Author: bugman
Date: Fri Oct 2 14:24:34 2015
New Revision: 27956
URL: http://svn.gna.org/viewcvs/relax?rev=27956&view=rev
Log:
Merged revisions
26141,26207,26313-26320,26349,26365,26388-26394,26396-26477,26479-26481,26484,26534-26537,26657-26658,26668-26669
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
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r26141 | bugman | 2014-10-02 15:53:19 +0200 (Thu, 02 Oct 2014) | 5 lines
Modified the PCS content testing base system.
The paramagnetic centre is now shifted to the origin, as this is the real
centre of the PCS physics.
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r26207 | bugman | 2014-10-08 12:10:04 +0200 (Wed, 08 Oct 2014) | 17 lines
Intermediate optimisation results are now stored by the frame order
auto-analysis.
The results from each minimise.grid_search and minimise.execute user
function call are now stored in
specially named directories located in the 'intermediate_results'
directory, which itself is located
in the auto-analysis results_dir directory. This allows intermediate
results to be more easily
analysed later on, which can be useful for optimising the optimisation
steps. These directories can
also be used for the pre_run_dir auto-analysis argument for subsequent
refinements from earlier
steps in the optimisation. The results stored include everything from the
results_output() method
and the count_sobol_points() and summarise() functions.
To allow this to work, the auto-analysis functions count_sobol_points() and
summarise() required
modification. Results files are now always loaded into a temporary data
pipe, rather switching to
the corresponding pipe, and the temporary data pipe is deleted after the
data has been extracted.
The original data pipe name is also stored and a switch back to that pipe
occurs at the end of each
function.
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r26313 | bugman | 2014-10-20 09:54:11 +0200 (Mon, 20 Oct 2014) | 7 lines
The simulation is now turned of for intermediate results in the frame order
auto-analysis.
The intermediate results are only for checking, so for these the full
pseudo-Brownian dynamics
simulations are not required. The simulation flag has been introduced into
the results_output()
method of the auto-analysis to control this.
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r26314 | bugman | 2014-10-20 11:52:52 +0200 (Mon, 20 Oct 2014) | 8 lines
The splitting of the rigid model grid search into rotation and translation
parts is now optional.
In the frame order auto-analysis, the rigid_grid_split argument has been
introduced. The
alternating algorithm of performing a grid search over the rotational space
followed by translation
is now optional and turned off by default. The reason is because the
global minimum is sometimes
missed with this shortcut algorithm.
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r26315 | bugman | 2014-10-20 14:45:24 +0200 (Mon, 20 Oct 2014) | 6 lines
Speed up of the Frame_order.test_auto_analysis system test.
The splitting of the rigid model grid search into rotation and translation
parts has been
reactivated.
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r26316 | bugman | 2014-10-20 15:11:58 +0200 (Mon, 20 Oct 2014) | 5 lines
Created the Optimisation.has_grid() method for the frame order
auto-analysis.
This is used to test if the optimisation settings object has a grid search
defined.
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r26317 | bugman | 2014-10-20 15:15:21 +0200 (Mon, 20 Oct 2014) | 7 lines
The grid search can now be skipped for the rigid model in the frame order
auto-analysis.
If the input 3D structures are close to the real solution, the grid search
over the translational
and rotation parameters of the rigid model could be skipped. This speeds
up the analysis and can
help find the real solution in problematic cases.
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r26318 | bugman | 2014-10-20 16:23:08 +0200 (Mon, 20 Oct 2014) | 6 lines
The intermediate results storing can now be turned off in the frame order
auto-analysis.
The new store_intermediate Boolean argument has been added to the analysis
to allow the storage of
these results to be turned on or off.
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r26319 | bugman | 2014-10-20 16:24:11 +0200 (Mon, 20 Oct 2014) | 5 lines
The intermediate results are no longer stored in the
Frame_order.test_auto_analysis system test.
This drops the test timing on one system from ~190 seconds to ~50 seconds.
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r26320 | bugman | 2014-10-20 16:45:49 +0200 (Mon, 20 Oct 2014) | 7 lines
The compression level for results files can now be set in the frame order
auto-analysis.
This is via the new argument results_compress_type, which is used to set
the compress_type argument
of the results.write user function. The results reading parts of the
auto-analysis have been
updated to allow uncompressed, bzip2 compressed, and gzip compressed files
to be handled.
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r26349 | bugman | 2014-10-22 15:22:03 +0200 (Wed, 22 Oct 2014) | 7 lines
Added a printout of the frame order model in the target function setup
function.
This is printed out when the minimise.calculate, minimise.grid_search, or
minimise.execute user
function are called, and is for better feedback, especially in the
auto-analysis where the
repetitive optimisations can be confusing.
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r26365 | bugman | 2014-10-23 11:34:29 +0200 (Thu, 23 Oct 2014) | 6 lines
Updated the frame order analysis for the structure.load_spins user function
changes.
The minimise_setup_atomic_pos() function of the
specific_analyses.frame_order.optimisation module
now handles the mixed type spin.pos variable correctly.
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r26388 | bugman | 2014-10-23 15:32:59 +0200 (Thu, 23 Oct 2014) | 5 lines
The data pipe containing a PCS subset is now optional in the frame order
auto-analysis.
This is for systems which have so little data that a subset makes no sense.
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r26389 | bugman | 2014-10-23 15:47:26 +0200 (Thu, 23 Oct 2014) | 3 lines
Missing import.
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r26390 | bugman | 2014-10-23 15:57:02 +0200 (Thu, 23 Oct 2014) | 12 lines
Redesigned the optimisation steps for the frame order auto-analysis.
The code has been significantly simplified as the optimisation for the PCS
subset and full data set
was the same. The code duplication has been eliminated by combining it
into the new optimisation()
method. The check for the PCS subset has also been expanded so that it is
skipped if the subset
data pipe is not supplied, even if an optimisation object for the subset
has been (this should
prevent strange errors when the auto-analysis is incorrectly used).
A side effect of this code merger is that the zooming grid search has now
been activated for the
full PCS data set. This is of great benefit when a PCS subset is not being
used.
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r26391 | bugman | 2014-10-23 16:19:39 +0200 (Thu, 23 Oct 2014) | 6 lines
The minimise.execute user function skip_preset flag is now False in the
frame order auto-analysis.
This is for the main model optimisation. Without this flag set, the grid
search for the pivot point
position for the rotor model was being skipped at the first zoom level.
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r26392 | bugman | 2014-10-23 16:32:15 +0200 (Thu, 23 Oct 2014) | 9 lines
The pivot point can now be excluded from the grid search in the frame order
auto-analysis.
If the initial pivot point is known to be reasonable, then it may be
possible to skip it in the grid
search for the rotor frame order model. This can lead to a speed up of the
analysis and can help
with stability. The pivot_search argument has been added to the
auto-analysis
Optimisation.add_grid() method to enable this. The get_grid_pivot_search()
method has also been
added to allow the auto-analysis to query this and turn it off if desired.
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r26393 | bugman | 2014-10-28 11:24:45 +0100 (Tue, 28 Oct 2014) | 5 lines
Updated the description of the frame_order.permute_axes user function.
This now includes the isotopic cone.
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r26394 | bugman | 2014-10-28 14:23:43 +0100 (Tue, 28 Oct 2014) | 6 lines
Replaced the table in the frame_order.permute_axes user function.
The original table was an old and incorrect version. This has been
replaced by the correct
permutation table.
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r26396 | bugman | 2014-11-01 12:36:07 +0100 (Sat, 01 Nov 2014) | 7 lines
Added some old relax scripts for both simulating and predicting the frame
order matrix elements.
These were used for the initial implementation of the pseudo-ellipse frame
order model back in July
2010. The scripts will be extended for all frame order models. The
simulated values could then be
used in unit tests of the frame order matrix code in lib.frame_order.
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r26397 | bugman | 2014-11-01 14:09:17 +0100 (Sat, 01 Nov 2014) | 6 lines
Updated the frame_order_simulate.py script for simulating frame order
matrix elements.
The MODEL variable has been added in preparation for supporting all model
types, and this is now
added to the file name. The Grace header is now also being automatically
generated.
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r26398 | bugman | 2014-11-01 14:42:40 +0100 (Sat, 01 Nov 2014) | 5 lines
Improvements for the Grace files produced by the frame_order_simulate.py
script.
The model name is now set as a variable and is used for the subheading.
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r26399 | bugman | 2014-11-01 14:44:03 +0100 (Sat, 01 Nov 2014) | 7 lines
Updated the frame_order_solution.py script for directly calculating the
frame order matrix elements.
The MODEL variable has been added in preparation for supporting all model
types, and this is now
added to the file name. The Grace header is now also being automatically
generated and this matches
that for the frame_order_simulation.py script.
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r26400 | bugman | 2014-11-01 17:00:00 +0100 (Sat, 01 Nov 2014) | 5 lines
Zero values can now be handled in the pseudo-ellipse 1st degree frame order
matrix function.
This is in
lib.frame_order.pseudo_ellipse.compile_1st_matrix_pseudo_ellipse().
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r26401 | bugman | 2014-11-01 17:01:58 +0100 (Sat, 01 Nov 2014) | 7 lines
Removed some unused code in the pseudo-ellipse 2nd degree frame order
matrix function.
This is the compile_2nd_matrix_pseudo_ellipse() function in the
lib.frame_order.pseudo_ellipse
module. The change should make the RDC part of the frame order analysis
for the pseudo-ellipse
model slightly faster.
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r26402 | bugman | 2014-11-01 17:57:15 +0100 (Sat, 01 Nov 2014) | 5 lines
Modified the rotate_daeg() function as this is independent of the degree of
the frame order matrix.
This is the lib.frame_order.matrix_ops.rotate_daeg() function.
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r26403 | bugman | 2014-11-01 18:00:21 +0100 (Sat, 01 Nov 2014) | 6 lines
Fix for the compile_1st_matrix_pseudo_ellipse() function.
This function of the lib.frame_order.pseudo_ellipse module now can rotate
the 1st degree frame order
matrix out of its eigenframe and into the PDB frame.
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r26404 | bugman | 2014-11-01 18:02:31 +0100 (Sat, 01 Nov 2014) | 5 lines
Created an executable Python script for mass converting the frame order
matrix Grace graphs.
The script converts the *.agr files to EPS and PNG files.
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r26405 | bugman | 2014-11-01 18:04:10 +0100 (Sat, 01 Nov 2014) | 6 lines
Modified the frame order matrix Grace graph to EPS/PNG format conversion
script.
The binary being called is now 'grace' rather than 'xmgrace'. This allows
different Grace versions
to be used.
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r26406 | bugman | 2014-11-01 20:13:38 +0100 (Sat, 01 Nov 2014) | 6 lines
Modified the frame order matrix Grace graph to EPS/PNG format conversion
script.
Grace is now used to create a PostScript file and then the ps2eps program
is called to convert to
EPS. This produces much better EPS files for inclusion into LaTeX
documents.
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r26407 | bugman | 2014-11-01 20:22:26 +0100 (Sat, 01 Nov 2014) | 8 lines
Redesign of the frame_order_solution.py script for calculating the frame
order matrix elements.
This script now loops over all models, all motional frame orientations, and
all order parameters to
generate the Grace graphs of all 1st and 2nd degree frame order matrix
elements. Therefore the
script only needs to be executed once. The script also now calculates a
point at zero (slightly
shifted to 0.01 to avoid artifacts).
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r26408 | bugman | 2014-11-01 20:24:24 +0100 (Sat, 01 Nov 2014) | 6 lines
Added all of the Grace graphs produced by the frame_order_solution.py
script.
These are the graphs of the 1st and 2nd degree frame order matrix elements,
calculated using the
functions in lib.frame_order.
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r26409 | bugman | 2014-11-02 15:39:25 +0100 (Sun, 02 Nov 2014) | 8 lines
Updated frame_order_simulate.py to be much faster in simulating the frame
order matrix elements.
The script also matches the Grace file output of the
frame_order_solution.py script. The inside()
method has been renamed for the pseudo-ellipse and the infrastructure for
adding support for the
other frame order models has been added. By shifting calculations outside
of the loops, the script
is now many orders of magnitude faster.
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r26410 | bugman | 2014-11-02 22:14:36 +0100 (Sun, 02 Nov 2014) | 4 lines
Implemented the compile_1st_matrix_rotor() function.
This is for the lib.frame_order.rotor module. The function will calculate
the 1st degree in-frame
frame order matrix for the rotor model.
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r26411 | bugman | 2014-11-02 22:14:38 +0100 (Sun, 02 Nov 2014) | 4 lines
Created the Grace graphs for the rotor model 1st degree frame order matrix
elements.
These are the values calculated directly from the lib.frame_order modules.
The graphs were
previously all zeros.
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r26412 | bugman | 2014-11-02 22:14:41 +0100 (Sun, 02 Nov 2014) | 4 lines
Implemented the compile_1st_matrix_free_rotor() function.
This is for the lib.frame_order.free_rotor module. The function will
calculate the 1st degree
in-frame frame order matrix for the free rotor model.
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r26413 | bugman | 2014-11-02 22:14:43 +0100 (Sun, 02 Nov 2014) | 4 lines
Created the Grace graphs for the free rotor model 1st degree frame order
matrix elements.
These are the values calculated directly from the lib.frame_order modules.
The graphs were
previously all zeros.
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r26414 | bugman | 2014-11-02 22:14:45 +0100 (Sun, 02 Nov 2014) | 4 lines
Implemented the compile_1st_matrix_iso_cone() function.
This is for the lib.frame_order.iso_cone module. The function will
calculate the 1st degree
in-frame frame order matrix for the isotropic cone model.
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r26415 | bugman | 2014-11-02 22:14:48 +0100 (Sun, 02 Nov 2014) | 4 lines
Created the Grace graphs for the isotropic cone model 1st degree frame
order matrix elements.
These are the values calculated directly from the lib.frame_order modules.
The graphs were
previously all zeros.
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r26416 | bugman | 2014-11-02 22:14:50 +0100 (Sun, 02 Nov 2014) | 4 lines
Implemented the compile_1st_matrix_iso_cone_torsionless() function.
This is for the lib.frame_order.iso_cone_torsionless module. The function
will calculate the 1st
degree in-frame frame order matrix for the torsionless isotropic cone model.
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r26417 | bugman | 2014-11-02 22:14:52 +0100 (Sun, 02 Nov 2014) | 4 lines
Created the Grace graphs for the torsionless isotropic cone 1st degree
frame order matrix elements.
These are the values calculated directly from the lib.frame_order modules.
The graphs were
previously all zeros.
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r26418 | bugman | 2014-11-02 22:14:55 +0100 (Sun, 02 Nov 2014) | 4 lines
Implemented the compile_1st_matrix_iso_cone_free_rotor() function.
This is for the lib.frame_order.iso_cone_free_rotor module. The function
will calculate the 1st
degree in-frame frame order matrix for the free rotor isotropic cone model.
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r26419 | bugman | 2014-11-02 22:14:57 +0100 (Sun, 02 Nov 2014) | 4 lines
Created the Grace graphs for the free rotor isotropic cone 1st degree frame
order matrix elements.
These are the values calculated directly from the lib.frame_order modules.
The graphs were
previously all zeros.
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r26420 | bugman | 2014-11-02 22:14:59 +0100 (Sun, 02 Nov 2014) | 1 line
Docstring fixes for the new compile_1st_matrix_iso_cone() function.
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r26421 | bugman | 2014-11-02 22:45:54 +0100 (Sun, 02 Nov 2014) | 4 lines
A minor speed up for the frame_order_simulate.py script.
The angles are now being calculated at the very start prior to the main
loop, removing repetitive
calculations.
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r26422 | bugman | 2014-11-02 22:45:56 +0100 (Sun, 02 Nov 2014) | 5 lines
The frame_order_simulate.py script now uses
lib.text.progress.progress_meter().
This script for simulating the frame order matrix elements now uses the
standard progress meter in
relax to simplify the script. This should also speed up the calculations
as the progress printouts
were slowing down the calculations.
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r26423 | bugman | 2014-11-03 08:18:07 +0100 (Mon, 03 Nov 2014) | 7 lines
Simulation of the pseudo-ellipse frame order matrix elements.
This is for a simulation of 1,000,000 states for each angle increment, and
includes in-frame and
out-of-frame and varying of theta X, Y, and Z. The resultant Grace graphs
have been added to the
repository.
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r26424 | bugman | 2014-11-03 08:31:48 +0100 (Mon, 03 Nov 2014) | 4 lines
The frame order matrix element simulation script now uses the Kronecker
outer product.
This allows the frame order matrix to be in the same notation as that used
internally in relax. It
will cause the colours of the Sijkl_* curves to match between the
simulation and solution scripts.
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r26425 | bugman | 2014-11-06 13:47:49 +0100 (Thu, 06 Nov 2014) | 7 lines
Added the rotor model to the frame order matrix element simulation script.
The generated in-frame and out-of-frame Grace graphs containing the matrix
values for 1,000,000
simulation values have been added to the repository. The script was
modified so that the rotation
is generated by special rotation_*() methods which are aliased depending on
the model.
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r26426 | bugman | 2014-11-06 14:07:28 +0100 (Thu, 06 Nov 2014) | 7 lines
Added the free rotor model to the frame order matrix element simulation
script.
The generated in-frame and out-of-frame Grace graphs containing the matrix
values for 1,000,000
simulation values have been added to the repository. The
inside_free_rotor() method has been added
to always return True for the rotation generated by rotation_z_axis().
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r26427 | bugman | 2014-11-06 15:48:03 +0100 (Thu, 06 Nov 2014) | 6 lines
Simplifications and fixes for the 1st degree frame order matrix calculation
for the pseudo-ellipse.
The compile_1st_matrix_pseudo_ellipse() function of the
lib.frame_order.pseudo_ellipse module has
been significantly simplified by shifting a lot of maths outside of the
quadratic integration.
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r26428 | bugman | 2014-11-06 15:49:09 +0100 (Thu, 06 Nov 2014) | 5 lines
Updated all the calculated 1st degree frame order matrix graphs for the
pseudo-ellipse.
The changes are due to the fixes in the lib.frame_order.pseudo_ellipse
module.
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r26429 | bugman | 2014-11-06 19:49:04 +0100 (Thu, 06 Nov 2014) | 3 lines
Simplifications for all of the torsionless pseudo-ellipse frame order
matrix equations.
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r26430 | bugman | 2014-11-06 20:00:00 +0100 (Thu, 06 Nov 2014) | 6 lines
Implemented the compile_1st_matrix_pseudo_ellipse_torsionless() function.
This is for the lib.frame_order.pseudo_ellipse_torsionless module. The
function will calculate the
1st degree in-frame frame order matrix for the torsionless pseudo-ellipse
model.
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r27956 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_da...