relax SVN archive

Reverted r24495 as this is rubbish.

The pivot point needs to be initially guessed to centre the grid search for the pivot to a
reasonable 20 Angstrom box in the PDB space.

The command used was:
svn merge -r24495:r24494 .

.....
r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines
Changed paths:
M /branches/frame_order_cleanup/specific_analyses/frame_order/parameters.py

Modified the specific_analyses.frame_order.parameters.update_model() function.

The pivot parameters are now set to 0.0 if they do not currently exist. They were previously
excluded from this initialisation, but this is required for the frame order models if the pivot is
not initially fixed at a give location in the PDB space.
.....

Parallelised the frame order optimisation code to run on clusters or multi-core systems via OpenMPI.

The optimisation code has been split into the three standard parts of the multi-processor:

- Frame_order_memo is the new Memo object used to store data on the master for use when data is
returned from the slaves.

- Frame_order_minimise_command is the Slave_command which stored all required data for the
optimisation, is pickled and sent to a slave, sets up the target function, and then performs
optimisation.

- Frame_order_result_command is the Result_command initialised by the Slave_command on the slave for
pickling and returning results to the master.

To avoid pickling the target function class, which is not possible, the store_bc_data() and
target_fn_setup() functions of the specific_analyses.frame_order.optimisation module have been
redesigned to work with basic data structures rather than the target function class directly. The
target_fn_setup() function no longer returns an initialised target function class, but rather all
the data assembled prior to the initialisation. And the target function class was itself modified
so that pcs_theta and rdc_theta are always defined to allow the store_bc_data() function to be used
successfully.

This parallelisation currently only allows the Monte Carlo simulations to be run on slave
processors.

Constraints are now properly turned off in the minimise user function for the frame order analysis.

The A and b matrices from linear_constraints() are now set to None if they are returned as empty
arrays.

Turned on the optimisation flag for the Frame_order.test_cam_free_rotor system test.

This is to activate code paths currently not tested by the test suite.

Changed the minimisation in the frame order system tests where optimisation is activated.

The number of iterations is now set to 1 for speed testing, and the constraints are turned on.

Merged revisions 24511 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r24511 | bugman | 2014-07-10 16:02:25 +0200 (Thu, 10 Jul 2014) | 9 lines

Fix for the relaxation dispersion analysis Monte Carlo simulation printouts on clusters.

The multi-processor code was calling the print() function from the Slave_command.run() method,
however this runs on the slave processor. This has been shifted to the Results_command.run() method
which runs on the master once the results have been returned via the Results_command. Now the
printout of the simulation number and cluster ID will be visible when running via OpenMPI on a
cluster.
........

Merged revisions 24511 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r24511 | bugman | 2014-07-10 16:02:25 +0200 (Thu, 10 Jul 2014) | 9 lines

Fix for the relaxation dispersion analysis Monte Carlo simulation printouts on clusters.

The multi-processor code was calling the print() function from the Slave_command.run() method,
however this runs on the slave processor. This has been shifted to the Results_command.run() method
which runs on the master once the results have been returned via the Results_command. Now the
printout of the simulation number and cluster ID will be visible when running via OpenMPI on a
cluster.
........

Fix for the relaxation dispersion analysis Monte Carlo simulation printouts on clusters.

The multi-processor code was calling the print() function from the Slave_command.run() method,
however this runs on the slave processor. This has been shifted to the Results_command.run() method
which runs on the master once the results have been returned via the Results_command. Now the
printout of the simulation number and cluster ID will be visible when running via OpenMPI on a
cluster.

Removal of many unused imports in the disp_spin_speed branch.

These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find
all unused imports. The false positives also present in the trunk were ignored.

Removal of many unused imports in the frame_order_cleanup branch.

These were detected using the devel_scripts/find_unused_imports.py script which uses pylint to find
all unused imports. The false positives also present in the trunk were ignored. And the unused
imports in the dispersion code were also left for clean up the disp_spin_speed branch.