Author: bugman
Date: Fri Jun 6 08:39:27 2014
New Revision: 23671
URL: http://svn.gna.org/viewcvs/relax?rev=23671&view=rev
Log:
Expanded the CaM free-rotor isotropic cone 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 have been added to the repository.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_true.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_true.pdb.gz
(with props)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.bz2
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.log.bz2
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos.pdb.gz?rev=23671&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_fixed_piv.pdb.gz?rev=23671&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_true.pdb.gz?rev=23671&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/ave_pos_true.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.bz2?rev=23671&r1=23670&r2=23671&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.log.bz2?rev=23671&r1=23670&r2=23671&view=diff
==============================================================================
Binary files - no diff available.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.pdb.gz?rev=23671&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py?rev=23671&r1=23670&r2=23671&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
Fri Jun 6 08:39:27 2014
@@ -1,4 +1,4 @@
-# Script for optimising the free rotor frame order test model of CaM.
+# Script for optimising the isotropic cone free rotor frame order test model
of CaM.
# Python module imports.
from numpy import array
@@ -81,10 +81,8 @@
# Set the paramagnetic centre.
paramag.centre(pos=[35.934, 12.194, -4.206])
-# The optimisation settings.
-frame_order.num_int_pts(num=5000)
-
-# Check the minimum.
+# Check the minimum (at a very high quality to check that the chi-squared
value is zero).
+frame_order.num_int_pts(num=100000)
value.set(param='ave_pos_x', val=AVE_POS_X)
value.set(param='ave_pos_y', val=AVE_POS_Y)
value.set(param='ave_pos_z', val=AVE_POS_Z)
@@ -98,22 +96,34 @@
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
-# Optimise.
-#grid_search(inc=5)
-minimise('simplex')
+# Grid search (low quality for speed).
+frame_order.num_int_pts(num=100)
+grid_search(inc=[None, None, None, None, None, 11, 11, 11])
+
+# Iterative optimisation with increasing precision.
+num_int_pts = [100, 1000, 10000, 50000]
+func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+for i in range(len(num_int_pts)):
+ frame_order.num_int_pts(num=num_int_pts[i])
+ minimise('simplex', func_tol=func_tol[i])
# Store the result.
frame_order.pdb_model(ave_pos_file='ave_pos_fixed_piv.pdb.gz',
rep_file='frame_order_fixed_piv.pdb.gz', dist_file=None, force=True)
-# Optimise the pivot and model.
+# Optimise the pivot and model, again iterating with increasing precision.
frame_order.pivot(pivot, fix=False)
-minimise('simplex')
+num_int_pts = [100, 1000, 10000, 50000]
+func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+for i in range(len(num_int_pts)):
+ frame_order.num_int_pts(num=num_int_pts[i])
+ minimise('simplex', func_tol=func_tol[i])
-# Test Monte Carlo simulations.
+# Test Monte Carlo simulations (at low quality for speed).
+frame_order.num_int_pts(num=100)
monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
-minimise('simplex')
+minimise('simplex', func_tol=1e-2)
eliminate()
monte_carlo.error_analysis()
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_fixed_piv.pdb.gz?rev=23671&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_true.pdb.gz?rev=23671&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_true.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
r23671 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/