r11647 - /branches/bmrb/generic_fns/diffusion_tensor.py -- October 21, 2010 - 23:42

Author: bugman
Date: Thu Oct 21 23:42:05 2010
New Revision: 11647

URL: http://svn.gna.org/viewcvs/relax?rev=11647&view=rev
Log:
The prolate diffusion tensors are now correctly created from the BMRB files.


Modified:
    branches/bmrb/generic_fns/diffusion_tensor.py

Modified: branches/bmrb/generic_fns/diffusion_tensor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/diffusion_tensor.py?rev=11647&r1=11646&r2=11647&view=diff
==============================================================================
--- branches/bmrb/generic_fns/diffusion_tensor.py (original)
+++ branches/bmrb/generic_fns/diffusion_tensor.py Thu Oct 21 23:42:05 2010
@@ -37,6 +37,7 @@
 from generic_fns import pipes
 from generic_fns.angles import fold_spherical_angles
 from generic_fns.mol_res_spin import get_molecule_names, spin_loop
+from maths_fns.coord_transform import cartesian_to_spherical
 from maths_fns.rotation_matrix import R_to_euler_zyz
 from physical_constants import element_from_isotope, number_from_isotope
 from relax_errors import RelaxError, RelaxNoTensorError, RelaxStrError, 
RelaxTensorError, RelaxUnknownParamCombError, RelaxUnknownParamError
@@ -97,15 +98,15 @@
     if xy_match and yz_match:
         shape = ['sphere']
     elif xy_match:
+        shape = ['spheroid', 'prolate spheroid']
+        type = 'prolate'
+        Dpar = Di[2]
+        Dper = Di[0]
+    elif yz_match:
         shape = ['spheroid', 'oblate spheroid']
         type = 'oblate'
         Dpar = Di[0]
-        Dper = Di[1]
-    elif yz_match:
-        shape = ['spheroid', 'prolate spheroid']
-        type = 'prolate'
-        Dper = Di[0]
-        Dpar = Di[2]
+        Dper = Di[2]
     else:
         shape = ['ellipsoid']
 
@@ -119,11 +120,19 @@
     # Set the fixed flag.
     cdp.diff_tensor.fixed = True
 
-    # Set up the tensor.
+    # Sphere.
     if data['geometric_shape'] == 'sphere':
         sphere(params=Di[0], d_scale=1.0, param_types=1)
+
+    # Spheroid.
     elif data['geometric_shape'] in ['spheroid', 'oblate spheroid', 'prolate 
spheroid']:
-        spheroid(params=(Dpar, Dper, beta, gamma), d_scale=1.0, 
param_types=3, spheroid_type=type)
+        # The spherical angles.
+        r, theta, phi = cartesian_to_spherical(R[:, 2])
+
+        # Set up the tensor.
+        spheroid(params=(Dpar, Dper, theta, phi), d_scale=1.0, 
param_types=3, spheroid_type=type)
+
+    # Ellipsoid.
     elif data['geometric_shape'] == 'ellipsoid':
         ellipsoid(params=(Di[0], Di[1], Di[2], alpha, beta, gamma), 
d_scale=1.0, param_types=3)
 
@@ -693,7 +702,7 @@
         if sim_index == None:
             # Fold phi inside 0 and pi.
             if cdp.diff_tensor.phi >= pi:
-                theta, phi = fold_spherical_angles(cdp.diff_tensor.theta, 
cdp.diff_tensor.theta)
+                theta, phi = fold_spherical_angles(cdp.diff_tensor.theta, 
cdp.diff_tensor.phi)
                 cdp.diff_tensor.theta = theta
                 cdp.diff_tensor.phi = phi
 
@@ -1755,9 +1764,6 @@
     # Switch from the left handed to right handed universes (if needed).
     if norm(cross(R_new[:, 0], R_new[:, 1]) - R_new[:, 2]) > 1e-7:
         R_new[:, 2] = -R_new[:, 2]
-    
-    # Reverse the rotation.
-    R_new = transpose(R_new)
 
     # Euler angles (reverse rotation in the rotated axis system).
     gamma, beta, alpha = R_to_euler_zyz(R_new)
@@ -1774,7 +1780,7 @@
         beta = beta - pi
 
     # Return the values.
-    return Di, R_new, alpha, beta, gamma
+    return Di_sort, R_new, alpha, beta, gamma
 
 
 def test_params(num_params):