relax SVN archive

Modified the CaM frame order base system test script to catch a bug in the free rotor model.

The axis spherical angles are no longer set for the rotor or free rotor models, as they use the
alpha angle instead and the lack of the theta and phi parameters triggers the bug. The PDB
representation of the frame order motions is also now tested for all frame order models, as it was
turned off for the rigid, rotor and free rotor models and this is where the bug lies.

Parameter conversion for all of the CaM free rotor test data frame_order.py optimisation scripts.

The rotor axis spherical angles have been replaced by the axis alpha angle defining the rotor with
respect to the xy-plane.

Converted the 'free rotor' frame order model to the new axis_alpha parameter system.

The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle
alpha. The alpha parameter defines the rotor axis angle from the xy-plane.

Fix for a number of the frame order models which do not have parameter constraints.

This change to the grid_search() API method is similar to the change for the minimise() method
(r23211). The linear_constraint() function was returning A, b = [], [] for these models, but these
empty numpy arrays were causing the dot product with A to fail in the grid_search() API method.
These values are now caught and the constraint algorithm turned off.

Merged revisions 23675 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23675 | bugman | 2014-06-06 09:30:52 +0200 (Fri, 06 Jun 2014) | 10 lines

Bug fix for r23674, the compilation of the C modules now respects the user defined environment.

This is the patch from Justin (https://gna.org/users/jlec) attached to bug #22145
(https://gna.org/bugs/?22145).

The problem was that on Mac OS X (as well as other systems), that these environmental variables were
not defined and hence the scons commands would all fail with a KeyError and traceback. Now the keys
in the os.environ dictionary are being searched for before they are set.
........

Merged revisions 23674 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23674 | bugman | 2014-06-06 09:15:26 +0200 (Fri, 06 Jun 2014) | 7 lines

The compilation of the C modules now respects the user defined environment.

This is the patch from Justin (https://gna.org/users/jlec) attached to bug #22145
(https://gna.org/bugs/?22145). It has been modified to include a comment and remove a double empty
line.
........

Merged revisions 23651,23654,23657-23658,23662,23666-23667 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23651 | tlinnet | 2014-06-05 14:19:55 +0200 (Thu, 05 Jun 2014) | 52 lines

Added profiling script for testing the lib/dispersion/cr72.py file.

This script creates the relax datastructures, and issues the call to the target function.

It was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6022.

--------

Checked on MacBook Pro
2.4 GHz Intel Core i5
8 GB 1067 Mhz DDR3 RAM.
Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

Timing for:
2 fields
20 dispersion points
iterations of function call: 1000

Timed for simulating 1 or 100 clustered spins.

svn ls "^/tags"

For tag 3.2.2
svn switch ^/tags/3.2.2

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.168 0.000 0.198 0.000 cr72.py:100(r2eff_CR72)
1000 0.040 0.000 0.280 0.000 relax_disp.py:456(calc_CR72_chi2)
2000 0.028 0.000 0.039 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 16.810 0.000 19.912 0.000 cr72.py:100(r2eff_CR72)
1000 4.185 0.004 28.518 0.029 relax_disp.py:456(calc_CR72_chi2)
200000 3.018 0.000 4.144 0.000 chi2.py:32(chi2)

For tag 3.2.1
svn switch ^/tags/3.2.1

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.696 0.000 0.697 0.000 cr72.py:98(r2eff_CR72)
1000 0.038 0.000 0.781 0.001 relax_disp.py:456(calc_CR72_chi2)
2000 0.031 0.000 0.043 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 75.880 0.000 76.078 0.000 cr72.py:98(r2eff_CR72)
1000 4.201 0.004 85.519 0.086 relax_disp.py:456(calc_CR72_chi2)
200000 3.513 0.000 4.940 0.000 chi2.py:32(chi2)
........
r23654 | bugman | 2014-06-05 14:47:46 +0200 (Thu, 05 Jun 2014) | 3 lines

Changed the order of some instructions in the release checklist document.
........
r23657 | bugman | 2014-06-05 15:09:54 +0200 (Thu, 05 Jun 2014) | 6 lines

Backported the relax 3.2.2 CHANGES file changes to trunk.

The command used was:
svn merge -r23651:23652 svn+ssh://bugman@.../svn/relax/tags/3.2.2 .
........
r23658 | bugman | 2014-06-05 15:10:38 +0200 (Thu, 05 Jun 2014) | 3 lines

Added proper sectioning to the release checklist document.
........
r23662 | bugman | 2014-06-05 15:54:30 +0200 (Thu, 05 Jun 2014) | 3 lines

Added the upload script to the release checklist document.
........
r23666 | bugman | 2014-06-05 18:55:47 +0200 (Thu, 05 Jun 2014) | 6 lines

Modified the Sequence GUI input element used for the user function list arguments.

The first column is now of fixed with when titles are supplied. Previously when supplying titles,
the width would be tiny and no text would be visible.
........
r23667 | bugman | 2014-06-05 18:57:37 +0200 (Thu, 05 Jun 2014) | 6 lines

Added titles for all 3D coordinate user function arguments.

This is for the Sequence GUI input element, and affects the frame_order.average_position,
n_state_model.CoM and paramag.centre user functions.
........

Reverted the last two revisions (r23676 and r23677) as these killed the svnmerge properties.

The command used was:
svn merge -r23677:r23675 .

Merged revisions 23651 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23651 | tlinnet | 2014-06-05 14:19:55 +0200 (Thu, 05 Jun 2014) | 52 lines

Added profiling script for testing the lib/dispersion/cr72.py file.

This script creates the relax datastructures, and issues the call to the target function.

It was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6022.

--------

Checked on MacBook Pro
2.4 GHz Intel Core i5
8 GB 1067 Mhz DDR3 RAM.
Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

Timing for:
2 fields
20 dispersion points
iterations of function call: 1000

Timed for simulating 1 or 100 clustered spins.

svn ls "^/tags"

For tag 3.2.2
svn switch ^/tags/3.2.2

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.168 0.000 0.198 0.000 cr72.py:100(r2eff_CR72)
1000 0.040 0.000 0.280 0.000 relax_disp.py:456(calc_CR72_chi2)
2000 0.028 0.000 0.039 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 16.810 0.000 19.912 0.000 cr72.py:100(r2eff_CR72)
1000 4.185 0.004 28.518 0.029 relax_disp.py:456(calc_CR72_chi2)
200000 3.018 0.000 4.144 0.000 chi2.py:32(chi2)

For tag 3.2.1
svn switch ^/tags/3.2.1

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.696 0.000 0.697 0.000 cr72.py:98(r2eff_CR72)
1000 0.038 0.000 0.781 0.001 relax_disp.py:456(calc_CR72_chi2)
2000 0.031 0.000 0.043 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 75.880 0.000 76.078 0.000 cr72.py:98(r2eff_CR72)
1000 4.201 0.004 85.519 0.086 relax_disp.py:456(calc_CR72_chi2)
200000 3.513 0.000 4.940 0.000 chi2.py:32(chi2)
........

Merged revisions 23651 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23651 | tlinnet | 2014-06-05 14:19:55 +0200 (Thu, 05 Jun 2014) | 52 lines

Added profiling script for testing the lib/dispersion/cr72.py file.

This script creates the relax datastructures, and issues the call to the target function.

It was discussed in:
http://thread.gmane.org/gmane.science.nmr.relax.devel/6022.

--------

Checked on MacBook Pro
2.4 GHz Intel Core i5
8 GB 1067 Mhz DDR3 RAM.
Python Distribution -- Python 2.7.3 |EPD 7.3-2 (32-bit)|

Timing for:
2 fields
20 dispersion points
iterations of function call: 1000

Timed for simulating 1 or 100 clustered spins.

svn ls "^/tags"

For tag 3.2.2
svn switch ^/tags/3.2.2

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.168 0.000 0.198 0.000 cr72.py:100(r2eff_CR72)
1000 0.040 0.000 0.280 0.000 relax_disp.py:456(calc_CR72_chi2)
2000 0.028 0.000 0.039 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 16.810 0.000 19.912 0.000 cr72.py:100(r2eff_CR72)
1000 4.185 0.004 28.518 0.029 relax_disp.py:456(calc_CR72_chi2)
200000 3.018 0.000 4.144 0.000 chi2.py:32(chi2)

For tag 3.2.1
svn switch ^/tags/3.2.1

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
2000 0.696 0.000 0.697 0.000 cr72.py:98(r2eff_CR72)
1000 0.038 0.000 0.781 0.001 relax_disp.py:456(calc_CR72_chi2)
2000 0.031 0.000 0.043 0.000 chi2.py:32(chi2)

100 spins:
ncalls tottime percall cumtime percall filename:lineno(function)
200000 75.880 0.000 76.078 0.000 cr72.py:98(r2eff_CR72)
1000 4.201 0.004 85.519 0.086 relax_disp.py:456(calc_CR72_chi2)
200000 3.513 0.000 4.940 0.000 chi2.py:32(chi2)
........