins, the second is the structures, and the third is the atomic
coordinates.
@type atomic_pos: numpy rank-3 array
- @param paramag_centre: The paramagnetic centre position.
+ @param paramag_centre: The paramagnetic centre position in Angstrom.
@type paramag_centre: numpy rank-1, 3D array
@param unit_vector: The structure to fill with the electron spin to
nuclear spin unit vectors.
@type unit_vector: numpy rank-3 array
Modified: branches/bieri_gui/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/n_state_model.py?rev=11297&r1=11296&r2=11297&view=diff
==============================================================================
--- branches/bieri_gui/prompt/n_state_model.py (original)
+++ branches/bieri_gui/prompt/n_state_model.py Tue Jul 13 01:35:11 2010
@@ -163,6 +163,26 @@
n_state_model_obj._cone_pdb(cone_type=cone_type, scale=scale,
file=file, dir=dir, force=force)
+ def elim_no_prob(self):
+ """Eliminate the structures or states with no probability.
+
+ Examples
+ ~~~~~~~~
+
+ Simply type:
+
+ relax> n_state_model.elim_no_prob(N=8)
+ """
+
+ # Function intro text.
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "n_state_model.elim_no_prob()"
+ print(text)
+
+ # Execute the functional code.
+ n_state_model_obj._elim_no_prob()
+
+
def number_of_states(self, N=None):
"""Set the number of states in the N-state model.
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=11297&r1=11296&r2=11297&view=diff
==============================================================================
--- branches/bieri_gui/specific_fns/n_state_model.py (original)
+++ branches/bieri_gui/specific_fns/n_state_model.py Tue Jul 13 01:35:11 2010
@@ -61,6 +61,7 @@
# Place methods into the API.
self.overfit_deselect = self._overfit_deselect_dummy
+ self.return_conversion_factor = self._return_no_conversion_factor
self.test_grid_ops = self._test_grid_ops_general
@@ -175,16 +176,20 @@
if ('rdc' in data_types or 'pcs' in data_types) and not
(hasattr(cdp.align_tensors, 'fixed') and cdp.align_tensors.fixed):
pop_start = pop_start + 5*len(cdp.align_ids)
+ # The alignment parameters.
+ for i in range(5*len(cdp.align_ids)):
+ scaling_matrix[i, i] = 1.0
+
# Loop over the populations, and set the scaling factor.
if cdp.model in ['2-domain', 'population']:
- factor = 100.0
+ factor = 0.1
for i in xrange(pop_start, pop_start + (cdp.N-1)):
scaling_matrix[i, i] = factor
# The paramagnetic centre.
if hasattr(cdp, 'paramag_centre_fixed') and not
cdp.paramag_centre_fixed:
for i in range(-3, 0):
- scaling_matrix[i, i] = 1e10
+ scaling_matrix[i, i] = 1e2
# Return the matrix.
return scaling_matrix
@@ -537,6 +542,57 @@
cdp.paramagnetic_centre[0] = param_vector[-3]
cdp.paramagnetic_centre[1] = param_vector[-2]
cdp.paramagnetic_centre[2] = param_vector[-1]
+
+
+ def _elim_no_prob(self):
+ """Remove all structures or states which have no probability."""
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the model is setup.
+ if not hasattr(cdp, 'model'):
+ raise RelaxNoModelError('N-state')
+
+ # Test if there are populations.
+ if not hasattr(cdp, 'probs'):
+ raise RelaxError("The N-state model populations do not exist.")
+
+ # Loop over the structures.
+ i = 0
+ while 1:
+ # End condition.
+ if i == cdp.N - 1:
+ break
+
+ # No probability.
+ if cdp.probs[i] < 1e-5:
+ # Remove the probability.
+ cdp.probs.pop(i)
+
+ # Remove the structure.
+ cdp.structure.structural_data.pop(i)
+
+ # Eliminate bond vectors.
+ for spin in spin_loop():
+ # Position info.
+ if hasattr(spin, 'pos'):
+ spin.pos.pop(i)
+
+ # Vector info.
+ if hasattr(spin, 'xh_vect'):
+ spin.xh_vect.pop(i)
+ if hasattr(spin, 'bond_vect'):
+ spin.bond_vect.pop(i)
+
+ # Update N.
+ cdp.N -= 1
+
+ # Start the loop again without incrementing i.
+ continue
+
+ # Increment i.
+ i += 1
def _linear_constraints(self, data_types=None, scaling_matrix=None):
@@ -1674,8 +1730,8 @@
# The paramagnetic centre.
elif hasattr(cdp, 'paramag_centre_fixed') and not
cdp.paramag_centre_fixed and (n - i) <= 3:
- lower.append(-100e-10)
- upper.append(100e-10)
+ lower.append(-100)
+ upper.append(100)
# Otherwise this must be an alignment tensor component.
else:
@@ -1683,7 +1739,7 @@
upper.append(1e-3)
# Minimisation.
- self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
+ self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
def is_spin_param(self, name):
@@ -1701,6 +1757,22 @@
# All other parameters are global.
return False
+
+
+ def map_bounds(self, param, spin_id=None):
+ """Create bounds for the OpenDX mapping function.
+
+ @param param: The name of the parameter to return the lower
and upper bounds of.
+ @type param: str
+ @param spin_id: The spin identification string (unused).
+ @type spin_id: None
+ @return: The upper and lower bounds of the parameter.
+ @rtype: list of float
+ """
+
+ # Paramagnetic centre.
+ if search('^paramag_[xyz]$', param):
+ return [-100.0, 100.0]
def minimise(self, min_algor=None, min_options=None, func_tol=None,
grad_tol=None, max_iterations=None, constraints=False, scaling=True,
verbosity=0, sim_index=None, lower=None, upper=None, inc=None):
@@ -1767,7 +1839,14 @@
# Grid search.
if search('^[Gg]rid', min_algor):
- results = grid(func=model.func, args=(),
num_incs=min_options[0], lower=min_options[1], upper=min_options[2], A=A,
b=b, verbosity=verbosity)
+ # Scaling.
+ if scaling:
+ for i in xrange(len(param_vector)):
+ lower[i] = lower[i] / scaling_matrix[i, i]
+ upper[i] = upper[i] / scaling_matrix[i, i]
+
+ # The search.
+ results = grid(func=model.func, args=(), num_incs=inc,
lower=lower, upper=upper, A=A, b=b, verbosity=verbosity)
# Unpack the results.
param_vector, func, iter_count, warning = results
@@ -2043,6 +2122,23 @@
obj = getattr(cdp, obj_name)
obj[index] = value[i]
+ # The paramagnetic centre.
+ if search('^paramag_[xyz]$', obj_name):
+ # Init.
+ if not hasattr(cdp, 'paramagnetic_centre'):
+ cdp.paramagnetic_centre = zeros(3, float64)
+
+ # Set the coordinate.
+ if obj_name == 'paramag_x':
+ index = 0
+ elif obj_name == 'paramag_y':
+ index = 1
+ else:
+ index = 2
+
+ # Set the value in Angstrom.
+ cdp.paramagnetic_centre[index] = value[i]
+
# Set the spin parameters.
else:
for spin in spin_loop(spin_id):
r11297 - in /branches/bieri_gui: ./ maths_fns/ prompt/ specific_fns/