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 _______________________________________________________ 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> _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?22017> _______________________________________________ Message sent via/by Gna! http://gna.org/