Author: bugman
Date: Mon Oct 24 23:35:10 2011
New Revision: 14908
URL: http://svn.gna.org/viewcvs/relax?rev=14908&view=rev
Log:
Extended the N-state model analysis to allow a separate paramagnetic centre
per state.
Modified:
1.3/maths_fns/n_state_model.py
1.3/maths_fns/paramag_centre.py
1.3/specific_fns/n_state_model.py
Modified: 1.3/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/n_state_model.py?rev=14908&r1=14907&r2=14908&view=diff
==============================================================================
--- 1.3/maths_fns/n_state_model.py (original)
+++ 1.3/maths_fns/n_state_model.py Mon Oct 24 23:35:10 2011
@@ -22,13 +22,13 @@
# Python module imports.
from math import sqrt
-from numpy import array, dot, float64, ones, transpose, zeros
+from numpy import array, dot, float64, ones, rank, transpose, zeros
# relax module imports.
from alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy, dAi_dAxz,
dAi_dAyz, to_tensor
from chi2 import chi2, dchi2_element, d2chi2_element
from float import isNaN
-from paramag_centre import paramag_data
+from paramag_centre import vectors_single_centre, vectors_centre_per_state
from pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn, pcs_tensor
from physical_constants import pcs_constant
from rdc import ave_rdc_tensor, ave_rdc_tensor_dDij_dAmn, rdc_tensor
@@ -141,8 +141,8 @@
@type dip_const: numpy rank-1 array
@keyword atomic_pos: The atomic positions of all spins. The
first index is the spin systems j and the second is the structure or state c.
@type atomic_pos: numpy rank-3 array
- @keyword paramag_centre: The paramagnetic centre position.
- @type paramag_centre: numpy rank-1 array
+ @keyword paramag_centre: The paramagnetic centre position (or
positions).
+ @type paramag_centre: numpy rank-1, 3D array or rank-2, Nx3
array
@keyword scaling_matrix: The square and diagonal scaling matrix.
@type scaling_matrix: numpy rank-2 array
@keyword centre_fixed: A flag which if False will cause the
paramagnetic centre to be optimised.
@@ -1614,7 +1614,10 @@
"""Calculate the paramagnetic centre to spin vectors, distances and
constants."""
# Get the vectors and distances.
- paramag_data(self.atomic_pos, self.paramag_centre,
self.paramag_unit_vect, self.paramag_dist)
+ if rank(self.paramag_centre) == 1:
+ vectors_single_centre(self.atomic_pos, self.paramag_centre,
self.paramag_unit_vect, self.paramag_dist)
+ else:
+ vectors_centre_per_state(self.atomic_pos, self.paramag_centre,
self.paramag_unit_vect, self.paramag_dist)
# The PCS constants.
for i in range(self.num_align):
Modified: 1.3/maths_fns/paramag_centre.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/paramag_centre.py?rev=14908&r1=14907&r2=14908&view=diff
==============================================================================
--- 1.3/maths_fns/paramag_centre.py (original)
+++ 1.3/maths_fns/paramag_centre.py Mon Oct 24 23:35:10 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2010 Edward d'Auvergne
#
+# Copyright (C) 2010-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -27,8 +27,44 @@
from numpy.linalg import norm
-def paramag_data(atomic_pos, paramag_centre, unit_vector, r):
+def vectors_centre_per_state(atomic_pos, paramag_centre, unit_vector, r):
"""Calculate the electron spin to nuclear spin unit vectors and
distances.
+
+ This assumes that there is one paramagnetic centre per state of the
system.
+
+
+ @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 in Angstrom.
+ @type paramag_centre: numpy rank-2, Nx3 array
+ @param unit_vector: The structure to fill with the electron spin to
nuclear spin unit vectors.
+ @type unit_vector: numpy rank-3 array
+ @param r: The structure to fill with the electron spin to
nuclear spin distances.
+ @type r: numpy rank-2 array
+ """
+
+ # Loop over the spins.
+ for i in range(len(atomic_pos)):
+ # Loop over the states.
+ for c in range(len(atomic_pos[i])):
+ # The vector.
+ vect = atomic_pos[i, c] - paramag_centre[c]
+
+ # The length.
+ r[i, c] = norm(vect)
+
+ # The unit vector.
+ unit_vector[i, c] = vect / r[i, c]
+
+ # Convert the distances from Angstrom to meters.
+ r[i, c] = r[i, c] * 1e-10
+
+
+def vectors_single_centre(atomic_pos, paramag_centre, unit_vector, r):
+ """Calculate the electron spin to nuclear spin unit vectors and
distances.
+
+ This assumes that there is only one paramagnetic centre for all states
of the system.
+
@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
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=14908&r1=14907&r2=14908&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Mon Oct 24 23:35:10 2011
@@ -836,7 +836,7 @@
# The paramagnetic centre.
if hasattr(cdp, 'paramagnetic_centre'):
- paramag_centre = cdp.paramagnetic_centre
+ paramag_centre = array(cdp.paramagnetic_centre)
else:
paramag_centre = zeros(3, float64)
r14908 - in /1.3: maths_fns/n_state_model.py maths_fns/paramag_centre.py specific_fns/n_state_model.py