Author: bugman
Date: Tue Jul 29 11:40:25 2014
New Revision: 24799
URL: http://svn.gna.org/viewcvs/relax?rev=24799&view=rev
Log:
Updated the frame order optimisation results for the CaM torsionless,
pseudo-ellipse 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.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz
(with props)
Removed:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
Binary files - no diff available.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz?rev=24799&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz
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svn:mime-type = application/octet-stream
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
Binary files - no diff available.
Removed:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz?rev=24798&view=auto
==============================================================================
Binary file - no diff available.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py?rev=24799&r1=24798&r2=24799&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
Tue Jul 29 11:40:25 2014
@@ -101,12 +101,12 @@
state.save('frame_order_true', force=True)
# Grid search (low quality for speed).
-frame_order.num_int_pts(num=100)
+frame_order.num_int_pts(num=200)
minimise.grid_search(inc=[None, None, None, None, None, None, 7, 7, 7, 7, 7])
# Iterative optimisation with increasing precision.
-num_int_pts = [100, 1000, 10000, 50000]
-func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+num_int_pts = [1000, 10000, 50000]
+func_tol = [1e-2, 1e-3, 1e-4]
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise.execute('simplex', func_tol=func_tol[i])
@@ -119,14 +119,14 @@
# Optimise the pivot and model, again iterating with increasing precision.
frame_order.pivot(pivot, fix=False)
-num_int_pts = [100, 1000, 10000, 50000]
-func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+num_int_pts = [1000, 10000, 50000]
+func_tol = [1e-2, 1e-3, 1e-4]
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise.execute('simplex', func_tol=func_tol[i])
-# Test Monte Carlo simulations (at low quality for speed).
-frame_order.num_int_pts(num=100)
+# Test Monte Carlo simulations.
+frame_order.num_int_pts(num=10000)
monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz?rev=24799&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz?rev=24799&view=auto
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branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2?rev=24799&view=auto
==============================================================================
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branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2
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svn:mime-type = application/octet-stream
Removed:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz?rev=24798&view=auto
==============================================================================
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Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz?rev=24799&view=auto
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branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz?rev=24799&view=auto
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branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz?rev=24799&view=auto
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz?rev=24799&view=auto
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2?rev=24799&view=auto
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branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2
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svn:mime-type = application/octet-stream
Removed:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz?rev=24798&view=auto
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Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz?rev=24799&view=auto
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Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz?rev=24799&view=auto
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r24799 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/