relax SVN archive

Merged revisions 23881 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23881 | bugman | 2014-06-12 14:47:31 +0200 (Thu, 12 Jun 2014) | 8 lines

Better handling of the control-C keyboard interrupt signal in the relax test suite.

This includes two changes. The Python 2.7 and higher unittest.installHandler() function is now
called, when present, to terminate all tests using the unittest module control-C handler. The
second change is that the keyboard interrupt signal is caught in a try-except statement, a message
printed out, and the tests terminated. This should be an improvement for all systems.
........

Better handling of the control-C keyboard interrupt signal in the relax test suite.

This includes two changes. The Python 2.7 and higher unittest.installHandler() function is now
called, when present, to terminate all tests using the unittest module control-C handler. The
second change is that the keyboard interrupt signal is caught in a try-except statement, a message
printed out, and the tests terminated. This should be an improvement for all systems.

Large increase in speed for model TSMFK01 by changing target functions to use multidimensional numpy arrays in calculation.

This is done by restructuring data into multidimensional arrays of dimension [NE][NS][NM][NO][ND], which are
number of spins, number of magnetic field strength, number of offsets, maximum number of dispersion point.

The speed comes from using numpy ufunc operations.

The new version is 2.4X as fast per spin calculation, and 54X as fast for clustered analysis.

The different in timings for 3 spectrometer frequencies, calculated for 1 spin or 100 clustered spins with 1000 iterations are:

----
VERSION 3.2.2
----
1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.262 0.262 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 25.391 25.391 <string>:1(<module>)
----
New version
---

1 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.111 0.111 <string>:1(<module>)
100 spin:
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.468 0.468 <string>:1(<module>)

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Fix for the Frame_order.test_rigid_data_to_free_rotor_model system test.

As the free rotor has undergone a reparameterisation, the chi-squared value is now higher. The
value is reasonable as the free rotor can never model the rigid system.

Fix for the PDB representation generated by frame_order.pdb_model for the free rotor pseudo-ellipse.

Made unit tests for model TSMFK01 send in R20A and dw as a numpy array.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Modified lib function for model TSMFK01 to accept dw_orig as input and replaced functions to find math domain errors into maske replacements.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Modified target function for model TSMFK01, to send in dw as original parameter.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Modified profiling script to be used for model TSMFK01.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.

Indention fix in cr72.py and b14.py.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis.