Author: bugman
Date: Fri Sep 25 14:17:21 2015
New Revision: 27876
URL: http://svn.gna.org/viewcvs/relax?rev=27876&view=rev
Log:
Merged revisions 27854-27865 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27854 | bugman | 2015-06-23 18:14:57 +0200 (Tue, 23 Jun 2015) | 5 lines
Added Monte Carlo simulations to the N_state_model.test_absolute_T system
test.
This is to demonstrate a failure of the simulations in certain N-state
model setups.
........
r27855 | bugman | 2015-06-23 18:26:18 +0200 (Tue, 23 Jun 2015) | 5 lines
Added a missing call to monte_carlo.initial_values in the
N_state_model.test_absolute_T system test.
This fixes the commit of r27854, showing that there is not a problem with
the Monte Carlo simulations.
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r27856 | bugman | 2015-06-24 14:35:32 +0200 (Wed, 24 Jun 2015) | 9 lines
Added Monte Carlo and Bootstrap simulation support for the RDC and PCS Q
factor calculations.
The pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions
have been modified to
support Monte Carlo and Bootstrap simulations. The sim_index argument has
been added to allow the Q
factor for the given simulation number to be calculated. All of the Q
factor data structures in the
base data pipe now have *_sim equivalents for permanently storing the
simulation values. For the
simulation values, all the warnings have been silenced.
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r27857 | bugman | 2015-06-24 14:39:42 +0200 (Wed, 24 Jun 2015) | 9 lines
Added simulation support for the RDC and PCS Q factors in the N-state model
analysis.
This is for both Monte Carlo and Bootstrap simulation. The simulation RDC
and PCS values, as well
as the simulation back calculated values are now stored via the
minimise_bc_data() function of
specific_analyses.n_state_model.optimisation in the respective spin or
interatomic data containers.
The analysis specific API methods now send the sim_index value into
minimise_bc_data(), as well as
the pipe_control.rdc.q_factors() and pipe_control.pcs.q_factors() functions.
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r27858 | bugman | 2015-06-24 14:51:11 +0200 (Wed, 24 Jun 2015) | 3 lines
Removed some accidentally committed debugging printouts.
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r27859 | bugman | 2015-06-25 12:52:26 +0200 (Thu, 25 Jun 2015) | 5 lines
Silenced a warning in the N-state model optimisation if the verbosity is
set to zero.
This removes a repetitive warning from the Monte Carlo or Bootstrap
simulations.
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r27860 | bugman | 2015-06-25 16:00:59 +0200 (Thu, 25 Jun 2015) | 9 lines
Huge speed up for the Monte Carlo simulations in the N-state model analyses.
This speed up is also for Bootstrap simulations and the frame order
analysis. The change affects
the monte_carlo.initial_values user function. The alignment tensor
_update_object() method was very
inefficient when updating the Monte Carlo simulation data structures. For
each simulation, each of
the alignment tensor data structures were being updated for all
simulations. Now only the current
simulations is being updated. This speeds up the user function by many
orders of magnitude.
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r27861 | bugman | 2015-06-26 09:56:16 +0200 (Fri, 26 Jun 2015) | 6 lines
Added functions for calculating the geometric mean and standard deviation
to the relax library.
These are the geometric_mean() and geometric_std() functions of the
lib.statistics module. The
implementation is designed to be fast, using numpy array arithmetic rather
than Python loops.
........
r27862 | bugman | 2015-06-26 09:57:22 +0200 (Fri, 26 Jun 2015) | 3 lines
Removed some rubbish text from the new lib.statistics.geometric_*()
function docstrings.
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r27863 | bugman | 2015-06-26 10:33:34 +0200 (Fri, 26 Jun 2015) | 3 lines
Created a simple unit test for the new lib.statistics.geometric_mean()
function.
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r27864 | bugman | 2015-06-26 10:36:14 +0200 (Fri, 26 Jun 2015) | 3 lines
Addition of the file which should have been committed in the last commit
(r27863).
........
r27865 | bugman | 2015-06-26 10:38:27 +0200 (Fri, 26 Jun 2015) | 3 lines
Added a unit test for the new lib.statistics.geometric_std() function.
........
Added:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/test_statistics.py
- copied unchanged from r27865,
trunk/test_suite/unit_tests/_lib/test_statistics.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/data_store/align_tensor.py
branches/frame_order_cleanup/lib/statistics.py
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/pipe_control/rdc.py
branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
branches/frame_order_cleanup/specific_analyses/n_state_model/optimisation.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/absolute_T.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/__init__.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/data_store/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/data_store/align_tensor.py?rev=27876&r1=27875&r2=27876&view=diff
Modified: branches/frame_order_cleanup/lib/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/statistics.py?rev=27876&r1=27875&r2=27876&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=27876&r1=27875&r2=27876&view=diff
Modified: branches/frame_order_cleanup/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/rdc.py?rev=27876&r1=27875&r2=27876&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/n_state_model/api.py?rev=27876&r1=27875&r2=27876&view=diff
Modified:
branches/frame_order_cleanup/specific_analyses/n_state_model/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/n_state_model/optimisation.py?rev=27876&r1=27875&r2=27876&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/absolute_T.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/absolute_T.py?rev=27876&r1=27875&r2=27876&view=diff
Modified: branches/frame_order_cleanup/test_suite/unit_tests/_lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/__init__.py?rev=27876&r1=27875&r2=27876&view=diff
r27876 - in /branches/frame_order_cleanup: ./ data_store/ lib/ pipe_control/ specific_analyses/n_state_model/ test_suite/sys...