r20003 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/r1rho_on_res_dpl94.py -- June 09, 2013 - 22:46

Author: bugman
Date: Sun Jun  9 22:46:15 2013
New Revision: 20003

URL: http://svn.gna.org/viewcvs/relax?rev=20003&view=rev
Log:
Created the Relax_disp.test_r1rho_on_res_fixed_time_dpl94 system test.

This is the David, Perlman and London 1994 R1rho 2-site fast exchange model.

This commit follows step 7 of the relaxation dispersion model addition 
tutorial
(http://thread.gmane.org/gmane.science.nmr.relax.devel/3907).


Added:
    
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_dpl94.py
      - copied, changed from r20001, 
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
Modified:
    branches/relax_disp/test_suite/system_tests/relax_disp.py

Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=20003&r1=20002&r2=20003&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Sun Jun  9 
22:46:15 2013
@@ -513,6 +513,41 @@
             spin_index += 1
 
 
+    def test_r1rho_on_res_fixed_time_dpl94(self):
+        """Test the relaxation dispersion 'DPL94' model curve fitting to 
fixed time synthetic data."""
+
+        # Fixed time variable.
+        ds.fixed = True
+
+        # Execute the script.
+        self.interpreter.run(script_file=status.install_path + 
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_dpl94.py')
+
+        # The original parameters.
+        i0 = [100000.0, 20000.0]
+        r1rho_prime = [2.25, 24.0]
+        pA = 0.7
+        kex = 1000.0
+        delta_omega = [1.0, 2.0]
+        phi_ex = []
+        for i in range(2):
+            phi_ex.append(pA * (1.0 - pA) * delta_omega[i]**2)
+
+        # Switch to the 'DPL94' model data pipe, then check for each spin.
+        self.interpreter.pipe.switch('DPL94')
+        spin_index = 0
+        for spin, spin_id in spin_loop(return_id=True):
+            # Printout.
+            print("\nSpin %s." % spin_id)
+
+            # Check the fitted parameters.
+            self.assertAlmostEqual(spin.r2[0]/10, 
r1rho_prime[spin_index]/10, 2)
+            self.assertAlmostEqual(spin.phi_ex, phi_ex[spin_index], 2)
+            self.assertAlmostEqual(spin.kex/1000.0, kex/1000.0, 2)
+
+            # Increment the spin index.
+            spin_index += 1
+
+
     def test_r1rho_on_res_fixed_time_m61(self):
         """Test the relaxation dispersion 'M61' model curve fitting to fixed 
time synthetic data."""
 

Copied: 
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_dpl94.py
 (from r20001, 
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py)
URL: 
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_dpl94.py?p2=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_dpl94.py&p1=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py&r1=20001&r2=20003&rev=20003&view=diff
==============================================================================
--- 
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
 (original)
+++ 
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_dpl94.py
 Sun Jun  9 22:46:15 2013
@@ -1,4 +1,4 @@
-# Optimise the R1rho on-resonance synthetic data using the M61 model.
+# Optimise the R1rho on-resonance synthetic data using the DPL94 model.
 
 
 # Python module imports.
@@ -14,17 +14,13 @@
 #####################
 
 # The dispersion models.
-MODELS = ['R2eff', 'No Rex', 'M61']
+MODELS = ['R2eff', 'DPL94']
 
 # The grid search size (the number of increments per dimension).
 GRID_INC = 3
 
 # The number of Monte Carlo simulations to be used for error analysis at the 
end of the analysis.
 MC_NUM = 3
-
-# Fixed relaxation time period flag.
-if not hasattr(ds, 'fixed'):
-    ds.fixed = True
 
 
 # Set up the data pipe.
@@ -39,7 +35,7 @@
 pipe_bundle = 'relax_disp'
 pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
 
-# The path to the data files.
+# The path to the data files (use the M61 model data for now).
 data_path = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_on_res_m61'
 
 # Create the sequence data.
@@ -50,35 +46,27 @@
 spin.isotope(isotope='15N')
 
 # Set the relaxation dispersion experiment type.
-if ds.fixed:
-    relax_disp.exp_type('r1rho fixed')
-else:
-    relax_disp.exp_type('r1rho exponential')
+relax_disp.exp_type('r1rho fixed')
 
 # The spectral data - spectrum ID, peak lists, offset frequency (Hz), 
relaxation time period (s), baseplane RMSD estimate.
 data = []
-times = [0.00, 0.01, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.15]
-ncyc = [1, 2, 3, 4, 5, 6, 7, 8, 9]
-if ds.fixed:
-    times = [0.15]
-    ncyc = [9]
+times = [0.15]
+ncyc = [9]
 spin_lock = [1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 
6000]
 for spin_lock_index in range(len(spin_lock)):
     for time_index in range(len(times)):
         data.append(["nu_%s_ncyc%s" % (spin_lock[spin_lock_index], 
ncyc[time_index]), "nu_%s_ncyc%s.list" % (spin_lock[spin_lock_index], 
ncyc[time_index]), spin_lock[spin_lock_index], times[time_index], 200000.0])
 
 # Load the reference spectrum.
-if ds.fixed:
-    # Load the peak intensities and set the errors.
-    spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0], 
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='N', 
proton='HN')
-    spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0], 
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='NE1', 
proton='HE1')
-    spectrum.baseplane_rmsd(spectrum_id='ref', error=data[0][4])
+spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0], 
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='N', 
proton='HN')
+spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0], 
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='NE1', 
proton='HE1')
+spectrum.baseplane_rmsd(spectrum_id='ref', error=data[0][4])
 
-    # Set as the reference.
-    relax_disp.spin_lock_field(spectrum_id='ref', field=None)
+# Set as the reference.
+relax_disp.spin_lock_field(spectrum_id='ref', field=None)
 
-    # Set the spectrometer frequency.
-    spectrometer.frequency(id='ref', frq=800, units='MHz')
+# Set the spectrometer frequency.
+spectrometer.frequency(id='ref', frq=800, units='MHz')
 
 # Loop over the spectral data, loading it and setting the metadata.
 for i in range(len(data)):