relax SVN archive

Complete redesign of the CaM frame order data generation base script for speed and memory savings.

Although the rotated XH bond vector and atomic position code was very fast, the amount of memory
needed to store these in the spin containers and interatomic data containers was huge when N > 1e6.
The subsequent rdc.back_calc and pcs.back_calc user function calls would also take far too long.

Therefore the base script has been redesigned. The _create_distribution() method has been split
into four: _calculate_pcs(), _calculate_rdc(), _create_distribution(), and _pipe_setup().
The _pipe_setup() method is called first to set up the data pipe with all required data. Then the
_calculate_rdc() and _calculate_pcs() methods, and finally _create_distribution() if the DIST_PDB
flag is set.

The calls to the rdc.back_calc and pcs.back_calc user functions have been eliminated. Instead the
_calculate_rdc() and _calculate_pcs() methods calculate the averaged RDC and PCS themselves as numpy
array structures. Rather than storing the huge rotated vectors and atomic positions data
structures, the RDCs and PCSs are summed. These are then divided by self.N at the end to average
the values.

Compared to the old code, when N is set to 20 million the RAM usage drops from ~20 GB to ~65 MB.
The total run time is also decreased on one system from a few days to a few hours (an order or two
of magnitude).

Fix for variable num_points not set.

An attempt to fix the pipe_control/minimisy.py minimise() call to processor.run_queue().

It was thought that I was modifying the address of array class(back_calc).
But this does not seem to be the problem.

Turned of processor.run_queue() when using calc().

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

A weird behaviour was found when running the test-suite.

Somehow, queued jobs from the last test suite was not flushed and done.
Running the test-suite gave errors on almost all tests.

Inspecting systemtest which only used calc() for the dispersion API, showed that no jobs was queued
in the calculate() method, and the call to processor.run_queue(), was turned off, solving the problem.

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.