Re: r23831 - /branches/disp_spin_speed/lib/dispersion/cr72.py -- June 11, 2014

Hi Troels,

The test for 'no Rex' is still wrong:

    if kex == 1.0 or pA == 1:

This needs to be:

    if kex == 0.0 or pA == 1.0:

Regards,

Edward



On 11 June 2014 13:12,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Wed Jun 11 13:12:21 2014
New Revision: 23831

URL: http://svn.gna.org/viewcvs/relax?rev=23831&view=rev
Log:
Made the lib/cr72.py to a numpy multi dimensional numpy array calculation.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    branches/disp_spin_speed/lib/dispersion/cr72.py

Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=23831&r1=23830&r2=23831&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/cr72.py     (original)
+++ branches/disp_spin_speed/lib/dispersion/cr72.py     Wed Jun 11 13:12:21 
2014
@@ -105,19 +105,19 @@


     @keyword r20a:          The R20 parameter value of state A (R2 with no 
exchange).
-    @type r20a:             float
+    @type r20a:             numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword r20b:          The R20 parameter value of state B (R2 with no 
exchange).
-    @type r20b:             float
+    @type r20b:             numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword pA:            The population of state A.
     @type pA:               float
     @keyword dw:            The chemical exchange difference between 
states A and B in rad/s.
-    @type dw:               float
+    @type dw:               numpy array of rank [NE][NS][[NM][NO][ND]
     @keyword kex:           The kex parameter value (the exchange rate in 
rad/s).
     @type kex:              float
     @keyword cpmg_frqs:     The CPMG nu1 frequencies.
-    @type cpmg_frqs:        numpy rank-1 float array
+    @type cpmg_frqs:        numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword back_calc:     The array for holding the back calculated 
R2eff values.  Each element corresponds to one of the CPMG nu1 frequencies.
-    @type back_calc:        numpy rank-1 float array
+    @type back_calc:        numpy float array of rank [NE][NS][[NM][NO][ND]
     @keyword num_points:    The number of points on the dispersion curve, 
equal to the length of the cpmg_frqs and back_calc arguments.
     @type num_points:       int
     """
@@ -125,34 +125,16 @@
     # Flag to tell if values should be replaced if max_etapos in cosh 
function is violated.
     t_max_etapos = False

-    # Determine if calculating in numpy rank-1 float array, of higher 
dimensions.
-    rank_1 = True
-    if isinstance(num_points, ndarray):
-        rank_1 = False
-
     # Catch parameter values that will result in no exchange, returning 
flat R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
-    # For rank-1 float array.
-    if rank_1:
-        if dw == 0.0 or pA == 1.0 or kex == 0.0:
-            back_calc[:] = array([r20a]*num_points)
-            return
-
-    # For higher dimensions, return same structure.
-    else:
-       # Test if kex is zero.
-        if kex == 1.0:
+    # Test if pA or kex is zero.
+    if kex == 1.0 or pA == 1:
             back_calc[:] = r20a
             return

-        # Test if pA is 1.
-        if pA == 1.0:
-            back_calc[:] = r20a
-            return
-
-        # Test if dw is zero.
-        if allclose(dw, zeros(dw.shape)):
-            back_calc[:] = r20a
-            return
+    # Test if dw is zero.
+    if allclose(dw, zeros(dw.shape)):
+        back_calc[:] = r20a
+        return

     # The B population.
     pB = 1.0 - pA
@@ -187,28 +169,20 @@
     # Catch math domain error of cosh(val > 710).
     # This is when etapos > 710.
     if max(etapos) > 700:
-        if rank_1:
-            back_calc[:] = array([r20a]*num_points)
-            return
         # For higher dimensions, find the mask to replace values.
         # Reset to 1.0 and wait for replacement to later.
-        else:
-            # Set the flag to tell to replace values.
-            t_max_etapos = True
-            # Find the mask, where to replace values.
-            mask_max_etapos = masked_greater_equal(etapos, 700.0)
-            # To prevent math errors, set etapos to 1.
-            etapos[mask_max_etapos.mask] = 1.0
+        # Set the flag to tell to replace values.
+        t_max_etapos = True
+        # Find the mask, where to replace values.
+        mask_max_etapos = masked_greater_equal(etapos, 700.0)
+        # To prevent math errors, set etapos to 1.
+        etapos[mask_max_etapos.mask] = 1.0

     # The arccosh argument - catch invalid values.
     fact = Dpos * cosh(etapos) - Dneg * cos(etaneg)
     if min(fact) < 1.0:
-        if rank_1:
-            back_calc[:] = array([r20_kex]*num_points)
-            return
-        else:
-            back_calc[:] = r20_kex
-            return
+        back_calc[:] = r20_kex
+        return

     # Calculate R2eff.
     R2eff = r20_kex - cpmg_frqs * arccosh( fact )
@@ -224,4 +198,4 @@
         mask = isnan(R2eff)
         R2eff[mask] = 1e100

-    back_calc[:] = R2eff
+    back_calc[:] = R2eff


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Re: r23831 - /branches/disp_spin_speed/lib/dispersion/cr72.py

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