Author: bugman
Date: Tue Dec 11 16:55:42 2007
New Revision: 4183
URL: http://svn.gna.org/viewcvs/relax?rev=4183&view=rev
Log:
Modified the generic_fns.align_tensor.set() function to handle the Saupe and
prob matrix.
Modified:
branches/N_state_model/generic_fns/align_tensor.py
Modified: branches/N_state_model/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/align_tensor.py?rev=4183&r1=4182&r2=4183&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/align_tensor.py (original)
+++ branches/N_state_model/generic_fns/align_tensor.py Tue Dec 11 16:55:42
2007
@@ -691,16 +691,22 @@
The alignment tensor parameters can only be set when the data pipe
corresponds to model-free
analysis. The units of the parameters are:
- Hertz for Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz.
+ Unitless for Sxx, Syy, Szz, Sxxyy, Sxy, Sxz, Syz.
+ Unitless for Axx, Ayy, Azz, Axxyy, Axy, Axz, Ayz.
+ Unitless for Pxx, Pyy, Pzz, Pxxyy, Pxy, Pxz, Pyz.
Radians for all angles (alpha, beta, gamma).
- If a single geometric parameter is supplied, it must be one of Axx, Ayy,
Axy, Axz, Ayz. For the
- parameters Azz and Axxyy , it is not possible to determine how to use
the currently set values
- together with the supplied value to calculate the new internal
parameters. When supplying
- multiple geometric parameters, the set must belong to one of
-
+ If a single geometric parameter is supplied, it must be one of Bxx, Byy,
Bxy, Bxz, Byz, where B
+ is one of S, A, or P. For the parameters Bzz and Bxxyy, it is not
possible to determine how to
+ use the currently set values together with the supplied value to
calculate the new internal
+ parameters. When supplying multiple geometric parameters, the set must
belong to one of
+
+ {Sxx, Syy, Sxy, Sxz, Syz},
+ {Szz, Sxxyy, Sxy, Sxz, Syz}.
{Axx, Ayy, Axy, Axz, Ayz},
{Azz, Axxyy, Axy, Axz, Ayz}.
+ {Pxx, Pyy, Pxy, Pxz, Pyz},
+ {Pzz, Pxxyy, Pxy, Pxz, Pyz}.
"""
# Alias the current data pipe.
@@ -726,7 +732,7 @@
value[i] = default_value(object_names[i])
# Geometric parameter.
- if param[i] in ['Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz']:
+ if param[i] in ['Sxx', 'Syy', 'Szz', 'Sxxyy', 'Sxy', 'Sxz', 'Syz',
'Axx', 'Ayy', 'Azz', 'Axxyy', 'Axy', 'Axz', 'Ayz', 'Pxx', 'Pyy', 'Pzz',
'Pxxyy', 'Pxy', 'Pxz', 'Pyz']:
geo_params.append(param[i])
geo_values.append(value[i])
@@ -741,25 +747,76 @@
# A single geometric parameter.
if len(geo_params) == 1:
+ # Saupe order matrix.
+ #####################
+
+ # The single parameter Sxx.
+ if geo_params[0] == 'Sxx':
+ cdp.align_tensor[tensor].Sxx = geo_values[0]
+
+ # The single parameter Syy.
+ elif geo_params[0] == 'Syy':
+ cdp.align_tensor[tensor].Syy = geo_values[0]
+
+ # The single parameter Sxy.
+ elif geo_params[0] == 'Sxy':
+ cdp.align_tensor[tensor].Sxy = geo_values[0]
+
+ # The single parameter Sxz.
+ elif geo_params[0] == 'Sxz':
+ cdp.align_tensor[tensor].Sxz = geo_values[0]
+
+ # The single parameter Syz.
+ elif geo_params[0] == 'Syz':
+ cdp.align_tensor[tensor].Syz = geo_values[0]
+
+
+ # Alignment tensor.
+ ###################
+
# The single parameter Axx.
- if geo_params[0] == 'Axx':
- cdp.align_tensor[tensor].Axx = geo_values[0]
+ elif geo_params[0] == 'Axx':
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * geo_values[0]
# The single parameter Ayy.
elif geo_params[0] == 'Ayy':
- cdp.align_tensor[tensor].Ayy = geo_values[0]
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * geo_values[0]
# The single parameter Axy.
elif geo_params[0] == 'Axy':
- cdp.align_tensor[tensor].Axy = geo_values[0]
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * geo_values[0]
# The single parameter Axz.
elif geo_params[0] == 'Axz':
- cdp.align_tensor[tensor].Axz = geo_values[0]
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * geo_values[0]
# The single parameter Ayz.
elif geo_params[0] == 'Ayz':
- cdp.align_tensor[tensor].Ayz = geo_values[0]
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * geo_values[0]
+
+
+ # Probability tensor.
+ #####################
+
+ # The single parameter Pxx.
+ elif geo_params[0] == 'Pxx':
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * (geo_values[0] -
1.0/3.0)
+
+ # The single parameter Pyy.
+ elif geo_params[0] == 'Pyy':
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * (geo_values[0] -
1.0/3.0)
+
+ # The single parameter Pxy.
+ elif geo_params[0] == 'Pxy':
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * geo_values[0]
+
+ # The single parameter Pxz.
+ elif geo_params[0] == 'Pxz':
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * geo_values[0]
+
+ # The single parameter Pyz.
+ elif geo_params[0] == 'Pyz':
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * geo_values[0]
# Cannot set the single parameter.
else:
@@ -767,8 +824,40 @@
# 5 geometric parameters.
elif len(geo_params) == 5:
+ # The geometric parameter set {Sxx, Syy, Sxy, Sxz, Syz}.
+ if geo_params.count('Sxx') == 1 and geo_params.count('Syy') == 1 and
geo_params.count('Sxy') == 1 and geo_params.count('Sxz') == 1 and
geo_params.count('Syz') == 1:
+ # The parameters.
+ Sxx = geo_values[geo_params.index('Sxx')]
+ Syy = geo_values[geo_params.index('Syy')]
+ Sxy = geo_values[geo_params.index('Sxy')]
+ Sxz = geo_values[geo_params.index('Sxz')]
+ Syz = geo_values[geo_params.index('Syz')]
+
+ # Set the internal parameter values.
+ cdp.align_tensor[tensor].Sxx = Sxx
+ cdp.align_tensor[tensor].Syy = Syy
+ cdp.align_tensor[tensor].Sxy = Sxy
+ cdp.align_tensor[tensor].Sxz = Sxz
+ cdp.align_tensor[tensor].Syz = Syz
+
+ # The geometric parameter set {Szz, Sxxyy, Sxy, Sxz, Syz}.
+ elif geo_params.count('Szz') == 1 and geo_params.count('Sxxyy') == 1
and geo_params.count('Sxy') == 1 and geo_params.count('Sxz') == 1 and
geo_params.count('Syz') == 1:
+ # The parameters.
+ Szz = geo_values[geo_params.index('Szz')]
+ Sxxyy = geo_values[geo_params.index('Sxxyy')]
+ Sxy = geo_values[geo_params.index('Sxy')]
+ Sxz = geo_values[geo_params.index('Sxz')]
+ Syz = geo_values[geo_params.index('Syz')]
+
+ # Set the internal parameter values.
+ cdp.align_tensor[tensor].Sxx = -0.5*(Szz-Sxxyy)
+ cdp.align_tensor[tensor].Syy = -0.5*(Szz+Sxxyy)
+ cdp.align_tensor[tensor].Sxy = Sxy
+ cdp.align_tensor[tensor].Sxz = Sxz
+ cdp.align_tensor[tensor].Syz = Syz
+
# The geometric parameter set {Axx, Ayy, Axy, Axz, Ayz}.
- if geo_params.count('Axx') == 1 and geo_params.count('Ayy') == 1 and
geo_params.count('Axy') == 1 and geo_params.count('Axz') == 1 and
geo_params.count('Ayz') == 1:
+ elif geo_params.count('Axx') == 1 and geo_params.count('Ayy') == 1
and geo_params.count('Axy') == 1 and geo_params.count('Axz') == 1 and
geo_params.count('Ayz') == 1:
# The parameters.
Axx = geo_values[geo_params.index('Axx')]
Ayy = geo_values[geo_params.index('Ayy')]
@@ -777,11 +866,11 @@
Ayz = geo_values[geo_params.index('Ayz')]
# Set the internal parameter values.
- cdp.align_tensor[tensor].Axx = Axx
- cdp.align_tensor[tensor].Ayy = Ayy
- cdp.align_tensor[tensor].Axy = Axy
- cdp.align_tensor[tensor].Axz = Axz
- cdp.align_tensor[tensor].Ayz = Ayz
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * Axx
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * Ayy
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * Axy
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * Axz
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * Ayz
# The geometric parameter set {Azz, Axxyy, Axy, Axz, Ayz}.
elif geo_params.count('Azz') == 1 and geo_params.count('Axxyy') == 1
and geo_params.count('Axy') == 1 and geo_params.count('Axz') == 1 and
geo_params.count('Ayz') == 1:
@@ -793,11 +882,43 @@
Ayz = geo_values[geo_params.index('Ayz')]
# Set the internal parameter values.
- cdp.align_tensor[tensor].Axx = -0.5*(Azz-Axxyy)
- cdp.align_tensor[tensor].Ayy = -0.5*(Azz+Axxyy)
- cdp.align_tensor[tensor].Axy = Axy
- cdp.align_tensor[tensor].Axz = Axz
- cdp.align_tensor[tensor].Ayz = Ayz
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * -0.5*(Azz-Axxyy)
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * -0.5*(Azz+Axxyy)
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * Axy
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * Axz
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * Ayz
+
+ # The geometric parameter set {Pxx, Pyy, Pxy, Pxz, Pyz}.
+ elif geo_params.count('Pxx') == 1 and geo_params.count('Pyy') == 1
and geo_params.count('Pxy') == 1 and geo_params.count('Pxz') == 1 and
geo_params.count('Pyz') == 1:
+ # The parameters.
+ Pxx = geo_values[geo_params.index('Pxx')]
+ Pyy = geo_values[geo_params.index('Pyy')]
+ Pxy = geo_values[geo_params.index('Pxy')]
+ Pxz = geo_values[geo_params.index('Pxz')]
+ Pyz = geo_values[geo_params.index('Pyz')]
+
+ # Set the internal parameter values.
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * (Pxx - 1.0/3.0)
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * (Pyy - 1.0/3.0)
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * Pxy
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * Pxz
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * Pyz
+
+ # The geometric parameter set {Pzz, Pxxyy, Pxy, Pxz, Pyz}.
+ elif geo_params.count('Pzz') == 1 and geo_params.count('Pxxyy') == 1
and geo_params.count('Pxy') == 1 and geo_params.count('Pxz') == 1 and
geo_params.count('Pyz') == 1:
+ # The parameters.
+ Pzz = geo_values[geo_params.index('Pzz')]
+ Pxxyy = geo_values[geo_params.index('Pxxyy')]
+ Pxy = geo_values[geo_params.index('Pxy')]
+ Pxz = geo_values[geo_params.index('Pxz')]
+ Pyz = geo_values[geo_params.index('Pyz')]
+
+ # Set the internal parameter values.
+ cdp.align_tensor[tensor].Sxx = 3.0/2.0 * (-0.5*(Pzz-Pxxyy) -
1.0/3.0)
+ cdp.align_tensor[tensor].Syy = 3.0/2.0 * (-0.5*(Pzz+Pxxyy) -
1.0/3.0)
+ cdp.align_tensor[tensor].Sxy = 3.0/2.0 * Pxy
+ cdp.align_tensor[tensor].Sxz = 3.0/2.0 * Pxz
+ cdp.align_tensor[tensor].Syz = 3.0/2.0 * Pyz
# Unknown parameter combination.
else:
r4183 - /branches/N_state_model/generic_fns/align_tensor.py