Author: bugman
Date: Mon Nov 17 18:13:38 2014
New Revision: 26607
URL: http://svn.gna.org/viewcvs/relax?rev=26607&view=rev
Log:
Created a script and log file to demonstrate differences between alignment
tensor basis sets.
This shows that the inter-tensor angles and condition numbers are dependent
on the basis set used.
Added:
trunk/test_suite/shared_data/align_data/basis_sets/
trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.log
trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.py
Added:
trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.log
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.log?rev=26607&view=auto
==============================================================================
--- trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.log
(added)
+++ trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.log
Mon Nov 17 18:13:38 2014
@@ -0,0 +1,102 @@
+
+
+
+ relax repository checkout r26606
+ svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
+
+ Molecular dynamics by NMR data analysis
+
+ Copyright (C) 2001-2006 Edward d'Auvergne
+ Copyright (C) 2006-2014 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 = 'compare_basis_sets.py'
+----------------------------------------------------------------------------------------------------
+# Random tensors of {Axx, Ayy, Axy, Axz, Ayz} generated using
random.uniform(0, 1e-4).
+tensor1 = (5.4839183673166663e-05, 3.692459844061351e-05,
1.994164790083226e-05, 4.5945264935308495e-05, 1.0090119622465559e-05)
+tensor2 = (1.5832157768761617e-05, -4.9797877146095514e-05,
-3.6007226809999e-05, -3.8175058915299295e-05, 5.3131759988544946e-05)
+tensor3 = (3.892445496049645e-05, -1.7165585393754253e-05,
7.803231512226243e-05, -3.057296854986567e-05, 9.31348723610886e-05)
+tensor4 = (4.6720247808382186e-05, -9.140580842599e-05,
-3.415945182796103e-05, -1.7753928806205142e-05, 5.20457038882803e-05)
+
+# Create a N-state analysis data pipe.
+pipe.create('basis set comparison', 'N-state')
+
+# Load the tensors.
+align_tensor.init(tensor='t1', align_id='t1', params=tensor1)
+align_tensor.init(tensor='t2', align_id='t2', params=tensor2)
+align_tensor.init(tensor='t3', align_id='t3', params=tensor3)
+align_tensor.init(tensor='t4', align_id='t4', params=tensor4)
+
+# Inter-tensor angles.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+# SVD.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
+----------------------------------------------------------------------------------------------------
+
+relax> pipe.create(pipe_name='basis set comparison', pipe_type='N-state',
bundle=None)
+
+relax> align_tensor.init(tensor='t1', align_id='t1', domain=None,
params=(5.4839183673166663e-05, 3.692459844061351e-05, 1.994164790083226e-05,
4.5945264935308495e-05, 1.0090119622465559e-05), scale=1.0,
angle_units='deg', param_types=2, errors=False)
+
+relax> align_tensor.init(tensor='t2', align_id='t2', domain=None,
params=(1.5832157768761617e-05, -4.9797877146095514e-05,
-3.6007226809999e-05, -3.8175058915299295e-05, 5.3131759988544946e-05),
scale=1.0, angle_units='deg', param_types=2, errors=False)
+
+relax> align_tensor.init(tensor='t3', align_id='t3', domain=None,
params=(3.892445496049645e-05, -1.7165585393754253e-05,
7.803231512226243e-05, -3.057296854986567e-05, 9.31348723610886e-05),
scale=1.0, angle_units='deg', param_types=2, errors=False)
+
+relax> align_tensor.init(tensor='t4', align_id='t4', domain=None,
params=(4.6720247808382186e-05, -9.140580842599e-05, -3.415945182796103e-05,
-1.7753928806205142e-05, 5.20457038882803e-05), scale=1.0, angle_units='deg',
param_types=2, errors=False)
+
+relax> align_tensor.matrix_angles(basis_set=0, tensors=None)
+
+Data pipe: 'basis set comparison'
+
+5D angles in deg between the vectors {Sxx, Syy, Sxy, Sxz, Syz}:
+ t1 t2 t3 t4
+t1 0.0 112.4 76.4 100.1
+t2 112.4 0.0 66.7 25.7
+t3 76.4 66.7 0.0 67.6
+t4 100.1 25.7 67.6 0.0
+
+relax> align_tensor.matrix_angles(basis_set=1, tensors=None)
+
+Data pipe: 'basis set comparison'
+
+5D angles in deg between the vectors {Szz, Sxx-yy, Sxy, Sxz, Syz}:
+ t1 t2 t3 t4
+t1 0.0 110.3 74.0 98.8
+t2 110.3 0.0 64.7 24.0
+t3 74.0 64.7 0.0 64.5
+t4 98.8 24.0 64.5 0.0
+
+relax> align_tensor.svd(basis_set=0, tensors=None)
+
+Data pipe: 'basis set comparison'
+
+Singular values:
+ 2.5039e-04
+ 1.7709e-04
+ 1.0672e-04
+ 3.8501e-05
+
+Condition number: 6.50
+
+relax> align_tensor.svd(basis_set=1, tensors=None)
+
+Data pipe: 'basis set comparison'
+
+Singular values:
+ 3.0403e-04
+ 2.0155e-04
+ 1.2545e-04
+ 4.3542e-05
+
+Condition number: 6.98
+
Added:
trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.py?rev=26607&view=auto
==============================================================================
--- trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.py
(added)
+++ trunk/test_suite/shared_data/align_data/basis_sets/compare_basis_sets.py
Mon Nov 17 18:13:38 2014
@@ -0,0 +1,22 @@
+# Random tensors of {Axx, Ayy, Axy, Axz, Ayz} generated using
random.uniform(0, 1e-4).
+tensor1 = (5.4839183673166663e-05, 3.692459844061351e-05,
1.994164790083226e-05, 4.5945264935308495e-05, 1.0090119622465559e-05)
+tensor2 = (1.5832157768761617e-05, -4.9797877146095514e-05,
-3.6007226809999e-05, -3.8175058915299295e-05, 5.3131759988544946e-05)
+tensor3 = (3.892445496049645e-05, -1.7165585393754253e-05,
7.803231512226243e-05, -3.057296854986567e-05, 9.31348723610886e-05)
+tensor4 = (4.6720247808382186e-05, -9.140580842599e-05,
-3.415945182796103e-05, -1.7753928806205142e-05, 5.20457038882803e-05)
+
+# Create a N-state analysis data pipe.
+pipe.create('basis set comparison', 'N-state')
+
+# Load the tensors.
+align_tensor.init(tensor='t1', align_id='t1', params=tensor1)
+align_tensor.init(tensor='t2', align_id='t2', params=tensor2)
+align_tensor.init(tensor='t3', align_id='t3', params=tensor3)
+align_tensor.init(tensor='t4', align_id='t4', params=tensor4)
+
+# Inter-tensor angles.
+align_tensor.matrix_angles(basis_set=0)
+align_tensor.matrix_angles(basis_set=1)
+
+# SVD.
+align_tensor.svd(basis_set=0)
+align_tensor.svd(basis_set=1)
r26607 - in /trunk/test_suite/shared_data/align_data/basis_sets: ./ compare_basis_sets.log compare_basis_sets.py