Author: bugman Date: Fri Jun 6 08:38:25 2014 New Revision: 23670 URL: http://svn.gna.org/viewcvs/relax?rev=23670&view=rev Log: Expanded the 2nd 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 have been added to the repository. Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_fixed_piv.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_true.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_fixed_piv.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_true.pdb.gz (with props) Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.bz2 branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.log.bz2 branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos.pdb.gz URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/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_ellipse2/ave_pos_fixed_piv.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_fixed_piv.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_true.pdb.gz URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_true.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/ave_pos_true.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.bz2 URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.bz2?rev=23670&r1=23669&r2=23670&view=diff ============================================================================== Binary files - no diff available. Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.log.bz2 URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.log.bz2?rev=23670&r1=23669&r2=23670&view=diff ============================================================================== Binary files - no diff available. Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.pdb.gz URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py?rev=23670&r1=23669&r2=23670&view=diff ============================================================================== --- branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py (original) +++ branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py Fri Jun 6 08:38:25 2014 @@ -80,10 +80,8 @@ # 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) @@ -101,22 +99,34 @@ # 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, None, 7, 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] +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/pseudo_ellipse2/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_ellipse2/frame_order_fixed_piv.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_fixed_piv.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_true.pdb.gz URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_true.pdb.gz?rev=23670&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_true.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream