r12266 - /1.3/test_suite/shared_data/model_free/back_calc.py -- January 12, 2011 - 19:15

Author: bugman
Date: Wed Jan 12 19:15:25 2011
New Revision: 12266

URL: http://svn.gna.org/viewcvs/relax?rev=12266&view=rev
Log:
Created the spectral_density_mf_ext() function for the extended model-free 
theory.

This calculates the spectral density values at the given model-free parameter 
values.


Modified:
    1.3/test_suite/shared_data/model_free/back_calc.py

Modified: 1.3/test_suite/shared_data/model_free/back_calc.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/model_free/back_calc.py?rev=12266&r1=12265&r2=12266&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/model_free/back_calc.py (original)
+++ 1.3/test_suite/shared_data/model_free/back_calc.py Wed Jan 12 19:15:25 
2011
@@ -172,8 +172,6 @@
     @type s2:           float
     @keyword te:        The effective internal correlation time.
     @type te:           float
-    @keyword rex:       The chemical exchange factor.
-    @type rex:          float
     @keyword heteronuc: The heteronucleus type, i.e. 15N, 13C, etc.
     @type heteronuc:    str
     @return:            The spectral density values.  The first dimension of 
this 2D array are the different proton frequencies.  The second dimension is 
the 5 frequencies.
@@ -203,3 +201,62 @@
 
     # Return the spectral density values.
     return J
+
+
+def spectral_density_mf_ext(frq=None, tm=None, s2=1.0, s2f=1.0, tf=0.0, 
ts=0.0, heteronuc='15N'):
+    """Calculate the spectral density values using the extended Lipari and 
Szabo model-free theory.
+
+    @keyword frq:       The array of proton frequencies to calculate the 
spectral densities at.
+    @type frq:          numpy rank-1 array
+    @keyword tm:        The global correlation time in seconds.
+    @type tm:           float
+    @keyword s2:        The generalised order parameter (S2 = S2f*S2s).
+    @type s2:           float
+    @keyword s2f:       The generalised order parameter for the faster 
motion.
+    @type s2f:          float
+    @keyword tf:        The effective internal correlation time for the 
faster motion.
+    @type tf:           float
+    @keyword ts:        The effective internal correlation time for the 
slower motion.
+    @type ts:           float
+    @keyword heteronuc: The heteronucleus type, i.e. 15N, 13C, etc.
+    @type heteronuc:    str
+    @return:            The spectral density values.  The first dimension of 
this 2D array are the different proton frequencies.  The second dimension is 
the 5 frequencies.
+    @rtype:             numpy rank-2 array
+    """
+
+    # Initialise.
+    J = zeros((len(frq), 5), float64)
+
+    # Loop over the frequencies.
+    for i in range(len(frq)):
+        # Calculate the 5 effective frequencies.
+        omega = calc_omega(frq[i], heteronuc=heteronuc)
+
+        # Loop over the effective frequencies.
+        for j in range(5):
+            # tf_prime.
+            if tf == 0.0:
+                tf_prime = 0.0
+            else:
+                tf_prime = 1.0 / (1.0/tm + 1.0/tf)
+
+            # ts_prime.
+            if ts == 0.0:
+                ts_prime = 0.0
+            else:
+                ts_prime = 1.0 / (1.0/tm + 1.0/ts)
+
+            # The spectral density value, part 1.
+            part1 = s2 * tm / (1.0 + (tm*omega[j])**2)
+
+            # The spectral density value, part 2.
+            part2 = (1.0 - s2f) * tf_prime / (1.0 + (tf_prime*omega[j])**2)
+
+            # The spectral density value, part 3.
+            part3 = (s2f - s2) * ts_prime / (1.0 + (ts_prime*omega[j])**2)
+
+            # Combine it all.
+            J[i, j] = 0.4 * (part1 + part2 + part3)
+
+    # Return the spectral density values.
+    return J