Author: bugman
Date: Sat Oct 20 19:00:05 2012
New Revision: 17936
URL: http://svn.gna.org/viewcvs/relax?rev=17936&view=rev
Log:
Improvements to the Frame Order multi-processor testing script.
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py?rev=17936&r1=17935&r2=17936&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py
Sat Oct 20 19:00:05 2012
@@ -1,4 +1,11 @@
-# Script for testing out the multi-processor optimisation efficiency.
+"""Script for testing out the multi-processor optimisation efficiency.
+
+This script should be run from the directory where it is found with the
commands:
+
+$ ../../../../../relax multi_processor_test.py
+
+$ mpirun -n 3 ../../../../../relax --multi mpi4py multi_processor_test.py
+"""
# Python module imports.
from numpy import array, float64, transpose, zeros
@@ -8,184 +15,88 @@
from maths_fns.rotation_matrix import euler_to_R_zyz
-class Analysis:
- def __init__(self):
- """Execute the frame order analysis."""
+# Create the data pipe.
+pipe.create(pipe_name='frame order', pipe_type='frame order')
- # Optimise.
- self.optimisation()
+# Read the structures.
+structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
+structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..', set_mol_name='C-dom')
- # Load the original structure.
- self.original_structure()
+# Set up the 15N and 1H spins.
+structure.load_spins(spin_id='@N', ave_pos=False)
+structure.load_spins(spin_id='@H', ave_pos=False)
+spin.isotope(isotope='15N', spin_id='@N')
+spin.isotope(isotope='1H', spin_id='@H')
- # Domain transformation.
- self.transform()
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+dipole_pair.unit_vectors()
- # Display in pymol.
- self.pymol_display()
+# Loop over the alignments.
+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)
- # Save the state.
- state.save('frame_order', force=True)
+ # 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)
+ # The temperature and field strength.
+ temperature(id=ln[i], temp=303)
+ frq.set(id=ln[i], frq=900e6)
- def optimisation(self):
- """Optimise the frame order model."""
+# Load the N-domain tensors (the full tensors).
+script('../tensors.py')
- # Create the data pipe.
- pipe.create(pipe_name='frame order', pipe_type='frame order')
+# Define the domains.
+domain(id='N', spin_id=":1-78")
+domain(id='C', spin_id=":80-148")
- # Read the structures.
- structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..',
set_mol_name='C-dom')
+# The tensor domains and reductions.
+full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
+red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
+ids = ['dy', 'tb', 'tm', 'er']
+for i in range(len(full)):
+ # Initialise the reduced tensor.
+ align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0, 0, 0, 0))
- # Set up the 15N and 1H spins.
- structure.load_spins(spin_id='@N', ave_pos=False)
- structure.load_spins(spin_id='@H', ave_pos=False)
- spin.isotope(isotope='15N', spin_id='@N')
- spin.isotope(isotope='1H', spin_id='@H')
+ # Set the domain info.
+ align_tensor.set_domain(tensor=full[i], domain='N')
+ align_tensor.set_domain(tensor=red[i], domain='C')
- # Define the magnetic dipole-dipole relaxation interaction.
- dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
- dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 *
1e-10)
- dipole_pair.unit_vectors()
+ # Specify which tensor is reduced.
+ align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
- # Loop over the alignments.
- 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)
+# Select the model.
+frame_order.select_model('pseudo-ellipse')
- # 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)
+# Set the reference domain.
+frame_order.ref_domain('N')
- # The temperature and field strength.
- temperature(id=ln[i], temp=303)
- frq.set(id=ln[i], frq=900e6)
+# Set the initial pivot point.
+pivot = array([ 37.254, 0.5, 16.7465])
+frame_order.pivot(pivot, fix=True)
- # Load the N-domain tensors (the full tensors).
- script('../tensors.py')
+# Set the paramagnetic centre.
+paramag.centre(pos=[35.934, 12.194, -4.206])
- # Define the domains.
- domain(id='N', spin_id=":1-78")
- domain(id='C', spin_id=":80-148")
+# The optimisation settings.
+frame_order.num_int_pts(num=1000)
+frame_order.quad_int(flag=False)
- # The tensor domains and reductions.
- full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
- red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
- ids = ['dy', 'tb', 'tm', 'er']
- for i in range(len(full)):
- # Initialise the reduced tensor.
- align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0,
0, 0, 0))
+# Check the minimum.
+value.set(param='ave_pos_alpha', val=4.3434999280669997+0.1)
+value.set(param='ave_pos_beta', val=0.43544332764249905+0.1)
+value.set(param='ave_pos_gamma', val=3.8013235235956007+0.1)
+value.set(param='eigen_alpha', val=3.14159265358979311600+0.1)
+value.set(param='eigen_beta', val=0.96007997859534310869+0.1)
+value.set(param='eigen_gamma', val=4.03227550621962294031+0.1)
+value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0+0.1)
+value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0+0.1)
+value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0+0.1)
+calc()
+print("\nchi2: %s" % repr(cdp.chi2))
- # Set the domain info.
- align_tensor.set_domain(tensor=full[i], domain='N')
- align_tensor.set_domain(tensor=red[i], domain='C')
-
- # Specify which tensor is reduced.
- align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
-
- # Select the model.
- frame_order.select_model('pseudo-ellipse')
-
- # Set the reference domain.
- frame_order.ref_domain('N')
-
- # Set the initial pivot point.
- pivot = array([ 37.254, 0.5, 16.7465])
- frame_order.pivot(pivot, fix=True)
-
- # Set the paramagnetic centre.
- paramag.centre(pos=[35.934, 12.194, -4.206])
-
- # The optimisation settings.
- frame_order.num_int_pts(num=1000)
- frame_order.quad_int(flag=False)
-
- # Check the minimum.
- value.set(param='ave_pos_alpha', val=4.3434999280669997+0.1)
- value.set(param='ave_pos_beta', val=0.43544332764249905+0.1)
- value.set(param='ave_pos_gamma', val=3.8013235235956007+0.1)
- value.set(param='eigen_alpha', val=3.14159265358979311600+0.1)
- value.set(param='eigen_beta', val=0.96007997859534310869+0.1)
- value.set(param='eigen_gamma', val=4.03227550621962294031+0.1)
- value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0+0.1)
- value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0+0.1)
- value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0+0.1)
- calc()
- print("\nchi2: %s" % repr(cdp.chi2))
-
- # Optimise.
- #grid_search(inc=5)
- minimise('simplex', constraints=False)
-
- # Test Monte Carlo simulations.
- monte_carlo.setup(number=5)
- monte_carlo.create_data()
- monte_carlo.initial_values()
- minimise('simplex', constraints=False)
- eliminate()
- monte_carlo.error_analysis()
-
-
- def original_structure(self):
- """Load the original structure into a dedicated data pipe."""
-
- # Create a special data pipe for the original rigid body position.
- pipe.create(pipe_name='orig pos', pipe_type='frame order')
-
- # Load the structure.
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
-
- def pymol_display(self):
- """Display the results in PyMOL."""
-
- # Switch back to the main data pipe.
- pipe.switch('frame order')
-
- # Load the PDBs of the 2 domains.
- structure.read_pdb('1J7O_1st_NH.pdb', dir='..')
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
- # Create the cone PDB file.
- frame_order.cone_pdb(file='cone.pdb', force=True)
-
- # Set the domains.
- frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
- frame_order.domain_to_pdb(domain='C', pdb='1J7P_1st_NH_rot.pdb')
-
- # PyMOL.
- pymol.view()
- pymol.command('show spheres')
- pymol.cone_pdb('cone.pdb')
-
-
- def transform(self):
- """Transform the domain to the average position."""
-
- # Switch back to the main data pipe.
- pipe.switch('frame order')
-
- # The rotation matrix.
- R = zeros((3, 3), float64)
- euler_to_R_zyz(0.0, cdp.ave_pos_beta, cdp.ave_pos_gamma, R)
- print("Rotation matrix:\n%s\n" % R)
- R = transpose(R)
- print("Inverted rotation:\n%s\n" % R)
- pivot = cdp.pivot
-
- # Create a special data pipe for the average rigid body position.
- pipe.create(pipe_name='ave pos', pipe_type='frame order')
-
- # Load the structure.
- structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
-
- # Rotate all atoms.
- structure.rotate(R=R, origin=pivot)
-
- # Write out the new PDB.
- structure.write_pdb('ave_pos', force=True)
-
-
-# Execute the analysis.
-Analysis()
+# Optimise.
+minimise('simplex', constraints=False, max_iter=300)
r17936 - /branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/multi_processor_test.py