Author: bugman
Date: Fri Oct 2 13:56:22 2015
New Revision: 27952
URL: http://svn.gna.org/viewcvs/relax?rev=27952&view=rev
Log:
Merged revisions
25901,25905,25909,25918-25922,25926,25929-25931,25948-25956,25960-25961 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r25901 | bugman | 2014-09-18 17:53:33 +0200 (Thu, 18 Sep 2014) | 5 lines
Fix for the frame order system test optimisation printouts.
The cdp.num_int_pts variable is now called cdp.sobol_max_points.
........
r25905 | bugman | 2014-09-19 09:07:19 +0200 (Fri, 19 Sep 2014) | 6 lines
The starting time of the axis permutation model optimisations is now output.
This is in the frame order auto-analysis. This call to the time user
function occurred for the
normal models, so extending it to the permuted axes models makes the output
more consistent.
........
r25909 | bugman | 2014-09-19 09:56:34 +0200 (Fri, 19 Sep 2014) | 6 lines
Simplified the atomic position averaging warning in the frame order
analysis.
Instead of throwing a warning for each spin, one warning for all spins is
now given. This should
make the output a lot less verbose.
........
r25918 | bugman | 2014-09-19 11:55:07 +0200 (Fri, 19 Sep 2014) | 5 lines
The frame order minimise_setup_atomic_pos() function now accepts the
verbosity argument.
This is used to silence the warnings in user functions such as
frame_order.sobol_setup.
........
r25919 | bugman | 2014-09-19 12:04:28 +0200 (Fri, 19 Sep 2014) | 8 lines
Improvements for the frame order overfit_deselect() API method.
Three changes have been made: The print statements have been converted to
RelaxWarnings; the spin
IDs or spin ID pairs are now stored in a list and one RelaxWarning for the
missing PCS data and one
for the missing RDC data is now given; and the verbose flag is now used to
determine if a
RelaxWarning will be given.
........
r25920 | bugman | 2014-09-19 12:06:32 +0200 (Fri, 19 Sep 2014) | 3 lines
Fix for the previous commit - a bracket was missing preventing relax from
starting.
........
r25921 | bugman | 2014-09-19 12:08:36 +0200 (Fri, 19 Sep 2014) | 3 lines
Change to the position averaging warning in the minimise_setup_atomic_pos()
frame order function.
........
r25922 | bugman | 2014-09-19 12:18:57 +0200 (Fri, 19 Sep 2014) | 6 lines
Improvements for the printout from the update_model() frame order function.
A list of updated parameters is now created and everything is printed on a
single line at the end.
The printout is therefore much more compact.
........
r25926 | bugman | 2014-09-19 18:26:26 +0200 (Fri, 19 Sep 2014) | 9 lines
Spun out part of the frame_order.pdb_model user function into the new
frame_order.simulate.
The new user function arguments required for properly creating the
pseudo-Brownian dynamics
simulation would have made the frame_order.pdb_model user function too
complicated. Therefore this
part has been spun out into the new frame_order.simulate user function.
The frame_order.simulate
frontend fully describes the algorithm that will be used to simulate the
dynamic content of the PCS
and RDC data, and warns that not all modes of motion are visible and
present.
........
r25929 | bugman | 2014-09-19 18:33:01 +0200 (Fri, 19 Sep 2014) | 6 lines
Updated the frame order auto-analysis to call the new frame_order.simulate
user function.
Although not implemented yet, this allows the user function to create the
simulation PDB file in the
future.
........
r25930 | bugman | 2014-09-19 18:41:29 +0200 (Fri, 19 Sep 2014) | 3 lines
Small fix for the new frame_order.simulate user function backend.
........
r25931 | bugman | 2014-09-19 18:43:15 +0200 (Fri, 19 Sep 2014) | 6 lines
Updated the base script for the Frame_order.test_cam_* system tests.
The frame_order.simulate user function is now called directly after the
frame_order.pdb_model user
function.
........
r25948 | bugman | 2014-09-22 11:52:24 +0200 (Mon, 22 Sep 2014) | 17 lines
Created the backend framework for the frame_order.simulate user function.
The backend specific_analyses.frame_order.uf.simulate() function performs
all data checks required,
prepares the output file object, assembles the frame order parameter values
and pivot point, and
creates a copy of the structural object object with the ensemble collapsed
into a single model.
All this data is then passed into the new
lib.frame_order.simulation.brownian() function. This
initialises all required data structures and the structural object. The
main loop of the simulation
is also implemented, taking snapshots at every fixed number of steps and
terminating the loop once
the total number of snapshots are reached. The snapshot consists of
copying the original unrotated
structural model and rotating it into the new position. The rotation is
currently the identity
matrix.
The old specific_analyses.frame_order.geometric.create_distribution() stub
function has been
deleted.
........
r25949 | bugman | 2014-09-22 12:04:58 +0200 (Mon, 22 Sep 2014) | 5 lines
Decreased the time required for the Frame_order.test_cam_* system tests.
The frame_order.simulate user function now only creates a total of 20
snapshots rather than 1000.
........
r25950 | bugman | 2014-09-22 12:19:36 +0200 (Mon, 22 Sep 2014) | 7 lines
Added new arguments to the frame order auto-analysis for the
frame_order.simulate user function.
These are the brownian_step_size, brownian_snapshot and brownian_total
arguments which are passed
directly into the frame_order.simulate user function. This gives the user
more control, as well as
allowing the test suite to speed up this part of the analysis.
........
r25951 | bugman | 2014-09-22 12:21:31 +0200 (Mon, 22 Sep 2014) | 6 lines
Huge speed up for the Frame_order.test_auto_analysis user function.
The pseudo-Brownian dynamics simulation via the frame_order.simulate user
function has been
massively speed up to allow the test to be almost as fast as before.
........
r25952 | bugman | 2014-09-22 12:26:32 +0200 (Mon, 22 Sep 2014) | 7 lines
Spun out the code for shifting to the average frame order position into a
new function.
The old code of the create_ave_pos() of the
specific_analyses.frame_order.geometric module has been
shifted into the new average_position() function. This will allow the code
to be reused by other
parts of relax to obtain the average frame order structures.
........
r25953 | bugman | 2014-09-22 12:28:49 +0200 (Mon, 22 Sep 2014) | 6 lines
Implemented the shifting to the average position for the
frame_order.simulate user function backend.
This simply sends the structural object into the new average_position()
function of the
specific_analyses.frame_order.geometric module.
........
r25954 | bugman | 2014-09-22 13:50:37 +0200 (Mon, 22 Sep 2014) | 6 lines
Improvements for the frame_order.simulate user function.
The rigid model is now skipped, the PDB file closed, and some printouts for
better user feedback
have been added.
........
r25955 | bugman | 2014-09-22 13:52:54 +0200 (Mon, 22 Sep 2014) | 6 lines
Changed the default PDB file name for the frame_order.simulate user
function to 'simulate.pdb'.
The '*.bz2' extension has been dropped so that the file is quicker to
create and does not need to be
decompressed for loading into molecular viewers.
........
r25956 | bugman | 2014-09-22 15:08:06 +0200 (Mon, 22 Sep 2014) | 7 lines
Created the specific_analyses.frame_order.geometric.generate_axis_system()
function.
This is now used by most parts of the frame order analysis to generate the
full 3D eigenframe of the
motions. Previously this was implemented each time the frame or major axis
was required. This
replicated and highly inconsistent code has been eliminated.
........
r25960 | bugman | 2014-09-22 17:00:37 +0200 (Mon, 22 Sep 2014) | 6 lines
Fix for the new
specific_analyses.frame_order.geometric.generate_axis_system() function.
The rotor and free rotor models were not correctly handled and the returned
eigenframe was the zero
matrix.
........
r25961 | bugman | 2014-09-23 09:26:08 +0200 (Tue, 23 Sep 2014) | 11 lines
Implemented the pseudo-Brownian frame order dynamics simulation for the
single motion models.
This uses the same logic as in the
test_suite/shared_data/frame_order/cam/*/generate_distribution.py
scripts which were used to generate all of the test suite data. However
rather than using a random
rotation matrix, a random 3D vector is used to rotate a fixed angle. And
the rotation is used to
rotate the current state to state i+1. The rotation for the state is
decomposed into torsion-tilt
angles once shifted into the motional eigenframe, the violations checked
for as the state shifted to
the boundary, then the new state reconstructed from the corrected
torsion-tilt angles, and then it
is shifted from the motional eigenframe to the PDB frame.
........
Added:
trunk/lib/frame_order/simulation.py
- copied, changed from r25956,
branches/frame_order_cleanup/lib/frame_order/simulation.py
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/lib/frame_order/__init__.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/geometric.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
trunk/user_functions/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/__init__.py?rev=27952&r1=27951&r2=27952&view=diff
Copied: trunk/lib/frame_order/simulation.py (from r25956,
branches/frame_order_cleanup/lib/frame_order/simulation.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/simulation.py?p2=trunk/lib/frame_order/simulation.py&p1=branches/frame_order_cleanup/lib/frame_order/simulation.py&r1=25956&r2=27952&rev=27952&view=diff
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/geometric.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27952&r1=27951&r2=27952&view=diff
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27952&r1=27951&r2=27952&view=diff
Modified: trunk/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/frame_order.py?rev=27952&r1=27951&r2=27952&view=diff
r27952 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ test_suite/system_tests/ test_suite/sy...