relax SVN archive

Merged revisions 23616-23622 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23616 | bugman | 2014-06-03 11:16:38 +0200 (Tue, 03 Jun 2014) | 6 lines

Created a new CaM frame order test data set.

This is for the rotor model with a very small torsion angle of 1 degree, and will be used as a
comparison to the rigid model and for testing the performance of the rotor model for an edge case.
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r23617 | bugman | 2014-06-03 11:18:44 +0200 (Tue, 03 Jun 2014) | 7 lines

Updated the frame order representations in all of the frame_order.py scripts for the CaM test data.

All PDB files are now gzipped to save space, the old pymol.cone_pdb user function calls replaced
with pymol.frame_order, and an average domain PDB file for the exact solution is now created in all
cases.
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r23618 | bugman | 2014-06-03 11:20:51 +0200 (Tue, 03 Jun 2014) | 3 lines

The minimisation constraints are now turned on for all CaM test data frame_order.py optimisation scripts.
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r23619 | bugman | 2014-06-03 11:24:59 +0200 (Tue, 03 Jun 2014) | 6 lines

Updated the rotor CaM test data frame_order.py script for the parameter reduction.

The rotor axis {theta, phi} polar angles have been replaced by the single axis alpha angle. This
now matches the script for the 2nd rotor model.
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r23620 | bugman | 2014-06-03 11:26:59 +0200 (Tue, 03 Jun 2014) | 3 lines

Fix for a fatal typo in r23618.
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r23621 | bugman | 2014-06-03 11:47:09 +0200 (Tue, 03 Jun 2014) | 7 lines

Updated the parameters in all of the frame_order.py scripts for the CaM test data.

The parameters are now specified at the top of the script as variables. All scripts now handle the
change to the translation + CoM rotation for the average domain position rather than having a pure
rotation about a fixed pivot, which is no longer supported.
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r23622 | bugman | 2014-06-03 11:49:00 +0200 (Tue, 03 Jun 2014) | 3 lines

Fix for a missing import in the isotropic cone CaM test data frame_order.py scripts.
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Merged revisions 23613-23615 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23613 | bugman | 2014-06-03 08:53:25 +0200 (Tue, 03 Jun 2014) | 5 lines

Optimisation of the rotor model to the rigid CaM frame order test data.

The optimisation script and all results files have been added to the repository.
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r23614 | bugman | 2014-06-03 09:00:25 +0200 (Tue, 03 Jun 2014) | 4 lines

Increased the grid search bounds for the frame order average domain translation.

Instead of being a 10 Angstrom box centred at {0, 0, 0}, now the translation search has been
increased to a 100 Angstrom box.
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r23615 | bugman | 2014-06-03 09:16:09 +0200 (Tue, 03 Jun 2014) | 8 lines

Proper edge case handling and slight speed up of the frame order PCS integration functions.

The case whereby no Sobol' points in the numerical integration lie within the motional distribution
is now caught and the rotation matrix set to the motional eigenframe to simulate the rigid state.
As the code for averaging the PCS was changed, it was also simplified by removing an unnecessary
loop over all spins. This should speed up the PCS integration by a tiny amount.
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Merged revisions 23612 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23612 | bugman | 2014-05-30 12:49:16 +0200 (Fri, 30 May 2014) | 3 lines

Preformed a frame order analysis on the rigid CaM test data set.

This is to demonstrate that everything is operating correctly.
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Merged revisions 23611 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23611 | bugman | 2014-05-30 11:48:40 +0200 (Fri, 30 May 2014) | 4 lines

Preformed a frame order analysis on a number of the CaM test data sets.

This includes the rotor, isotropic cone, and pseudo-ellipse, and the analyses demonstrate a common
bug between all these models.
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Merged revisions 23544 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23544 | bugman | 2014-05-28 17:47:55 +0200 (Wed, 28 May 2014) | 7 lines

Attempt to speed up the pseudo-elliptic frame order models.

The quasi-random numerical integration of the PCS for the pseudo-ellipse has been modified so that
the torsion angle check for each Sobol' point is preformed before the tmax_pseudo_ellipse() function
call. A new check that the tilt angle is less than cone_theta_y, the larger of the two cone angles,
has also been added to avoid tmax_pseudo_ellipse() when the theta tilt angle is outside of an
isotropic cone defined by cone_theta_y.
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Merged revisions 23427-23430,23466-23467 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23427 | bugman | 2014-05-26 17:00:03 +0200 (Mon, 26 May 2014) | 3 lines

The minimisation verbosity flag now effects the frame order RelaxWarning about turning constraints off.
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r23428 | bugman | 2014-05-26 18:15:06 +0200 (Mon, 26 May 2014) | 3 lines

Preformed a frame order analysis on the 2nd CaM free-rotor model test data.

This is to check that everything is operating as expected.
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r23429 | bugman | 2014-05-26 19:07:55 +0200 (Mon, 26 May 2014) | 4 lines

Small speed up for the frame order target functions for most models.

The rotation matrix corresponding to each Sobol' point for the numerical integration is now
pre-calculated during target function initialisation rather than once for each function call.
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r23430 | bugman | 2014-05-26 19:08:02 +0200 (Mon, 26 May 2014) | 5 lines

Updates for some of the frame order system tests for the rotation matrix pre-calculation change.

As the rotation matrix is being pre-calculated, one consequence is that the Sobol' angles are now
full 64-bit precision rather than 32-bit. Therefore this changes the chi-squared value a little,
requiring updates to the tests.
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r23466 | bugman | 2014-05-27 13:54:09 +0200 (Tue, 27 May 2014) | 3 lines

Preformed a frame order analysis on the CaM free-rotor mode test data set.

This is to demonstrate that everything is operating correctly.
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r23467 | bugman | 2014-05-27 13:54:14 +0200 (Tue, 27 May 2014) | 3 lines

Preformed a frame order analysis on the CaM free-rotor mode test data set with missing data.

This is to demonstrate that everything is operating correctly.
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Merged revisions 23394-23407,23411,23421-23424 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23394 | bugman | 2014-05-24 09:11:48 +0200 (Sat, 24 May 2014) | 5 lines

Improved the value setting in the optimisation() method of the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
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r23395 | bugman | 2014-05-24 09:14:53 +0200 (Sat, 24 May 2014) | 9 lines

Changed the average domain position parameter values in the CaM frame order system tests.

This is in the base script used by all scripts in test_suite/system_tests/scripts/frame_order/cam/.
The translation vector coordinates are now set, as well as the CoM Euler angle rotations. These
come from the log file of the test_suite/shared_data/frame_order/cam/superimpose.py script, and are
needed due to the simplification of the average domain position mechanics now mimicking the Kabsch
superimposition algorithm.
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r23396 | bugman | 2014-05-24 09:16:28 +0200 (Sat, 24 May 2014) | 6 lines

The CaM frame order system test mesg_opt_debug() method not prints out the translation vector.

This is printed out at the end of all CaM frame order system tests to help with debugging when the
test fails.
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r23397 | bugman | 2014-05-24 09:32:21 +0200 (Sat, 24 May 2014) | 16 lines

Change for how the CaM frame order system test scripts handle the average domain position rotation.

The trick of pre-rotating the 3D coordinates was used to solve the {a, b, g} -> {0, b', g'} angle
conversion problem in the rotor models no longer works now that the average domain position
mechanics has been simplified. Instead, high precision optimised b' and g' values are now set, and
the ave_pos_alpha value set to None.

The high precision parameters were obtained with the frame_order.py script located in the directory
test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target function was modified so
that the translation vector is hard-coded to [-20.859750185691549, -2.450606987447843,
-2.191854570352916] and the axis theta and phi angles to 0.96007997859534299767 and
4.0322755062196229403. These parameters were then commented out for the model in the module
specific_analyses.frame_order.parameters so only b' and g' were optimised. Iterative optimisation
was used with increasing precision, ending up with high precision using 10,000 Sobol' points.
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r23398 | bugman | 2014-05-24 10:03:22 +0200 (Sat, 24 May 2014) | 5 lines

Updated a number of the CaM frame order system tests for the higher precision data.

The new data results in chi-squared values at the real solution to be much closer to zero.
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r23399 | bugman | 2014-05-24 10:09:39 +0200 (Sat, 24 May 2014) | 5 lines

Change for how the CaM frame order free-rotor pseudo-ellipse test script handle the average position.

This should have been updated earlier (r23397).
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r23400 | bugman | 2014-05-24 10:10:46 +0200 (Sat, 24 May 2014) | 6 lines

Added FIXME comments to the 2nd free-rotor CaM frame order model system test scripts.

These explain the steps required to obtain the correct b' and g' average domain position rotation
angles.
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r23401 | bugman | 2014-05-24 11:47:05 +0200 (Sat, 24 May 2014) | 4 lines

Large increase in precision for the CaM frame order isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23402 | bugman | 2014-05-25 08:49:33 +0200 (Sun, 25 May 2014) | 4 lines

Large increase in precision for the CaM frame order free-rotor, isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23403 | bugman | 2014-05-25 09:39:39 +0200 (Sun, 25 May 2014) | 7 lines

Updated the CaM frame order free-rotor model test data set for testing for missing data.

This is the data in test_suite/shared_data/frame_order/cam/free_rotor_missing_data. To simplify the
copying of data from test_suite/shared_data/frame_order/cam/free_rotor and then the deletion of
data, the missing.py script was created to automate the process. The generate_distribution.py
script and some of the files it creates were removed from the repository so it is clearer how the
data has been created.
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r23404 | bugman | 2014-05-26 09:05:05 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the 2nd CaM frame order free-rotor, isotropic cone model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23405 | bugman | 2014-05-26 09:05:09 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the CaM frame order free-rotor, pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23406 | bugman | 2014-05-26 09:05:12 +0200 (Mon, 26 May 2014) | 4 lines

Large increase in precision for the CaM frame order pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23407 | bugman | 2014-05-26 09:48:42 +0200 (Mon, 26 May 2014) | 5 lines

Updated a number of the CaM frame order system tests for the higher precision data.

The new data results in chi-squared values at the real solution to be much closer to zero. The
free-rotor pseudo-ellipse models might need investigation however as the chi-squared values have
increased.
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r23411 | bugman | 2014-05-26 11:43:18 +0200 (Mon, 26 May 2014) | 6 lines

Elimination of the error_flag variable from the frame order analysis.

This flag is used to activate some old code paths which have now been deleted as they are never
used.
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r23421 | bugman | 2014-05-26 15:20:04 +0200 (Mon, 26 May 2014) | 10 lines

Optimisation of the average domain position for the CaM frame order free-rotor models.

The log file that shows the optimisation of the average domain position for the free-rotor models
has been added to the repository for reference. This is for the simple free-rotor model, but the
optimised position holds for the isotropic cone and pseudo-ellipse model data too.

To perform the optimisation, the axis_theta and axis_phi parameters were removed from the model and
hardcoded into the target function. As the rotor axis is know, this allows the average domain
position to be optimised in isolation. Visual inspection of the results confirmed the position to
be correct.
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r23422 | bugman | 2014-05-26 15:23:37 +0200 (Mon, 26 May 2014) | 6 lines

Fixes for the 2nd frame order free-rotor system tests.

The average domain position parameters are now set to the correct values, matching those in the
relax log file frame_order_ave_pos_opt.log in test_suite/shared_data/frame_order/cam/free_rotor2.
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r23423 | bugman | 2014-05-26 15:37:55 +0200 (Mon, 26 May 2014) | 3 lines

Updated the 2nd CaM free-rotor frame order system tests for the correct average domain position.

The chi-squared values are now significantly lower.
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r23424 | bugman | 2014-05-26 16:24:42 +0200 (Mon, 26 May 2014) | 5 lines

Increased the precision of the chi-squared value testing in the CaM frame order system tests.

The check_chi2 method has been modified so that the chi-squared value is no longer scaled, and the
precision has been increased from 1 significant figure to 4. All of the tests have been updated to
match.
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Merged revisions 23326,23347,23354-23355,23387-23388,23391 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23326 | bugman | 2014-05-22 12:13:26 +0200 (Thu, 22 May 2014) | 4 lines

Parameter update for the 2nd rotor CaM frame order test model optimisation script.

The Euler angles for the rotation about the motional pivot have been replaced by the translation
vector and Euler angle CoM rotation parameters.
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r23347 | bugman | 2014-05-22 18:26:47 +0200 (Thu, 22 May 2014) | 4 lines

Large increase in precision for the 2nd CaM frame order free rotor model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 999,999 and the numpy.float128 data averaging has been used.
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r23354 | bugman | 2014-05-22 18:37:42 +0200 (Thu, 22 May 2014) | 4 lines

Updated the CaM frame order test model superimposition script.

The Ca2+ atoms are now deleted from the structures before superimposition so that the centroid
matches that used in the frame order analysis.
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r23355 | bugman | 2014-05-22 18:46:51 +0200 (Thu, 22 May 2014) | 5 lines

The average domain rotation centroid is printed out when setting up the frame order target functions.

This is to help the user understand what is happening in the analysis.
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r23387 | bugman | 2014-05-23 16:55:52 +0200 (Fri, 23 May 2014) | 6 lines

Faster clearing of numpy arrays in the lib.frame_order modules.

The x[:] = 0.0 notation is now used to set all elements to zero, rather than nested looping over all
dimensions. This however has a negligible effect on the test suite timings.
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r23388 | bugman | 2014-05-23 17:38:34 +0200 (Fri, 23 May 2014) | 4 lines

Large increase in precision for the CaM frame order pseudo-ellipse model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
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r23391 | bugman | 2014-05-23 20:09:10 +0200 (Fri, 23 May 2014) | 3 lines

Missing import from the trunk merge.
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Merged revisions 23241-23245,23251-23253,23256-23258,23280-23283,23309,23321-23322 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23241 | bugman | 2014-05-19 15:10:15 +0200 (Mon, 19 May 2014) | 5 lines

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.
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r23242 | bugman | 2014-05-19 16:13:24 +0200 (Mon, 19 May 2014) | 5 lines

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.
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r23243 | bugman | 2014-05-19 16:54:19 +0200 (Mon, 19 May 2014) | 4 lines

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.
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r23244 | bugman | 2014-05-19 18:11:12 +0200 (Mon, 19 May 2014) | 9 lines

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).
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r23245 | bugman | 2014-05-19 20:10:33 +0200 (Mon, 19 May 2014) | 5 lines

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.
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r23251 | bugman | 2014-05-20 11:09:21 +0200 (Tue, 20 May 2014) | 21 lines

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).
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r23252 | bugman | 2014-05-20 11:48:11 +0200 (Tue, 20 May 2014) | 7 lines

Large increase in accuracy of the RDC and PCS averaging.

This is for the CaM frame order test data generation base script. By storing the RDCs and PCSs in
numpy.float128 arrays, a 64-bit system is required, and then using numpy.average(), the average
value can be calculated with a much higher accuracy. As N becomes larger, the averaging introduces
greater and greater amounts of truncation artifacts. So this change alleviates this. However a lot
more RAM is now required.
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r23253 | bugman | 2014-05-20 11:48:13 +0200 (Tue, 20 May 2014) | 4 lines

Changed the progress meter updating for the CaM frame order test data generation base script.

The spinner was far too fast, updating every 5 increments, and is now updated every 250. And the
total number is now only printed every 10,000 increments.
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r23256 | bugman | 2014-05-20 13:47:33 +0200 (Tue, 20 May 2014) | 20 lines

Reverted r23252 as this uses far, far too much RAM, and there is a better solution.

The command used was:
svn merge -r23252:r23251 .

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r23252 | bugman | 2014-05-20 11:48:11 +0200 (Tue, 20 May 2014) | 7 lines
Changed paths:
M /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/generate_base.py

Large increase in accuracy of the RDC and PCS averaging.

This is for the CaM frame order test data generation base script. By storing the RDCs and PCSs in
numpy.float128 arrays, a 64-bit system is required, and then using numpy.average(), the average
value can be calculated with a much higher accuracy. As N becomes larger, the averaging introduces
greater and greater amounts of truncation artifacts. So this change alleviates this. However a lot
more RAM is now required.
.....
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r23257 | bugman | 2014-05-20 13:47:59 +0200 (Tue, 20 May 2014) | 3 lines

Improvements to the progress meter for the CaM frame order test data generation base script.

Commas are now printed between the thousands and the numbers are now right justified.
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r23258 | bugman | 2014-05-20 13:57:31 +0200 (Tue, 20 May 2014) | 9 lines

Large increase in accuracy of the RDC and PCS averaging.

This is for the CaM frame order test data generation base script. By summing the RDCs and PCSs into
1D numpy.float128 arrays (for this, a 64-bit system is required), and then dividing by N at the end,
the average value can be calculated with a much higher accuracy. As N becomes larger, the
numerical averaging introduces greater and greater amounts of truncation artifacts. So this change
alleviates this.

This change is what r23252 should have been.
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r23280 | bugman | 2014-05-21 09:24:28 +0200 (Wed, 21 May 2014) | 5 lines

Fix for the RDC and PCS averaging in the CaM frame order test data generation base script.

For the double rotor model, or any multiple motional mode model, the averaging was incorrect.
Instead of dividing by N, the values should be divided by N**M, where M is the number of motional
modes.
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r23281 | bugman | 2014-05-21 09:24:31 +0200 (Wed, 21 May 2014) | 9 lines

Huge increase in precision for the CaM frame order free rotor model test data.

The higher precision is because the number structures in the distribution is now twenty million
rather than one million, and the much higher precision numpy.float128 averaging of the updated data
generation base script has been used.

This data should allow for a much better estimate of the beta and gamma average domain position
parameter values for the free rotor models which are affected by the collapse of the alpha parameter
to zero.
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r23282 | bugman | 2014-05-21 09:24:34 +0200 (Wed, 21 May 2014) | 5 lines

Huge increase in precision for the CaM frame order double rotor model test data.

The higher precision is because the number structures in the distribution is now over twenty million
(4500**2) rather than a quarter of a million (500**2). And the much higher precision numpy.float128
averaging of the updated data generation base script has been used.
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r23283 | bugman | 2014-05-21 09:59:51 +0200 (Wed, 21 May 2014) | 3 lines

Fix for the constraint deactivation in the frame order minimisation when no constraints are present.

This problem was introduced at r23211.
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r23309 | bugman | 2014-05-21 17:06:17 +0200 (Wed, 21 May 2014) | 4 lines

Deletion of the frame_order.quad_int user function.

This no longer has a purpose, as the incredibly slow quadratic integration code has been removed
from relax.
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r23321 | bugman | 2014-05-22 08:58:54 +0200 (Thu, 22 May 2014) | 4 lines

Huge increase in precision for the CaM frame order rotor model test data.

The higher precision is because the number structures in the distribution is now 20 million rather
than 166,666, and the numpy.float128 data averaging has been used.
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r23322 | bugman | 2014-05-22 08:59:00 +0200 (Thu, 22 May 2014) | 4 lines

Large increase in precision for the 2nd CaM frame order rotor model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1,000,001 and the numpy.float128 data averaging has been used.
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Merged revisions 23208-23211 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23208 | bugman | 2014-05-16 16:36:45 +0200 (Fri, 16 May 2014) | 7 lines

Updated the CaM frame order test model superimposition script.

The structure.superimpose user function is now correctly called. The output log file has been added
to the repository as it contains the correct translation and Euler rotation information needed for
the test models.
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r23209 | bugman | 2014-05-16 16:55:55 +0200 (Fri, 16 May 2014) | 6 lines

Parameter update for the isotropic cone CaM frame order test model optimisation script.

The Euler angles for the rotation about the motional pivot have been replaced by the translation
vector and Euler angle CoM rotation parameters.
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r23210 | bugman | 2014-05-17 18:03:44 +0200 (Sat, 17 May 2014) | 1 line

Removed an unused import and an extra blank line.
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r23211 | bugman | 2014-05-17 18:03:46 +0200 (Sat, 17 May 2014) | 5 lines

Fix for a number of the frame order models which do not have parameter constraints.

The linear_constraint() function was returning A, b = [], [] for these models, but these empty numpy
arrays were causing the minfx library (https://gna.org/projects/minfx/) to fail. These values are
now caught and the constraint algorithm turned off in the minimise() specific API method.
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