Author: bugman
Date: Thu Oct 1 21:23:53 2015
New Revision: 27929
URL: http://svn.gna.org/viewcvs/relax?rev=27929&view=rev
Log:
Merged revisions 23641-23646 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23641 | bugman | 2014-06-04 19:21:24 +0200 (Wed, 04 Jun 2014) | 6 lines
Removed a terrible hack for handling the frame order analysis without
constraints.
This is no longer needed as the log-barrier method is now used to constrain
the optimisation, so
that the torsion angle can no longer be negative.
........
r23642 | bugman | 2014-06-04 19:36:43 +0200 (Wed, 04 Jun 2014) | 6 lines
Constraints are now implemented in the frame order grid search.
This is useful for the pseudo-elliptic models as the cone theta_x < theta_y
constraint halves the
optimisation space.
........
r23643 | bugman | 2014-06-05 08:36:47 +0200 (Thu, 05 Jun 2014) | 10 lines
Expanded the CaM rotor test data frame_order.py optimisation script.
The optimisation is now implemented as in the auto-analysis, with an
iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the
function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is
now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now
much lower.
The results of the new optimisation are included.
........
r23644 | bugman | 2014-06-05 08:51:23 +0200 (Thu, 05 Jun 2014) | 10 lines
Expanded the CaM pseudo-ellipse test data frame_order.py optimisation
script.
The optimisation is now implemented as in the auto-analysis, with an
iterative increase in accuracy
of the quasi-random numerical integration together with an decrease of the
function tolerance cutoff
for optimisation. The accuracy of the initial chi-squared calculation is
now much higher. And the
accuracy of the initial grid search and the Monte Carlo simulations is now
much lower.
The results of the new optimisation are included.
........
r23645 | bugman | 2014-06-05 10:28:34 +0200 (Thu, 05 Jun 2014) | 9 lines
Added one more iteration for the zooming optimisation of the frame order
auto-analysis.
This is to improve the speed of optimisation when all RDC and PCS data is
being used. The previous
iterations where with [100, 1000, 200000] Sobol' integration points and
[1e-2, 1e-3, 1e-4] function
tolerances. This has been increased to [100, 1000, 10000, 100000] and
[1e-2, 1e-3, 5e-3, 1e-4].
The final number of points has been decreased as that level of accuracy
does not appear to be
necessary. These are also only default values that the user can change for
themselves.
........
r23646 | bugman | 2014-06-05 10:50:12 +0200 (Thu, 05 Jun 2014) | 6 lines
Updated the CaM frame order data generation base script to print out more
information.
This is for the first axis system so that the same amount of information as
the second system is
printed.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_true.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_true.pdb.gz
- copied unchanged from r23646,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor/ave_pos_true.pdb.gz
Removed:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos.pdb
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_fixed_piv.pdb
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_true.pdb
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos.pdb
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_fixed_piv.pdb
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_true.pdb
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_true.pdb.gz
[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=27929&r1=27928&r2=27929&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=27929&r1=27928&r2=27929&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=27929&r1=27928&r2=27929&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=27929&r1=27928&r2=27929&view=diff
Removed:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos.pdb?rev=27928&view=auto
Removed:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_fixed_piv.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_fixed_piv.pdb?rev=27928&view=auto
Removed:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_true.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/ave_pos_true.pdb?rev=27928&view=auto
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.bz2?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.log.bz2?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_fixed_piv.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order_true.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
Removed: trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos.pdb?rev=27928&view=auto
Removed:
trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_fixed_piv.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_fixed_piv.pdb?rev=27928&view=auto
Removed: trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_true.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/ave_pos_true.pdb?rev=27928&view=auto
Modified: trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.bz2?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.log.bz2?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_fixed_piv.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_true.pdb.gz?rev=27929&r1=27928&r2=27929&view=diff
r27929 - in /trunk: ./ auto_analyses/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/ test_suite/shar...