relax SVN archive

Math-domain catching for model CR72.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

The skipping of test when num_points > 0, is a bad implementation.
If such a case should show, it is best to catch the wrong input for the
calculations. This is best done with a check before running the calculations.

Math-domain catching for model: 'NS CPMG 2-site expanded'.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.

Modified the CaM frame order test data generation base script to conserve computer RAM.

The XH vector and atomic position data structures for all N rotations are now of the numpy.float32
rather than numpy.float64 type. The main change is to calculate the averaged RDCs and averaged PCSs
separately, deleting the N-sized data structures once the data files are written.

Huge speed up of the CaM frame order test data generation base script.

By using multidimensional numpy arrays to store the atomic positions and XH unit vectors of all
spins, and performing the rotations on these structures using numpy.tensordot(), the calculations
are now a factor of 10 times faster. The progress meter had to be changed to show every 1000 rather
than 100 iterations.

The rotations of the positions and vectors are now performed sequentially, accidentally fixing a bug
with the double motion models (i.e. the 'double rotor' model).

Modification of the structure loading part of the CaM frame order data generation base script.

The structures are now only loaded if the DIST_PDB flag is set, as they are only used for generating
the 3D distribution of structures. This saves a lot of time and computer memory.

Fix for the RDC error setting in the CaM frame order test data generation base script.

The rdc_err data structure is located in the interatomic data containers, no the spin containers.

Increased the precision of all the data in the CaM frame order test data generation base script.

These have all been converted from float16 to float64 numpy types.

Math-domain catching for model CR72.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.

Math-domain catching for model B14.

task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.
These can be found via the --numpy-raise function to the systemtests.

To make the code look clean, the class object "back_calc" is no longer
being updated per time point, but is updated in the relax_disp target function in
one go.

Merged revisions 23230,23232,23234-23236 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23230 | bugman | 2014-05-19 11:57:56 +0200 (Mon, 19 May 2014) | 7 lines

Exposed the backend verbosity flag of the structure.read_* user functions.

This allows the user to silence these user functions, which can be very useful when loading many
3D structures in the scripting UI mode. This change is for the structure.read_gaussian,
structure.read_pdb, and structure.read_xyz user functions.
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r23232 | bugman | 2014-05-19 12:09:17 +0200 (Mon, 19 May 2014) | 7 lines

Expanded the structure.delete user function to add the 'verbosity' and 'spin_info' arguments.

The verbosity argument, when set to zero, allows all output to be suppressed. The spin_info flag
allows the deletion of spin and interatomic data to now be turned off, so that only 3D data is
deleted.
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r23234 | bugman | 2014-05-19 12:21:31 +0200 (Mon, 19 May 2014) | 5 lines

The new structure.delete 'verbosity' argument is now propagated into the structural object.

This allows the printouts to now be completely suppressed.
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r23235 | bugman | 2014-05-19 12:25:49 +0200 (Mon, 19 May 2014) | 5 lines

The structure.read_* user function 'verbosity' argument is now passed into the structural object.

This allows another printout to be silenced.
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r23236 | bugman | 2014-05-19 12:29:36 +0200 (Mon, 19 May 2014) | 5 lines

The structure.read_* user function 'verbosity' argument is now passed into lib.io.open_read_file().

This allows all printouts from these three user functions to be suppressed.
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