Author: bugman
Date: Fri Jun 7 17:01:44 2013
New Revision: 19952
URL: http://svn.gna.org/viewcvs/relax?rev=19952&view=rev
Log:
Added a log file for the data generation script for the r1rho_on_res
dispersion data.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.log
Modified:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.py
Added:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.log
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.log?rev=19952&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.log
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.log
Fri Jun 7 17:01:44 2013
@@ -1,0 +1,401 @@
+
+
+
+ relax repository checkout r19950
+
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp
+
+ Molecular dynamics by NMR data analysis
+
+ Copyright (C) 2001-2006 Edward d'Auvergne
+ Copyright (C) 2006-2013 the relax development team
+
+This is free software which you are welcome to modify and redistribute under
the conditions of the
+GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
+and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
+
+Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
+the prompt.
+
+Processor fabric: Uni-processor.
+
+script = 'generate.py'
+----------------------------------------------------------------------------------------------------
+"""Simulate relaxation curves for an on resonance R1rho-type experiment
using the M61 model.
+
+This is the Meiboom 1961 model for 2-site fast exchange. The equation is:
+
+ phi_ex * kex
+ R1rho = R1rho' + ----------------- ,
+ kex^2 + omega_e^2
+
+where R1rho' is the R1rho value in the absence of exchange,
+
+ phi_ex = pA * pB * delta_omega^2 ,
+
+kex is the chemical exchange rate constant, pA and pB are the populations of
states A and B, delta_omega is the chemical shift difference between the two
states (in rad/s), and omega_e is the effective field in the rotating frame.
+
+To run the script, simply type:
+
+$ ../../../../relax generate.py --tee generate.log
+"""
+
+# Python module imports.
+from math import exp, pi
+
+# relax module imports.
+from lib.software.sparky import write_list
+
+
+# Setup for 2 spin systems.
+i0 = [100000.0, 20000.0] # Initial peak intensities.
+times = [0.00, 0.01, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.15] # The
relaxation delay times in seconds.
+spin_lock = [1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500,
6000] # The spin-lock field strengths in Hz.
+r1rho_prime = [2.25, 24.0] # The R1rho' value per spin.
+pA = 0.7
+kex = 1000.0
+delta_omega = [1.0, 2.0] # The chemical shift difference in ppm.
+frq = -81.1177503272
+
+# Setup for the Sparky peak list.
+res_names = ['Trp', 'Trp']
+res_nums = [1, 1]
+atom1_names = ['N', 'NE1']
+atom2_names = ['HN', 'HE1']
+w1 = [122.454, 111.978]
+w2 = [8.397, 8.720]
+
+# Loop over the spin-lock fields.
+for spin_lock_index in range(len(spin_lock)):
+ # Loop over the relaxation times.
+ for time_index in range(len(times)):
+ # Loop over the spins.
+ intensities = []
+ for spin_index in range(len(r1rho_prime)):
+ # Phi of exchange.
+ phi_ex = pA * (1.0 - pA) * (delta_omega[spin_index]*frq*2*pi)**2
+
+ # The rate.
+ rx = r1rho_prime[spin_index] + (phi_ex * kex) / (kex**2 +
(2*pi*spin_lock[spin_lock_index])**2)
+
+ # The peak intensity.
+ intensities.append(i0[spin_index] * exp(-rx*times[time_index]))
+
+ # Printout.
+ if time_index == 8:
+ print("Phi_ex: %s" % phi_ex)
+ print("Rex: %s" % ((phi_ex * kex) / (kex**2 +
(2*pi*spin_lock[spin_lock_index])**2)))
+ print("Rate: %s" % rx)
+ print("Intensity: %s\n" % intensities[spin_index])
+
+ # Create a Sparky .list file.
+ write_list(file_prefix='nu_%s_ncyc%s' % (spin_lock[spin_lock_index],
time_index+1), dir=None, res_names=res_names, res_nums=res_nums,
atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2,
data_height=intensities)
+----------------------------------------------------------------------------------------------------
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 1.34768160399
+Rate: 3.59768160399
+Intensity: 58295.0943799
+
+Phi_ex: 218208.075056
+Rex: 5.39072641595
+Rate: 29.390726416
+Intensity: 243.441968112
+
+Creating the Sparky list file.
+Opening the file 'nu_1000_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.607304697825
+Rate: 2.85730469783
+Intensity: 65142.3243322
+
+Phi_ex: 218208.075056
+Rex: 2.4292187913
+Rate: 26.4292187913
+Intensity: 379.594938867
+
+Creating the Sparky list file.
+Opening the file 'nu_1500_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.343280843119
+Rate: 2.59328084312
+Intensity: 67773.9606198
+
+Phi_ex: 218208.075056
+Rex: 1.37312337247
+Rate: 25.3731233725
+Intensity: 444.752988783
+
+Creating the Sparky list file.
+Opening the file 'nu_2000_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.220198573247
+Rate: 2.47019857325
+Intensity: 69036.8486186
+
+Phi_ex: 218208.075056
+Rex: 0.880794292986
+Rate: 24.880794293
+Intensity: 478.84090798
+
+Creating the Sparky list file.
+Opening the file 'nu_2500_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.153104510584
+Rate: 2.40310451058
+Intensity: 69735.1510176
+
+Phi_ex: 218208.075056
+Rex: 0.612418042334
+Rate: 24.6124180423
+Intensity: 498.510596619
+
+Creating the Sparky list file.
+Opening the file 'nu_3000_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.112568765524
+Rate: 2.36256876552
+Intensity: 70160.4576619
+
+Phi_ex: 218208.075056
+Rex: 0.450275062096
+Rate: 24.4502750621
+Intensity: 510.783741016
+
+Creating the Sparky list file.
+Opening the file 'nu_3500_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.08622716364
+Rate: 2.33622716364
+Intensity: 70438.2268935
+
+Phi_ex: 218208.075056
+Rex: 0.34490865456
+Rate: 24.3449086546
+Intensity: 518.920791691
+
+Creating the Sparky list file.
+Opening the file 'nu_4000_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.0681527135511
+Rate: 2.31815271355
+Intensity: 70629.4558357
+
+Phi_ex: 218208.075056
+Rex: 0.272610854204
+Rate: 24.2726108542
+Intensity: 524.578941391
+
+Creating the Sparky list file.
+Opening the file 'nu_4500_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.0552168047922
+Rate: 2.30521680479
+Intensity: 70766.6373147
+
+Phi_ex: 218208.075056
+Rex: 0.220867219169
+Rate: 24.2208672192
+Intensity: 528.666326276
+
+Creating the Sparky list file.
+Opening the file 'nu_5000_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.0456417407937
+Rate: 2.29564174079
+Intensity: 70868.349602
+
+Phi_ex: 218208.075056
+Rex: 0.182566963175
+Rate: 24.1825669632
+Intensity: 531.712275792
+
+Creating the Sparky list file.
+Opening the file 'nu_5500_ncyc9.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc1.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc2.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc3.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc4.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc5.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc6.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc7.list' for writing.
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc8.list' for writing.
+Phi_ex: 54552.018764
+Rex: 0.0383568663066
+Rate: 2.28835686631
+Intensity: 70945.8319828
+
+Phi_ex: 218208.075056
+Rex: 0.153427465226
+Rate: 24.1534274652
+Intensity: 534.041436693
+
+Creating the Sparky list file.
+Opening the file 'nu_6000_ncyc9.list' for writing.
+
Modified:
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.py?rev=19952&r1=19951&r2=19952&view=diff
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.py
(original)
+++
branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res/generate.py
Fri Jun 7 17:01:44 2013
@@ -14,7 +14,7 @@
To run the script, simply type:
-$ ../../../../relax generate.py
+$ ../../../../relax generate.py --tee generate.log
"""
# Python module imports.
r19952 - in /branches/relax_disp/test_suite/shared_data/dispersion/r1rho_on_res: generate.log generate.py