Author: bugman
Date: Wed Jul 9 16:20:51 2014
New Revision: 24496
URL: http://svn.gna.org/viewcvs/relax?rev=24496&view=rev
Log:
Added a profiling script and log file for the free rotor frame order model.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py
- copied, changed from r24495,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_iso_cone.py
Copied:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py
(from r24495,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_iso_cone.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py?p2=branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py&p1=branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_iso_cone.py&r1=24495&r2=24496&rev=24496&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_iso_cone.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py
Wed Jul 9 16:20:51 2014
@@ -2,7 +2,7 @@
The user functions below were obtained by running:
-$ ./relax -sd Frame_order.test_cam_iso_cone | grep "relax>" > log
+$ ./relax -sd Frame_order.test_cam_free_rotor | grep "relax>" > log
To profile, set the profiling flag in the 'relax' file.
"""
@@ -16,8 +16,8 @@
# All the user functions from the Frame_order.test_cam_pseudo_ellipse system
test until the first target function call.
pipe.create(pipe_name='frame order', pipe_type='frame order', bundle=None)
-structure.read_pdb(file='1J7O_1st_NH.pdb',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/',
read_mol=None, set_mol_name='N-dom', read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)
-structure.read_pdb(file='1J7P_1st_NH_rot.pdb',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/',
read_mol=None, set_mol_name='C-dom', read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)
+structure.read_pdb(file='1J7O_1st_NH.pdb',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/',
read_mol=None, set_mol_name='N-dom', read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)
+structure.read_pdb(file='1J7P_1st_NH_rot.pdb',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/',
read_mol=None, set_mol_name='C-dom', read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)
structure.load_spins(spin_id='@N', mol_name_target=None, ave_pos=False)
structure.load_spins(spin_id='@H', mol_name_target=None, ave_pos=False)
spin.isotope(isotope='15N', spin_id='@N', force=False)
@@ -25,23 +25,23 @@
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True, pipe=None)
interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041e-10,
unit='meter')
interatom.unit_vectors(ave=True)
-rdc.read(align_id='dy', file='rdc_dy.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
-pcs.read(align_id='dy', file='pcs_dy_subset.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
+rdc.read(align_id='dy', file='rdc_dy.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
+pcs.read(align_id='dy', file='pcs_dy_subset.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
spectrometer.temperature(id='dy', temp=303)
spectrometer.frequency(id='dy', frq=900000000.0, units='Hz')
-rdc.read(align_id='tb', file='rdc_tb.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
-pcs.read(align_id='tb', file='pcs_tb_subset.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
+rdc.read(align_id='tb', file='rdc_tb.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
+pcs.read(align_id='tb', file='pcs_tb_subset.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
spectrometer.temperature(id='tb', temp=303)
spectrometer.frequency(id='tb', frq=900000000.0, units='Hz')
-rdc.read(align_id='tm', file='rdc_tm.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
-pcs.read(align_id='tm', file='pcs_tm_subset.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
+rdc.read(align_id='tm', file='rdc_tm.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
+pcs.read(align_id='tm', file='pcs_tm_subset.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
spectrometer.temperature(id='tm', temp=303)
spectrometer.frequency(id='tm', frq=900000000.0, units='Hz')
-rdc.read(align_id='er', file='rdc_er.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
-pcs.read(align_id='er', file='pcs_er_subset.txt',
dir='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/iso_cone',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
+rdc.read(align_id='er', file='rdc_er.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
data_type='D', spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
sep=None, neg_g_corr=False, absolute=False)
+pcs.read(align_id='er', file='pcs_er_subset.txt',
dir='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=None,
spin_num_col=None, spin_name_col=5, data_col=6, error_col=7, sep=None,
spin_id=None)
spectrometer.temperature(id='er', temp=303)
spectrometer.frequency(id='er', frq=900000000.0, units='Hz')
-script(file='/data/relax/branches/frame_order_cleanup2/test_suite/shared_data/frame_order/cam/tensors.py',
dir=None)
+script(file='/data/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/tensors.py',
dir=None)
align_tensor.init(tensor='Dy N-dom', align_id='dy', domain=None,
params=(0.000622191953772, 1.35210609663e-05, -0.000133742852942,
0.000756743581636, 0.000550729840729), scale=1.0, angle_units='deg',
param_types=2, errors=False)
align_tensor.init(tensor='Dy N-dom', align_id='dy', domain=None,
params=(2.35766523882e-05, 2.51785772774e-05, 1.99369755031e-05,
1.86674275393e-05, 2.01343581166e-05), scale=1.0, angle_units='deg',
param_types=2, errors=True)
align_tensor.init(tensor='Tb N-dom', align_id='tb', domain=None,
params=(0.000617222650166, -0.000438128542649, -0.000375477068228,
0.000760687126774, 0.00034129025543), scale=1.0, angle_units='deg',
param_types=2, errors=False)
@@ -68,28 +68,24 @@
align_tensor.set_domain(tensor='Er N-dom', domain='N')
align_tensor.set_domain(tensor='Er C-dom', domain='C')
align_tensor.reduction(full_tensor='Er N-dom', red_tensor='Er C-dom')
-frame_order.select_model(model='iso cone')
+frame_order.select_model(model='free rotor')
frame_order.ref_domain(ref='N')
-frame_order.pivot(pivot=array([ 37.254001617431641, 0.5 ,
16.746500015258789], dtype=float64), order=1, fix=True)
+frame_order.pivot(pivot=array([ 39.482819802779524, 3.255542739800277,
14.265680648645716]), order=1, fix=False)
paramag.centre(pos=[35.934, 12.194, -4.206], atom_id=None, pipe=None,
verbosity=1, fix=True, ave_pos=True, force=False)
frame_order.num_int_pts(num=2000)
value.set(val=-21.269217407269576, param='ave_pos_x', index=0, spin_id=None,
error=False)
value.set(val=-3.122610661328414, param='ave_pos_y', index=0, spin_id=None,
error=False)
value.set(val=-2.400652421655998, param='ave_pos_z', index=0, spin_id=None,
error=False)
-value.set(val=5.623469076122531, param='ave_pos_alpha', index=0,
spin_id=None, error=False)
-value.set(val=0.435439405668396, param='ave_pos_beta', index=0,
spin_id=None, error=False)
-value.set(val=5.081265529106499, param='ave_pos_gamma', index=0,
spin_id=None, error=False)
-value.set(val=0.960079978595343, param='axis_theta', index=0, spin_id=None,
error=False)
-value.set(val=4.032275506219623, param='axis_phi', index=0, spin_id=None,
error=False)
-value.set(val=0.6, param='cone_theta', index=0, spin_id=None, error=False)
-value.set(val=0.9, param='cone_sigma_max', index=0, spin_id=None,
error=False)
+value.set(val=0.19740471457956135, param='ave_pos_beta', index=0,
spin_id=None, error=False)
+value.set(val=4.662231310426542, param='ave_pos_gamma', index=0,
spin_id=None, error=False)
+value.set(val=-0.6109933365884923, param='axis_alpha', index=0,
spin_id=None, error=False)
# Set up the target function for direct calculation.
model, param_vector, scaling_matrix = target_fn_setup(sim_index=None,
verbosity=1)
# Make repeated function calls.
-N = 2000
+N = 200
print("Function calls.")
for i in range(N):
print(i)
r24496 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/timings/profiling_free_rotor.py