Hi Ed.
This now fails:
Relax_disp.test_bug_21460_disp_cluster_fail
"/Users/tlinnet/software/disp_spin_speed/specific_analyses/relax_disp/data.py",
line 1863, in plot_disp_curves
point = cpmg_frqs_new[ei][mi][oi][di]
IndexError: list index out of range
Do you have an idea?
Best
Troels
-------------------
---------------------
- The 'R2eff' model -
---------------------
relax> pipe.copy(pipe_from='origin - relax_disp (Thu Jan 2 13:46:44
2014)', pipe_to='R2eff - relax_disp (Thu Jan 2 13:46:44 2014)',
bundle_to='relax_disp (Thu Jan 2 13:46:44 2014)')
relax> pipe.switch(pipe_name='R2eff - relax_disp (Thu Jan 2 13:46:44
2014)')
relax> relax_disp.select_model(model='R2eff')
The model for determining the R2eff/R1rho values from peak intensities.
relax> calc(verbosity=1)
Calculating the R2eff/R1rho values for fixed relaxation time period data.
Spin ':459@N'.
Results writing
===============
relax>
relax_disp.plot_disp_curves(dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff',
num_points=1000, extend=500.0, force=True)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/disp_459_N.agr'
for writing.
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/grace2images.py'
for writing.
relax>
relax_disp.write_disp_curves(dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff',
force=True)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/disp_459_N.out'
for writing.
relax> value.write(param='r2eff', file='r2eff.out',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff',
scaling=1.0, comment=None, bc=False, force=True)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/r2eff.out'
for writing.
relax> grace.write(x_data_type='res_num', y_data_type='r2eff',
spin_id=None, plot_data='value', file='r2eff.agr',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff',
force=True, norm=False)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/r2eff.agr'
for writing.
relax> results.write(file='results',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff',
compress_type=1, force=True)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/R2eff/results.bz2'
for writing.
----------------------
- The 'No Rex' model -
----------------------
relax> pipe.copy(pipe_from='origin - relax_disp (Thu Jan 2 13:46:44
2014)', pipe_to='No Rex - relax_disp (Thu Jan 2 13:46:44 2014)',
bundle_to='relax_disp (Thu Jan 2 13:46:44 2014)')
relax> pipe.switch(pipe_name='No Rex - relax_disp (Thu Jan 2 13:46:44
2014)')
relax> relax_disp.select_model(model='No Rex')
The model for no chemical exchange relaxation.
relax> value.copy(pipe_from='R2eff - relax_disp (Thu Jan 2 13:46:44
2014)', pipe_to='No Rex - relax_disp (Thu Jan 2 13:46:44 2014)',
param='r2eff')
Optimisation
============
Nesting and model equivalence checks
------------------------------------
No model nesting or model equivalence detected.
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
Fitting to the spin block [':459@N']
------------------------------------
Unconstrained grid search size: 9 (constraints may decrease this size).
Grid search
~~~~~~~~~~~
Searching through 9 grid nodes.
k: 0 xk: [ 0.5, 0.5] fk: 436.862516468
k: 3 xk: [ 0.5, 1.25] fk: 406.49758716
Optimised parameter values:
r2 (SQ CPMG - 0.00059977 MHz) 5.000000000000000
r2 (SQ CPMG - 599.77212354 MHz) 12.500000000000000
relax> minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-05, grad_tol=None, max_iter=1000,
constraints=True, scaling=True, verbosity=1)
Fitting to the spin block [':459@N']
------------------------------------
Logarithmic barrier function
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
k: 0 xk: [ 0.5, 1.25] fk: 406.49758716
Entering sub-algorithm.
Simplex minimisation
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: [ 0.5, 1.25] fk: 406.443271114
Parameter values: [0.0021207261241890383, 0.89458126560725759]
Function value: 1.2065517126305849
Iterations: 43
Function calls: 83
Gradient calls: 0
Hessian calls: 0
Warning: None
k: 1 xk: [ 0.002120726124, 0.8945812656] fk: 1.20356618386
Entering sub-algorithm.
Simplex minimisation
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: [ 0.002120726124, 0.8945812656] fk: 1.20336591206
Parameter values: [0.00022841489930163758, 0.89459438262210345]
Function value: 1.1986979999438134
Iterations: 23
Function calls: 48
Gradient calls: 0
Hessian calls: 0
Warning: None
k: 2 xk: [0.0002284148993, 0.8945943826] fk: 1.19844299599
Entering sub-algorithm.
Simplex minimisation
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: [0.0002284148993, 0.8945943826] fk: 1.19844554603
Parameter values: [0.00022841489930163758, 0.89459438262210345]
Function value: 1.1984455460281873
Iterations: 9
Function calls: 21
Gradient calls: 0
Hessian calls: 0
Warning: None
k: 3 xk: [0.0002284148993, 0.8945943826] fk: 1.19844895966
Entering sub-algorithm.
Simplex minimisation
~~~~~~~~~~~~~~~~~~~~
k: 0 xk: [0.0002284148993, 0.8945943826] fk: 1.19844302149
Parameter values: [0.00022841489930163758, 0.89459438262210345]
Function value: 1.1984430214890309
Iterations: 9
Function calls: 21
Gradient calls: 0
Hessian calls: 0
Warning: None
Parameter values: [0.00022841489930163758, 0.89459438262210345]
Function value: 1.1984429959886356
Iterations: 84
Function calls: 173
Gradient calls: 0
Hessian calls: 0
Warning: None
Optimised parameter values:
r2 (SQ CPMG - 0.00059977 MHz) 0.002284148993016
r2 (SQ CPMG - 599.77212354 MHz) 8.945943826221034
relax> eliminate(function=None, args=None)
Results writing
===============
relax>
relax_disp.plot_disp_curves(dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/No
Rex', num_points=1000, extend=500.0, force=True)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmppeiu5o/No
Rex/disp_459_N.agr' for writing.
Traceback (most recent call last):
File
"/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py",
line 926, in test_bug_21460_disp_cluster_fail
relax_disp.Relax_disp(pipe_name="origin - relax_disp (Thu Jan 2
13:46:44 2014)", pipe_bundle="relax_disp (Thu Jan 2 13:46:44 2014)",
results_dir=self.tmpdir, models=['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site
expanded'], grid_inc=3, mc_sim_num=5, modsel='AIC', pre_run_dir=None,
insignificance=1.0, numeric_only=False, mc_sim_all_models=False,
eliminate=True)
File
"/Users/tlinnet/software/disp_spin_speed/auto_analyses/relax_disp.py", line
124, in __init__
self.run()
File
"/Users/tlinnet/software/disp_spin_speed/auto_analyses/relax_disp.py", line
494, in run
self.write_results(path=path, model=model)
File
"/Users/tlinnet/software/disp_spin_speed/auto_analyses/relax_disp.py", line
541, in write_results
self.interpreter.relax_disp.plot_disp_curves(dir=path, force=True)
File "/Users/tlinnet/software/disp_spin_speed/prompt/uf_objects.py", line
223, in __call__
self._backend(*new_args, **uf_kargs)
File
"/Users/tlinnet/software/disp_spin_speed/specific_analyses/relax_disp/data.py",
line 1863, in plot_disp_curves
point = cpmg_frqs_new[ei][mi][oi][di]
IndexError: list index out of range
----------------------------------------------------------------------
Ran 1 test in 0.121s
Idea to fix systemtest?