Author: bugman Date: Wed Jul 9 10:05:34 2014 New Revision: 24484 URL: http://svn.gna.org/viewcvs/relax?rev=24484&view=rev Log: Added the full optimisation results for the double rotor test data. This is for the CaM frame order test data using the new frame_order.py optimisation script. Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos_fixed_piv.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos_sim.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos_true.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.bz2 (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.log.bz2 (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_fixed_piv.bz2 (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_fixed_piv.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_sim.pdb.gz (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_true.bz2 (with props) branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_true.pdb.gz (with props) Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos.pdb.gz URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos.pdb.gz?rev=24484&view=auto ============================================================================== Binary file - no diff available. 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Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/ave_pos_true.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.bz2 URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.bz2?rev=24484&view=auto ============================================================================== Binary file - no diff available. Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.bz2 ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Added: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.log.bz2 URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.log.bz2?rev=24484&view=auto ============================================================================== Binary file - no diff available. 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Propchange: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.pdb.gz ------------------------------------------------------------------------------ svn:mime-type = application/octet-stream Modified: branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py?rev=24484&r1=24483&r2=24484&view=diff ============================================================================== --- branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py (original) +++ branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py Wed Jul 9 10:05:34 2014 @@ -16,14 +16,14 @@ C_COM = array([26.837, -12.379, 28.342], float64) # The Z-axis as the inter CoM vector. - z_axis = N_COM - C_COM + z_axis = C_COM - N_COM disp = norm(z_axis) z_axis /= disp # The eigenframe (partly from the system_create.log file). eigensystem = transpose(array([ + [ -7.778375610280605e-01, 6.284649244351433e-01, -7.532653237683726e-04], [-0.487095774865268, -0.60362450312215, -0.63116968030708 ], - [ -7.778375610280605e-01, 6.284649244351433e-01, -7.532653237683726e-04], z_axis ], float64)) @@ -38,8 +38,8 @@ AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -21.269217407269576, -3.122610661328414, -2.400652421655998] AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623469076122531, 0.435439405668396, 5.081265529106499] EIGEN_ALPHA, EIGEN_BETA, EIGEN_GAMMA, PIVOT_DISP = eigen_system() -CONE_SIGMA_MAX = 10.5 * 2.0 * pi / 360.0 # 0.1832595714594046 -CONE_SIGMA_MAX_2 = 11.5 * 2.0 * pi / 360.0 # 0.20071286397934787 +CONE_SIGMA_MAX = 11.5 / 2.0 * 2.0 * pi / 360.0 # 0.20071286397934787 +CONE_SIGMA_MAX_2 = 10.5 / 2.0 * 2.0 * pi / 360.0 # 0.1832595714594046 # Create the data pipe. pipe.create(pipe_name='frame order', pipe_type='frame order') @@ -63,7 +63,7 @@ ln = ['dy', 'tb', 'tm', 'er'] for i in range(len(ln)): # Load the RDCs. - #rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4) + rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4) # The PCS. pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7) @@ -101,7 +101,7 @@ frame_order.ref_domain('N') # Set the initial pivot point. -pivot = array([ 26.837, -12.379, 28.342]) +pivot = array([41.739, 6.03, -0.764]) frame_order.pivot(pivot, fix=True) # Set the paramagnetic centre. @@ -130,12 +130,12 @@ state.save('frame_order_true', force=True) # Grid search (low quality for speed). -frame_order.num_int_pts(num=100) -grid_search(inc=[None, None, None, None, None, None, None, 7, 7, 7, 7, 7]) +frame_order.num_int_pts(num=200) +grid_search(inc=[21, 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, 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]) @@ -148,14 +148,14 @@ # 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, 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 (at low quality for speed). -frame_order.num_int_pts(num=100) +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/double_rotor/frame_order_fixed_piv.bz2 URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_fixed_piv.bz2?rev=24484&view=auto ============================================================================== Binary file - no diff available. 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