Author: bugman
Date: Wed Jun 5 22:31:56 2013
New Revision: 19876
URL: http://svn.gna.org/viewcvs/relax?rev=19876&view=rev
Log:
Added a directory and files for testing the white noise in relaxation data.
This includes scripts and graphs.
Added:
trunk/test_suite/shared_data/relaxation_data/white_noise/
trunk/test_suite/shared_data/relaxation_data/white_noise/curve.py
trunk/test_suite/shared_data/relaxation_data/white_noise/dist.agr
trunk/test_suite/shared_data/relaxation_data/white_noise/simulation.py
trunk/test_suite/shared_data/relaxation_data/white_noise/stats.py
Added: trunk/test_suite/shared_data/relaxation_data/white_noise/curve.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/relaxation_data/white_noise/curve.py?rev=19876&view=auto
==============================================================================
--- trunk/test_suite/shared_data/relaxation_data/white_noise/curve.py (added)
+++ trunk/test_suite/shared_data/relaxation_data/white_noise/curve.py Wed Jun
5 22:31:56 2013
@@ -1,0 +1,14 @@
+# Generate an exponential curve.
+
+from math import exp
+
+
+rx = 2.25
+i0 = 10000.0
+times = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
+
+intensities = []
+for i in range(len(times)):
+ intensities.append(i0 * exp(-rx*times[i]))
+
+print intensities
Added: trunk/test_suite/shared_data/relaxation_data/white_noise/dist.agr
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/relaxation_data/white_noise/dist.agr?rev=19876&view=auto
==============================================================================
--- trunk/test_suite/shared_data/relaxation_data/white_noise/dist.agr (added)
+++ trunk/test_suite/shared_data/relaxation_data/white_noise/dist.agr Wed Jun
5 22:31:56 2013
@@ -1,0 +1,550 @@
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Added: trunk/test_suite/shared_data/relaxation_data/white_noise/simulation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/relaxation_data/white_noise/simulation.py?rev=19876&view=auto
==============================================================================
--- trunk/test_suite/shared_data/relaxation_data/white_noise/simulation.py
(added)
+++ trunk/test_suite/shared_data/relaxation_data/white_noise/simulation.py
Wed Jun 5 22:31:56 2013
@@ -1,0 +1,67 @@
+"""Simulation of white noise through an exponential.
+
+To run the script, type:
+
+$ ../../../../relax simulation.py
+"""
+
+# relax module imports.
+from lib.statistics import bucket, gaussian
+from pipe_control.mol_res_spin import return_spin
+
+
+# Create the data pipe.
+pipe.create('white noise', 'relax_fit')
+
+# Add a single spin.
+spin.create(res_num=1, res_name='Gly', spin_name='N')
+
+# Get the spin.
+spin_cont = return_spin(':1@N')
+
+# Set up the synthetic peak intensities (rx = 2.25, i0 = 10000).
+cdp.spectrum_ids = ['ncyc_1', 'ncyc_2', 'ncyc_3', 'ncyc_4', 'ncyc_5',
'ncyc_6', 'ncyc_7', 'ncyc_8', 'ncyc_9', 'ncyc_10']
+times = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
+intensities = [7985.162187593771, 6376.281516217733, 5091.564206075492,
4065.6965974059913, 3246.5246735834976, 2592.4026064589157,
2070.0755268115263, 1652.9888822158653, 1319.9384318783023,
1053.9922456186434]
+cdp.relax_times = {}
+spin_cont.intensities = {}
+spin_cont.intensity_err = {}
+for i in range(len(times)):
+ cdp.relax_times[cdp.spectrum_ids[i]] = times[i]
+ spin_cont.intensities[cdp.spectrum_ids[i]] = intensities[i]
+ spin_cont.intensity_err[cdp.spectrum_ids[i]] = 1000.0
+
+# Set the relaxation curve type.
+relax_fit.select_model('exp')
+
+# Grid search.
+grid_search(inc=11)
+
+# Minimise.
+minimise('simplex', constraints=False)
+
+# Monte Carlo simulations.
+monte_carlo.setup(number=100000)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise('simplex', constraints=False)
+monte_carlo.error_analysis()
+
+# Bucket and write out the data.
+dist = bucket(spin_cont.rx_sim, lower=0, upper=5, inc=100, verbose=True)
+file = open('dist.agr', 'w')
+file.write("@target G0.S0\n@type xy\n")
+for i in range(len(dist)):
+ file.write("%s %s\n" % (dist[i][0], dist[i][1]))
+file.write("&\n")
+
+# The Gaussian distribution.
+file.write("@target G0.S1\n@type xy\n")
+for i in range(len(dist)):
+ pr = gaussian(dist[i][0], mu=2.25, sigma=spin_cont.rx_err)
+ file.write("%s %s\n" % (dist[i][0], pr*0.05))
+file.write("&\n")
+file.close()
+
+# Save the state.
+state.save('state', force=True)
Added: trunk/test_suite/shared_data/relaxation_data/white_noise/stats.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/relaxation_data/white_noise/stats.py?rev=19876&view=auto
==============================================================================
--- trunk/test_suite/shared_data/relaxation_data/white_noise/stats.py (added)
+++ trunk/test_suite/shared_data/relaxation_data/white_noise/stats.py Wed Jun
5 22:31:56 2013
@@ -1,0 +1,3 @@
+
+def bucket():
+ return []
r19876 - in /trunk/test_suite/shared_data/relaxation_data/white_noise: ./ curve.py dist.agr simulation.py stats.py