URL:
<http://gna.org/bugs/?22017>
Summary: LinAlgError, for all numerical CPMG models.
Project: relax
Submitted by: tlinnet
Submitted on: Wed 07 May 2014 03:07:49 PM UTC
Category: relax's source code
Specific analysis category: Relaxation dispersion
Priority: 7 - High
Severity: 4 - Important
Status: None
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Release: Repository: trunk
Discussion Lock: Any
Operating System: All systems
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Details:
Hi Edward.
The attached script, will make relax trip.
I am reading in fake R2eff points, and then do a back calculation with:
sfrq_1 = 599.8908617*1E6
ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60]
sfrq_2 = 499.8908617*1E6
ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50]
With the following dynamic parameters
['Ala', 1, 'N', {'r2': {r20_key_1:10, r20_key_2:11.5}, 'r2a': {r20_key_1:10,
r20_key_2:11.5}, 'r2b': {r20_key_1:10, r20_key_2:11.5}, 'kex': 1000, 'pA':
0.99, 'dw': 2} ]
#################3
relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
file='CPMG_599.9_1_N.txt', dir=None, disp_point_col=1, offset_col=None,
data_col=2, error_col=3, sep=None)
Opening the file 'CPMG_599.9_1_N.txt' for reading.
The following R2eff/R1rho data has been loaded into the relax data store:
# R2eff_key Disp_point R2eff
R2eff_error
sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
1.000000000000000 0.100000000000000
Traceback (most recent call last):
File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/multi/processor.py",
line 494, in run
self.callback.init_master(self)
File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/multi/__init__.py",
line 318, in default_init_master
self.master.run()
File "/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax.py", line 194,
in run
self.interpreter.run(self.script_file)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", line
275, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", line
569, in run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", line
468, in interact_script
exec_script(script_file, local)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/prompt/interpreter.py", line
347, in exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.6/runpy.py", line 140, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.6/runpy.py", line 34, in _run_code
exec code in run_globals
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py",
line 270, in <module>
r2effs = optimisation.back_calc_r2eff(spin=cur_spin, spin_id=cur_spin_id)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/specific_analyses/relax_disp/optimisation.py",
line 188, in back_calc_r2eff
chi2 = model.func(param_vector)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/target_functions/relax_disp.py",
line 1419, in func_ns_cpmg_2site_3D
return self.calc_ns_cpmg_2site_3D_chi2(R20A=R20, R20B=R20, dw=dw, pA=pA,
kex=kex)
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/target_functions/relax_disp.py",
line 542, in calc_ns_cpmg_2site_3D_chi2
r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=self.M0, r20a=R20A[r20_index],
r20b=R20B[r20_index], pA=pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA,
inv_tcpmg=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
back_calc=self.back_calc[0][si][mi][0],
num_points=self.num_disp_points[0][si][mi][0], power=self.power[0][mi])
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/lib/dispersion/ns_cpmg_2site_3d.py",
line 115, in r2eff_ns_cpmg_2site_3D
Rexpo = matrix_exponential(R*tcp[i])
File
"/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/lib/linear_algebra/matrix_exponential.py",
line 46, in matrix_exponential
W, V = eig(A)
File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", line 999,
in eig
_assertFinite(a)
File "/usr/lib64/python2.6/site-packages/numpy/linalg/linalg.py", line 144,
in _assertFinite
raise LinAlgError, "Array must not contain infs or NaNs"
LinAlgError: Array must not contain infs or NaNs
#########################
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wed 07 May 2014 03:07:49 PM UTC Name: cpmg_synthetic.py Size: 16kB
By: tlinnet
<http://gna.org/bugs/download.php?file_id=20667>
_______________________________________________________
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<http://gna.org/bugs/?22017>
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[bug #22017] LinAlgError, for all numerical CPMG models.