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{{infobox relax release| version = 4.0.0| prev = 3.3.9| next = 4.0.1| keywords = Frame order theory| type = Major feature| date = 7 October 2015| manual = yes}} == Description ==
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== Download ==
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== CHANGES file ==
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=== Features ===
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=== Changes ===
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* Updated the CaM frame order test model superimposition script. The [http://www.nmr-relax.com/manual/structure_superimpose.html 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.
* 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 The Euler angles for the rotation about the motional pivot have been replaced by the translation vector and Euler angle CoM rotation parameters.
* Fix for a number of the frame order models which do not have parameter constraints. The [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.parameters-module.html#linear_constraints linear_constraint() function] was returning A, b = [], [] for these models, but these empty numpy arrays were causing the [https://gna.org/projects/{{minfx/ homepage}} minfx library] to fail. These values are now caught and the constraint algorithm turned off in the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.api.Frame_order-class.html#minimise minimise() specific API method].
* 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.
* 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.
* Added a script for profiling the target function calls of the pseudo-ellipse frame order model.
* Added a timeit script and log file showing how numpy.cos() is 10 times slower than math.cos(). This is for single floats.
* Shifted the calculation of the θ<supsub>max</supsub> cone opening for the pseudo-ellipse outside of all loops. This is infrastructure change for potentially eliminating all of the looping for the PCS numeric integration in the future. It however slightly speeds up the pseudo-ellipse frame order model. Using 500 target function calls in the profiling_pseudo_ellipse.py script in test_suite/shared_data/frame_order/timings/, the time spent in the [http://www.nmr-relax.com/api/4.0/lib.frame_order.matrix_ops-module.html#pcs_pivot_motion_full_qr_int pcs_pivot_motion_full_qrint() function] decreases from 20.849 to 20.719 seconds.* Converted the torsionless pseudo-ellipse model to also use the [http://www.nmr-relax.com/api/4.0/lib.frame_order.pseudo_ellipse-module.html#tmax_pseudo_ellipse_array tmax_pseudo_ellipse_array() function]. This allows the calculation of the pseudo-elliptic cone opening θ<supsub>max</supsub> to be shifted outside of all loops.
* Created a profiling script and log file for the isotropic cone frame order model. This shows where the slow points of the model are, using 2000 target function calls.
* Increased the function call number to 500 in the pseudo-ellipse frame order model profiling script. The profiling log file has also been added to show where the slowness is - specifically that the numeric PCS integration takes almost the same amount of time as the RDC frame order matrix construction using the scipy.integrate.quad() function.
* Sent the verbosity argument to the minfx.grid.grid_split() function for the frame order analysis. This matches the relax trunk changes for the model-free analysis. The minfx function in the next release (1.0.8) will now be more verbose, so this will help with user feedback when running the model-free analysis on a cluster or multi-core system using MPI.
* Improvements for the parallelised grid search for the frame order analysis. As each grid point can take wildly different numbers of CPU cycles to calculate the chi-squared value for, the result of subdividing the grid search was that some subdivisions where incredibly quick while others required much larger amounts of time. To avoid this bad slave management, the grid points are now randomised. This means that the subdivisions will require about the same amount of time to optimise.
* Moved the setup of the target function data structures in the frame order analysis. This is for the [http://www.nmr-relax.com/manual/grid_search.html grid_search] and [http://www.nmr-relax.com/manual/minimise.html minimise] user functions. The target function data setup function has been renamed to [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html#target_fn_data_setup target_fn_data_setup()]. This is now called before the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation.Frame_order_grid_command-class.html Frame_order_grid_command] and [[http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation.Frame_order_minimise_command-class.html Frame_order_minimise_command] multi-processor objects are initialised, and all of the data is now passed into these functions. Although the code is uglier, this has the benefit that the [http://www.nmr-relax.com/api/4.0/specific_analyses.frame_order.optimisation-module.html#target_fn_data_setup target_fn_data_setup() function] will only be called once. This data setup requires a lot of time, so for a large cluster, this can be a large time saving for the grid search.
* Modified the frame_order_free_start.py script to better mimic the [http://www.nmr-relax.com/api/4.0/auto_analyses.frame_order-module.html frame order auto-analysis].
* Updated the frame order optimisation results for the 2<sup>nd</sup> CaM free rotor test data. The optimisation in the frame_order.py is now of higher precision with the number of Sobol' numeric integration points significantly increased, especially for the Monte Carlo simulations. The new frame order representation files have been added to the repository, as well as the intermediate state files.
* Created the Grace graphs for the double rotor model 1<sup>st</sup> degree frame order matrix. These are the values calculated directly from the [http://www.nmr-relax.com/api/4.0/lib.frame_order-module.html lib.frame_order modules]. The graphs were previously all zeros.
* Recreated all of the simulated pseudo-ellipse frame order matrix element graphs. These are now in the Kronecker product notation so that they will match the graphs calculated using the [http://www.nmr-relax.com/api/4.0/lib.frame_order.pseudo_ellipse-module.html relax lib.frame_order.pseudo_ellipse module].
* Fix for the [http://www.nmr-relax.com/api/4.0/lib.frame_order.pseudo_ellipse-module.html#part_int_daeg1_pseudo_ellipse_22 pseudo-ellipse 1<sup>st</sup> degree frame order matrix Daeg22 ᛞ<sub>22</sub> element].
* Updated all of the pseudo-ellipse 1<sup>st</sup> degree frame order matrix graphs for the recent fix.
* Converted the Sobol' rotation matrices to float32 in the frame order target function. This is to conserve huge amounts of memory to allow for more Sobol' points to be used. For example for the models which use 3D Sobol' points (isotropic cone and pseudo-ellipse), a maximum of 50000 Sobol' points requires 50000000 to be created, using about 15 Gb of RAM.
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=== Bugfixes ===
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== Links ==
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* [http://wiki.nmr-relax.com/Relax_4.0.0 Official release notes on the relax wiki].
* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2514 |text=Gna! news item]}}.
* [http://article.gmane.org/gmane.science.nmr.relax.announce/68 Gmane mailing list archive].
* [https://mail.gna.org/public/relax-announce/2015-10/msg00001.html Local archives].
* [https://marc.info/?l=relax-announce&m=144376869310289144485916126262&w=2 Mailing list ARChives (MARC)].
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== Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/4.0/ The relax 4.0 API documentation]
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[[Category:Relaxation dispersion Frame order analysis]]