relax SVN archive

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)
........

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.

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.

Updated the CaM 2-site to rotor model frame_order.py optimisation script for the parameter reduction.

The rotor frame order model axis spherical angles have now been converted to a single alpha angle.

Expanded all remaining CaM test data frame_order.py optimisation scripts.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

Expanded the CaM free-rotor isotropic cone test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation have been added to the repository.

Expanded the 2nd CaM pseudo-ellipse test data frame_order.py optimisation script.

The optimisation is now implemented as in the auto-analysis, with an iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now much lower.

The results of the new optimisation have been added to the repository.

Updated the 3 Frame_order.test_cam_rotor2* system tests for the higher quality data.

Important fix for the 2nd rotor model of the CaM frame order test data.

The tilt angle was not set, and therefore the old data matched the non-tilted 1st rotor model. All
PCS and RDC data has been regenerated to the highest quality using 20,000,000 structures.

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.