Edward, I created a minfx-py fink package and a test package for relax-py updated to the new 1.3.2 source. Unfortunately, I am seeing a lot of failures in the testsuite on powerpc-apple-darwin9. The results are appended below. I'll try i386-apple-darwin9 tonight. This compares to 1.3.0 without minfx which showed no failures. Jack relax --test-suite Function intros have been enabled. ############################# # System / functional tests # ############################# F....................FF.FFF..............E................. ====================================================================== ERROR: Test the reading of an NMRView peak list. ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> residue.create(res_num=70, res_name=None, mol_id=None) relax> residue.create(res_num=72, res_name=None, mol_id=None) relax> spin.name(spin_id=None, name='N') relax> relax_fit.read(file='cNTnC.xpk', dir='/sw/lib/relax-py25/test_suite/shared_data/peak_lists', relax_time=0.017600000000000001, format='sparky', heteronuc='N', proton='HN', int_col=None) Sparky formatted data file. Opening the file '/sw/lib/relax-py25/test_suite/shared_data/peak_lists/cNTnC.xpk' for reading. Number of header lines found: 2 Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/nmrview.py", line 60, in test_read_peak_list self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk", dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", relax_time=0.0176) File "/sw/lib/relax-py25/prompt/relax_fit.py", line 193, in read relax_fit_obj.read(file=file, dir=dir, relax_time=relax_time, format=format, heteronuc=heteronuc, proton=proton, int_col=int_col) File "/sw/lib/relax-py25/specific_fns/relax_fit.py", line 1034, in read intensity.read(file=file, dir=dir, format=format, heteronuc=heteronuc, proton=proton, int_col=int_col, assign_func=self.assign_function) File "/sw/lib/relax-py25/generic_fns/intensity.py", line 284, in read res_num, H_name, X_name, intensity = intensity_fn(file_data[i]) File "/sw/lib/relax-py25/generic_fns/intensity.py", line 95, in intensity_sparky raise RelaxError, "Improperly formatted Sparky file." RelaxError: RelaxError: Improperly formatted Sparky file. ====================================================================== FAIL: The user function angles(). ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='Ap4Aase.seq', dir='/sw/lib/relax-py25/test_suite/shared_data', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/Ap4Aase.seq' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 PRO None None None 3 LEU None None None 4 GLY None None None 5 SER None None None 6 MET None None None 7 ASP None None None 8 SER None None None 9 PRO None None None 10 PRO None None None 11 GLU None None None 12 GLY None None None 13 TYR None None None 14 ARG None None None 15 ARG None None None 16 ASN None None None 17 VAL None None None 18 GLY None None None 19 ILE None None None 20 CYS None None None 21 LEU None None None 22 MET None None None 23 ASN None None None 24 ASN None None None 25 ASP None None None 26 LYS None None None 27 LYS None None None 28 ILE None None None 29 PHE None None None 30 ALA None None None 31 ALA None None None 32 SER None None None 33 ARG None None None 34 LEU None None None 35 ASP None None None 36 ILE None None None 37 PRO None None None 38 ASP None None None 39 ALA None None None 40 TRP None None None 41 GLN None None None 42 MET None None None 43 PRO None None None 44 GLN None None None 45 GLY None None None 46 GLY None None None 47 ILE None None None 48 ASP None None None 49 GLU None None None 50 GLY None None None 51 GLU None None None 52 ASP None None None 53 PRO None None None 54 ARG None None None 55 ASN None None None 56 ALA None None None 57 ALA None None None 58 ILE None None None 59 ARG None None None 60 GLU None None None 61 LEU None None None 62 ARG None None None 63 GLU None None None 64 GLU None None None 65 THR None None None 66 GLY None None None 67 VAL None None None 68 THR None None None 69 SER None None None 70 ALA None None None 71 GLU None None None 72 VAL None None None 73 ILE None None None 74 ALA None None None 75 GLU None None None 76 VAL None None None 77 PRO None None None 78 TYR None None None 79 TRP None None None 80 LEU None None None 81 THR None None None 82 TYR None None None 83 ASP None None None 84 PHE None None None 85 PRO None None None 86 PRO None None None 87 LYS None None None 88 VAL None None None 89 ARG None None None 90 GLU None None None 91 LYS None None None 92 LEU None None None 93 ASN None None None 94 ILE None None None 95 GLN None None None 96 TRP None None None 97 GLY None None None 98 SER None None None 99 ASP None None None 100 TRP None None None 101 LYS None None None 102 GLY None None None 103 GLN None None None 104 ALA None None None 105 GLN None None None 106 LYS None None None 107 TRP None None None 108 PHE None None None 109 LEU None None None 110 PHE None None None 111 LYS None None None 112 PHE None None None 113 THR None None None 114 GLY None None None 115 GLN None None None 116 ASP None None None 117 GLN None None None 118 GLU None None None 119 ILE None None None 120 ASN None None None 121 LEU None None None 122 LEU None None None 123 GLY None None None 124 ASP None None None 125 GLY None None None 126 SER None None None 127 GLU None None None 128 LYS None None None 129 PRO None None None 130 GLU None None None 131 PHE None None None 132 GLY None None None 133 GLU None None None 134 TRP None None None 135 SER None None None 136 TRP None None None 137 VAL None None None 138 THR None None None 139 PRO None None None 140 GLU None None None 141 GLN None None None 142 LEU None None None 143 ILE None None None 144 ASP None None None 145 LEU None None None 146 THR None None None 147 VAL None None None 148 GLU None None None 149 PHE None None None 150 LYS None None None 151 LYS None None None 152 PRO None None None 153 VAL None None None 154 TYR None None None 155 LYS None None None 156 GLU None None None 157 VAL None None None 158 LEU None None None 159 SER None None None 160 VAL None None None 161 PHE None None None 162 ALA None None None 163 PRO None None None 164 HIS None None None 165 LEU None None relax> structure.read_pdb(file='Ap4Aase_res1-12.pdb', dir='/sw/lib/relax-py25/test_suite/shared_data/structures', model=1, parser='scientific') Scientific Python PDB parser. Loading structure 1 from the PDB file. Structure('/sw/lib/relax-py25/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb', model=1): Peptide chain of length 12 relax> structure.load_spins(spin_id='@N', ave_pos=True) Adding the following spins to the relax data store. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY 1 N None 2 PRO 11 N None 3 LEU 28 N None 4 GLY 51 N None 5 SER 59 N None 6 MET 71 N None 7 ASP 91 N None 8 SER 104 N None 9 PRO 116 N None 10 PRO 133 N None 11 GLU 150 N None 12 GLY 167 N relax> structure.vectors(attached='H', spin_id=None, struct_index=None, verbosity=1, ave=True, unit=True) Extracting vectors from the single structure. Calculating the unit vectors. The attached atom is a proton. RelaxWarning: No attached atom could be found (atom ID ':1@1&@N'). RelaxWarning: No attached atom could be found (atom ID ':2@11&@N'). Extracted N-H vectors for ':3@28&@N'. Extracted N-H vectors for ':4@51&@N'. Extracted N-H vectors for ':5@59&@N'. Extracted N-H vectors for ':6@71&@N'. Extracted N-H vectors for ':7@91&@N'. Extracted N-H vectors for ':8@104&@N'. RelaxWarning: No attached atom could be found (atom ID ':9@116&@N'). RelaxWarning: No attached atom could be found (atom ID ':10@133&@N'). Extracted N-H vectors for ':11@150&@N'. Extracted N-H vectors for ':12@167&@N'. RelaxWarning: Either the spin number or name must be set for the spin ':13' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':14' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':15' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':16' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':17' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':18' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':19' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':20' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':21' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':22' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':23' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':24' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':25' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':26' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':27' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':28' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':29' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':30' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':31' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':32' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':33' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':34' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':35' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':36' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':37' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':38' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':39' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':40' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':41' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':42' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':43' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':44' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':45' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':46' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':47' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':48' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':49' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':50' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':51' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':52' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':53' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':54' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':55' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':56' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':57' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':58' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':59' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':60' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':61' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':62' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':63' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':64' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':65' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':66' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':67' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':68' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':69' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':70' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':71' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':72' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':73' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':74' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':75' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':76' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':77' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':78' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':79' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':80' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':81' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':82' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':83' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':84' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':85' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':86' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':87' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':88' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':89' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':90' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':91' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':92' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':93' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':94' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':95' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':96' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':97' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':98' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':99' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':100' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':101' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':102' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':103' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':104' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':105' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':106' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':107' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':108' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':109' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':110' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':111' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':112' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':113' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':114' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':115' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':116' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':117' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':118' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':119' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':120' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':121' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':122' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':123' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':124' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':125' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':126' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':127' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':128' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':129' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':130' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':131' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':132' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':133' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':134' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':135' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':136' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':137' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':138' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':139' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':140' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':141' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':142' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':143' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':144' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':145' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':146' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':147' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':148' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':149' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':150' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':151' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':152' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':153' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':154' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':155' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':156' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':157' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':158' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':159' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':160' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':161' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':162' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':163' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':164' to identify the corresponding atom in the structure. RelaxWarning: Either the spin number or name must be set for the spin ':165' to identify the corresponding atom in the structure. relax> diffusion_tensor.init(params=(16980000.0, 14170000.0, 67.174000000000007, -83.718000000000004), time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=3, spheroid_type=None, fixed=True) relax> sequence.display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True) Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY 1 N None 2 PRO 11 N None 3 LEU 28 N None 4 GLY 51 N None 5 SER 59 N None 6 MET 71 N None 7 ASP 91 N None 8 SER 104 N None 9 PRO 116 N None 10 PRO 133 N None 11 GLU 150 N None 12 GLY 167 N None 13 TYR None None None 14 ARG None None None 15 ARG None None None 16 ASN None None None 17 VAL None None None 18 GLY None None None 19 ILE None None None 20 CYS None None None 21 LEU None None None 22 MET None None None 23 ASN None None None 24 ASN None None None 25 ASP None None None 26 LYS None None None 27 LYS None None None 28 ILE None None None 29 PHE None None None 30 ALA None None None 31 ALA None None None 32 SER None None None 33 ARG None None None 34 LEU None None None 35 ASP None None None 36 ILE None None None 37 PRO None None None 38 ASP None None None 39 ALA None None None 40 TRP None None None 41 GLN None None None 42 MET None None None 43 PRO None None None 44 GLN None None None 45 GLY None None None 46 GLY None None None 47 ILE None None None 48 ASP None None None 49 GLU None None None 50 GLY None None None 51 GLU None None None 52 ASP None None None 53 PRO None None None 54 ARG None None None 55 ASN None None None 56 ALA None None None 57 ALA None None None 58 ILE None None None 59 ARG None None None 60 GLU None None None 61 LEU None None None 62 ARG None None None 63 GLU None None None 64 GLU None None None 65 THR None None None 66 GLY None None None 67 VAL None None None 68 THR None None None 69 SER None None None 70 ALA None None None 71 GLU None None None 72 VAL None None None 73 ILE None None None 74 ALA None None None 75 GLU None None None 76 VAL None None None 77 PRO None None None 78 TYR None None None 79 TRP None None None 80 LEU None None None 81 THR None None None 82 TYR None None None 83 ASP None None None 84 PHE None None None 85 PRO None None None 86 PRO None None None 87 LYS None None None 88 VAL None None None 89 ARG None None None 90 GLU None None None 91 LYS None None None 92 LEU None None None 93 ASN None None None 94 ILE None None None 95 GLN None None None 96 TRP None None None 97 GLY None None None 98 SER None None None 99 ASP None None None 100 TRP None None None 101 LYS None None None 102 GLY None None None 103 GLN None None None 104 ALA None None None 105 GLN None None None 106 LYS None None None 107 TRP None None None 108 PHE None None None 109 LEU None None None 110 PHE None None None 111 LYS None None None 112 PHE None None None 113 THR None None None 114 GLY None None None 115 GLN None None None 116 ASP None None None 117 GLN None None None 118 GLU None None None 119 ILE None None None 120 ASN None None None 121 LEU None None None 122 LEU None None None 123 GLY None None None 124 ASP None None None 125 GLY None None None 126 SER None None None 127 GLU None None None 128 LYS None None None 129 PRO None None None 130 GLU None None None 131 PHE None None None 132 GLY None None None 133 GLU None None None 134 TRP None None None 135 SER None None None 136 TRP None None None 137 VAL None None None 138 THR None None None 139 PRO None None None 140 GLU None None None 141 GLN None None None 142 LEU None None None 143 ILE None None None 144 ASP None None None 145 LEU None None None 146 THR None None None 147 VAL None None None 148 GLU None None None 149 PHE None None None 150 LYS None None None 151 LYS None None None 152 PRO None None None 153 VAL None None None 154 TYR None None None 155 LYS None None None 156 GLU None None None 157 VAL None None None 158 LEU None None None 159 SER None None None 160 VAL None None None 161 PHE None None None 162 ALA None None None 163 PRO None None None 164 HIS None None None 165 LEU None None relax> angle_diff_frame() RelaxWarning: No angles could be calculated for the spin ':1&:GLY@1&@N'. RelaxWarning: No angles could be calculated for the spin ':2&:PRO@11&@N'. RelaxWarning: No angles could be calculated for the spin ':9&:PRO@116&@N'. RelaxWarning: No angles could be calculated for the spin ':10&:PRO@133&@N'. RelaxWarning: No angles could be calculated for the spin ':13&:TYR'. RelaxWarning: No angles could be calculated for the spin ':14&:ARG'. RelaxWarning: No angles could be calculated for the spin ':15&:ARG'. RelaxWarning: No angles could be calculated for the spin ':16&:ASN'. RelaxWarning: No angles could be calculated for the spin ':17&:VAL'. RelaxWarning: No angles could be calculated for the spin ':18&:GLY'. RelaxWarning: No angles could be calculated for the spin ':19&:ILE'. RelaxWarning: No angles could be calculated for the spin ':20&:CYS'. RelaxWarning: No angles could be calculated for the spin ':21&:LEU'. RelaxWarning: No angles could be calculated for the spin ':22&:MET'. RelaxWarning: No angles could be calculated for the spin ':23&:ASN'. RelaxWarning: No angles could be calculated for the spin ':24&:ASN'. RelaxWarning: No angles could be calculated for the spin ':25&:ASP'. RelaxWarning: No angles could be calculated for the spin ':26&:LYS'. RelaxWarning: No angles could be calculated for the spin ':27&:LYS'. RelaxWarning: No angles could be calculated for the spin ':28&:ILE'. RelaxWarning: No angles could be calculated for the spin ':29&:PHE'. RelaxWarning: No angles could be calculated for the spin ':30&:ALA'. RelaxWarning: No angles could be calculated for the spin ':31&:ALA'. RelaxWarning: No angles could be calculated for the spin ':32&:SER'. RelaxWarning: No angles could be calculated for the spin ':33&:ARG'. RelaxWarning: No angles could be calculated for the spin ':34&:LEU'. RelaxWarning: No angles could be calculated for the spin ':35&:ASP'. RelaxWarning: No angles could be calculated for the spin ':36&:ILE'. RelaxWarning: No angles could be calculated for the spin ':37&:PRO'. RelaxWarning: No angles could be calculated for the spin ':38&:ASP'. RelaxWarning: No angles could be calculated for the spin ':39&:ALA'. RelaxWarning: No angles could be calculated for the spin ':40&:TRP'. RelaxWarning: No angles could be calculated for the spin ':41&:GLN'. RelaxWarning: No angles could be calculated for the spin ':42&:MET'. RelaxWarning: No angles could be calculated for the spin ':43&:PRO'. RelaxWarning: No angles could be calculated for the spin ':44&:GLN'. RelaxWarning: No angles could be calculated for the spin ':45&:GLY'. RelaxWarning: No angles could be calculated for the spin ':46&:GLY'. RelaxWarning: No angles could be calculated for the spin ':47&:ILE'. RelaxWarning: No angles could be calculated for the spin ':48&:ASP'. RelaxWarning: No angles could be calculated for the spin ':49&:GLU'. RelaxWarning: No angles could be calculated for the spin ':50&:GLY'. RelaxWarning: No angles could be calculated for the spin ':51&:GLU'. RelaxWarning: No angles could be calculated for the spin ':52&:ASP'. RelaxWarning: No angles could be calculated for the spin ':53&:PRO'. RelaxWarning: No angles could be calculated for the spin ':54&:ARG'. RelaxWarning: No angles could be calculated for the spin ':55&:ASN'. RelaxWarning: No angles could be calculated for the spin ':56&:ALA'. RelaxWarning: No angles could be calculated for the spin ':57&:ALA'. RelaxWarning: No angles could be calculated for the spin ':58&:ILE'. RelaxWarning: No angles could be calculated for the spin ':59&:ARG'. RelaxWarning: No angles could be calculated for the spin ':60&:GLU'. RelaxWarning: No angles could be calculated for the spin ':61&:LEU'. RelaxWarning: No angles could be calculated for the spin ':62&:ARG'. RelaxWarning: No angles could be calculated for the spin ':63&:GLU'. RelaxWarning: No angles could be calculated for the spin ':64&:GLU'. RelaxWarning: No angles could be calculated for the spin ':65&:THR'. RelaxWarning: No angles could be calculated for the spin ':66&:GLY'. RelaxWarning: No angles could be calculated for the spin ':67&:VAL'. RelaxWarning: No angles could be calculated for the spin ':68&:THR'. RelaxWarning: No angles could be calculated for the spin ':69&:SER'. RelaxWarning: No angles could be calculated for the spin ':70&:ALA'. RelaxWarning: No angles could be calculated for the spin ':71&:GLU'. RelaxWarning: No angles could be calculated for the spin ':72&:VAL'. RelaxWarning: No angles could be calculated for the spin ':73&:ILE'. RelaxWarning: No angles could be calculated for the spin ':74&:ALA'. RelaxWarning: No angles could be calculated for the spin ':75&:GLU'. RelaxWarning: No angles could be calculated for the spin ':76&:VAL'. RelaxWarning: No angles could be calculated for the spin ':77&:PRO'. RelaxWarning: No angles could be calculated for the spin ':78&:TYR'. RelaxWarning: No angles could be calculated for the spin ':79&:TRP'. RelaxWarning: No angles could be calculated for the spin ':80&:LEU'. RelaxWarning: No angles could be calculated for the spin ':81&:THR'. RelaxWarning: No angles could be calculated for the spin ':82&:TYR'. RelaxWarning: No angles could be calculated for the spin ':83&:ASP'. RelaxWarning: No angles could be calculated for the spin ':84&:PHE'. RelaxWarning: No angles could be calculated for the spin ':85&:PRO'. RelaxWarning: No angles could be calculated for the spin ':86&:PRO'. RelaxWarning: No angles could be calculated for the spin ':87&:LYS'. RelaxWarning: No angles could be calculated for the spin ':88&:VAL'. RelaxWarning: No angles could be calculated for the spin ':89&:ARG'. RelaxWarning: No angles could be calculated for the spin ':90&:GLU'. RelaxWarning: No angles could be calculated for the spin ':91&:LYS'. RelaxWarning: No angles could be calculated for the spin ':92&:LEU'. RelaxWarning: No angles could be calculated for the spin ':93&:ASN'. RelaxWarning: No angles could be calculated for the spin ':94&:ILE'. RelaxWarning: No angles could be calculated for the spin ':95&:GLN'. RelaxWarning: No angles could be calculated for the spin ':96&:TRP'. RelaxWarning: No angles could be calculated for the spin ':97&:GLY'. RelaxWarning: No angles could be calculated for the spin ':98&:SER'. RelaxWarning: No angles could be calculated for the spin ':99&:ASP'. RelaxWarning: No angles could be calculated for the spin ':100&:TRP'. RelaxWarning: No angles could be calculated for the spin ':101&:LYS'. RelaxWarning: No angles could be calculated for the spin ':102&:GLY'. RelaxWarning: No angles could be calculated for the spin ':103&:GLN'. RelaxWarning: No angles could be calculated for the spin ':104&:ALA'. RelaxWarning: No angles could be calculated for the spin ':105&:GLN'. RelaxWarning: No angles could be calculated for the spin ':106&:LYS'. RelaxWarning: No angles could be calculated for the spin ':107&:TRP'. RelaxWarning: No angles could be calculated for the spin ':108&:PHE'. RelaxWarning: No angles could be calculated for the spin ':109&:LEU'. RelaxWarning: No angles could be calculated for the spin ':110&:PHE'. RelaxWarning: No angles could be calculated for the spin ':111&:LYS'. RelaxWarning: No angles could be calculated for the spin ':112&:PHE'. RelaxWarning: No angles could be calculated for the spin ':113&:THR'. RelaxWarning: No angles could be calculated for the spin ':114&:GLY'. RelaxWarning: No angles could be calculated for the spin ':115&:GLN'. RelaxWarning: No angles could be calculated for the spin ':116&:ASP'. RelaxWarning: No angles could be calculated for the spin ':117&:GLN'. RelaxWarning: No angles could be calculated for the spin ':118&:GLU'. RelaxWarning: No angles could be calculated for the spin ':119&:ILE'. RelaxWarning: No angles could be calculated for the spin ':120&:ASN'. RelaxWarning: No angles could be calculated for the spin ':121&:LEU'. RelaxWarning: No angles could be calculated for the spin ':122&:LEU'. RelaxWarning: No angles could be calculated for the spin ':123&:GLY'. RelaxWarning: No angles could be calculated for the spin ':124&:ASP'. RelaxWarning: No angles could be calculated for the spin ':125&:GLY'. RelaxWarning: No angles could be calculated for the spin ':126&:SER'. RelaxWarning: No angles could be calculated for the spin ':127&:GLU'. RelaxWarning: No angles could be calculated for the spin ':128&:LYS'. RelaxWarning: No angles could be calculated for the spin ':129&:PRO'. RelaxWarning: No angles could be calculated for the spin ':130&:GLU'. RelaxWarning: No angles could be calculated for the spin ':131&:PHE'. RelaxWarning: No angles could be calculated for the spin ':132&:GLY'. RelaxWarning: No angles could be calculated for the spin ':133&:GLU'. RelaxWarning: No angles could be calculated for the spin ':134&:TRP'. RelaxWarning: No angles could be calculated for the spin ':135&:SER'. RelaxWarning: No angles could be calculated for the spin ':136&:TRP'. RelaxWarning: No angles could be calculated for the spin ':137&:VAL'. RelaxWarning: No angles could be calculated for the spin ':138&:THR'. RelaxWarning: No angles could be calculated for the spin ':139&:PRO'. RelaxWarning: No angles could be calculated for the spin ':140&:GLU'. RelaxWarning: No angles could be calculated for the spin ':141&:GLN'. RelaxWarning: No angles could be calculated for the spin ':142&:LEU'. RelaxWarning: No angles could be calculated for the spin ':143&:ILE'. RelaxWarning: No angles could be calculated for the spin ':144&:ASP'. RelaxWarning: No angles could be calculated for the spin ':145&:LEU'. RelaxWarning: No angles could be calculated for the spin ':146&:THR'. RelaxWarning: No angles could be calculated for the spin ':147&:VAL'. RelaxWarning: No angles could be calculated for the spin ':148&:GLU'. RelaxWarning: No angles could be calculated for the spin ':149&:PHE'. RelaxWarning: No angles could be calculated for the spin ':150&:LYS'. RelaxWarning: No angles could be calculated for the spin ':151&:LYS'. RelaxWarning: No angles could be calculated for the spin ':152&:PRO'. RelaxWarning: No angles could be calculated for the spin ':153&:VAL'. RelaxWarning: No angles could be calculated for the spin ':154&:TYR'. RelaxWarning: No angles could be calculated for the spin ':155&:LYS'. RelaxWarning: No angles could be calculated for the spin ':156&:GLU'. RelaxWarning: No angles could be calculated for the spin ':157&:VAL'. RelaxWarning: No angles could be calculated for the spin ':158&:LEU'. RelaxWarning: No angles could be calculated for the spin ':159&:SER'. RelaxWarning: No angles could be calculated for the spin ':160&:VAL'. RelaxWarning: No angles could be calculated for the spin ':161&:PHE'. RelaxWarning: No angles could be calculated for the spin ':162&:ALA'. RelaxWarning: No angles could be calculated for the spin ':163&:PRO'. RelaxWarning: No angles could be calculated for the spin ':164&:HIS'. RelaxWarning: No angles could be calculated for the spin ':165&:LEU'. Class containing all the spin system specific data. Objects: element: 'N' name: 'N' num: 1 pos: array([ 8.442, 10.188, 6.302]) select: True Class containing all the spin system specific data. Objects: element: 'N' name: 'N' num: 11 pos: array([ 5.613, 8.385, 7.943]) select: True Class containing all the spin system specific data. Objects: alpha: 2.8102691247870468 attached_atom: 'H' element: 'N' name: 'N' num: 28 pos: array([ 4.074, 6.099, 5.719]) select: True xh_vect: array([ 0.40899187, -0.80574458, 0.42837054]) Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/angles.py", line 104, in test_angles self.assertAlmostEqual(cdp.mol[0].res[i].spin[0].xh_vect[j], xh_vects[i][j]) AssertionError: 0.40899187042469931 != -1.6863286833629661e+272 within 7 places ====================================================================== FAIL: Constrained BFGS opt, backtracking line search {S2=0.970, te=2048, Rex=0.149} ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 ALA None None relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, file='r1.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, file='r2.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, file='noe.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out' for reading. relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0, file='r1.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0, file='r2.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0, file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None, fixed=True) relax> value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None) relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None) relax> value.set(val='15N', param='heteronucleus', spin_id=None) relax> value.set(val='1H', param='proton', spin_id=None) relax> model_free.select_model(model='m4', spin_id=None) relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None) relax> minimise(*args=('bfgs', 'back'), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1) Only the model-free parameters for single spins will be used. Fitting to spin ':2&:ALA' ~~~~~~~~~~~~~~~~~~~~~~~~ Method of Multipliers ~~~~~~~~~~~~~~~~~~~~ k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Parameter values: array([ 0.90905502, 74.36929555, 1.22310091]) Function value: -1447.7789206950388 Iterations: 37 Function calls: 93 Gradient calls: 38 Hessian calls: 0 Warning: None k: 1 xk: array([ 0.90905502, 74.36929555, 1.22310091]) fk: 48.121412825285702 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 0.90905502, 74.36929555, 1.22310091]) fk: 46.071579585447914 Parameter values: array([ 9.89561039e-01, 4.08922110e+02, 1.27899123e-01]) Function value: 1.5767185057428068 Iterations: 38 Function calls: 259 Gradient calls: 39 Hessian calls: 0 Warning: None k: 2 xk: array([ 9.89561039e-01, 4.08922110e+02, 1.27899123e-01]) fk: 3.626551745580596 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 9.89561039e-01, 4.08922110e+02, 1.27899123e-01]) fk: 3.626551745580596 Parameter values: array([ 9.74034731e-01, 8.37698106e+02, 1.23106917e-01]) Function value: 2.1800782005407622 Iterations: 31 Function calls: 201 Gradient calls: 32 Hessian calls: 0 Warning: None k: 3 xk: array([ 9.74034731e-01, 8.37698106e+02, 1.23106917e-01]) fk: 2.1800782005407622 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 9.74034731e-01, 8.37698106e+02, 1.23106917e-01]) fk: 2.1800782005407622 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 7.5991121570503778e-22 Iterations: 42 Function calls: 98 Gradient calls: 43 Hessian calls: 0 Warning: None k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 7.5991121570503778e-22 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 7.5991121570503778e-22 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 1.9022883080402212e-24 Iterations: 6 Function calls: 26 Gradient calls: 7 Hessian calls: 0 Warning: None k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.9022883080402212e-24 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.9022883080402212e-24 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 1.8533903598853284e-24 Iterations: 2 Function calls: 18 Gradient calls: 3 Hessian calls: 0 Warning: None Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 1.8533903598853284e-24 Iterations: 156 Function calls: 695 Gradient calls: 162 Hessian calls: 0 Warning: None Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 301, in test_opt_constr_bfgs_back_S2_0_970_te_2048_Rex_0_149 self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, h_count, warning) File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1046, in value_test self.assertEqual(spin.iter, iter, msg=mesg) AssertionError: Optimisation failure. System: Darwin Release: 9.5.0 Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC Win32 version: Distribution: Architecture: 32bit Machine: Power Macintosh Processor: powerpc Python version: 2.5.2 numpy version: 1.1.1 s2: 0.9699999999999861 te: 2047.9999999978033 rex: 0.14900000000028032 chi2: 1.8533903598853284e-24 iter: 156 f_count: 695 g_count: 162 h_count: 0 warning: None ====================================================================== FAIL: Constrained BFGS opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 ALA None None relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, file='r1.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, file='r2.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, file='noe.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out' for reading. relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0, file='r1.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0, file='r2.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0, file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None, fixed=True) relax> value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None) relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None) relax> value.set(val='15N', param='heteronucleus', spin_id=None) relax> value.set(val='1H', param='proton', spin_id=None) relax> model_free.select_model(model='m4', spin_id=None) relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None) relax> minimise(*args=('bfgs', 'mt'), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1) Only the model-free parameters for single spins will be used. Fitting to spin ':2&:ALA' ~~~~~~~~~~~~~~~~~~~~~~~~ Method of Multipliers ~~~~~~~~~~~~~~~~~~~~ k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Parameter values: array([ 0.90905506, 74.36943011, 1.22310156]) Function value: -1447.7789206948671 Iterations: 22 Function calls: 50 Gradient calls: 50 Hessian calls: 0 Warning: None k: 1 xk: array([ 0.90905506, 74.36943011, 1.22310156]) fk: 48.121371716752257 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 0.90905506, 74.36943011, 1.22310156]) fk: 46.071517922561874 Parameter values: array([ 9.94936631e-01, 8.81385060e+01, -3.79281070e-05]) Function value: 1.9644199905707935 Iterations: 38 Function calls: 128 Gradient calls: 128 Hessian calls: 0 Warning: The gradient at point 0 of this line search is positive, ie p is not a descent direction and the line search will not work. (fatal minimisation error). k: 2 xk: array([ 9.94936631e-01, 8.81385060e+01, -3.79281070e-05]) fk: 144.63923664803443 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.94936631e-01, 8.81385060e+01, -3.79281070e-05]) fk: 4.0147053471508878 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: -7.1927064951510456e-05 Iterations: 56 Function calls: 129 Gradient calls: 129 Hessian calls: 0 Warning: None k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.6264773549380294e-20 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.6264773549380294e-20 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 2.6808864830250424e-21 Iterations: 1 Function calls: 4 Gradient calls: 4 Hessian calls: 0 Warning: None k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 2.6808864830250424e-21 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 2.6808864830250424e-21 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 4.8056261450870388e-23 Iterations: 2 Function calls: 7 Gradient calls: 7 Hessian calls: 0 Warning: None k: 5 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 4.8056261450870388e-23 Entering sub-algorithm. Quasi-Newton BFGS minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 4.8056261450870388e-23 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 4.8056261450870388e-23 Iterations: 1 Function calls: 59 Gradient calls: 59 Hessian calls: 0 Warning: None Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 4.8056261450870388e-23 Iterations: 120 Function calls: 377 Gradient calls: 377 Hessian calls: 0 Warning: None Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 355, in test_opt_constr_bfgs_mt_S2_0_970_te_2048_Rex_0_149 self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, h_count, warning) File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047, in value_test self.assertEqual(spin.f_count, f_count, msg=mesg) AssertionError: Optimisation failure. System: Darwin Release: 9.5.0 Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC Win32 version: Distribution: Architecture: 32bit Machine: Power Macintosh Processor: powerpc Python version: 2.5.2 numpy version: 1.1.1 s2: 0.9700000000000607 te: 2048.0000000115510 rex: 0.14899999999885080 chi2: 4.8056261450870388e-23 iter: 120 f_count: 377 g_count: 377 h_count: 0 warning: None ====================================================================== FAIL: Constrained coordinate descent opt, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 ALA None None relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, file='r1.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, file='r2.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, file='noe.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out' for reading. relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0, file='r1.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0, file='r2.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0, file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None, fixed=True) relax> value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None) relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None) relax> value.set(val='15N', param='heteronucleus', spin_id=None) relax> value.set(val='1H', param='proton', spin_id=None) relax> model_free.select_model(model='m4', spin_id=None) relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None) relax> minimise(*args=('cd', 'mt'), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1) Only the model-free parameters for single spins will be used. Fitting to spin ':2&:ALA' ~~~~~~~~~~~~~~~~~~~~~~~~ Method of Multipliers ~~~~~~~~~~~~~~~~~~~~ k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Entering sub-algorithm. Back-and-forth coordinate descent minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Parameter values: array([ 0.90905609, 74.37463254, 1.22289922]) Function value: -1447.7789199590425 Iterations: 25 Function calls: 75 Gradient calls: 75 Hessian calls: 0 Warning: None k: 1 xk: array([ 0.90905609, 74.37463254, 1.22289922]) fk: 48.120438129522014 Entering sub-algorithm. Back-and-forth coordinate descent minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 0.90905609, 74.37463254, 1.22289922]) fk: 46.070117173804164 Parameter values: array([ 9.70000218e-01, 2.04801529e+03, 1.48994731e-01]) Function value: -2.0503209554858945 Iterations: 89 Function calls: 284 Gradient calls: 284 Hessian calls: 0 Warning: None k: 2 xk: array([ 9.70000218e-01, 2.04801529e+03, 1.48994731e-01]) fk: 2.3195995262977486e-10 Entering sub-algorithm. Back-and-forth coordinate descent minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000218e-01, 2.04801529e+03, 1.48994731e-01]) fk: 2.3195995262977486e-10 Parameter values: array([ 9.70000218e-01, 2.04800873e+03, 1.48997054e-01]) Function value: 1.2998777447179547e-10 Iterations: 18 Function calls: 136 Gradient calls: 136 Hessian calls: 0 Warning: None k: 3 xk: array([ 9.70000218e-01, 2.04800873e+03, 1.48997054e-01]) fk: 1.2998777447179547e-10 Entering sub-algorithm. Back-and-forth coordinate descent minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000218e-01, 2.04800873e+03, 1.48997054e-01]) fk: 1.2998777447179547e-10 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01]) Function value: 2.3477234248531005e-18 Iterations: 65 Function calls: 184 Gradient calls: 184 Hessian calls: 0 Warning: None k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01]) fk: 2.3477234248531005e-18 Entering sub-algorithm. Back-and-forth coordinate descent minimisation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01]) fk: 2.3477234248531005e-18 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01]) Function value: 2.3477234248531005e-18 Iterations: 1 Function calls: 78 Gradient calls: 78 Hessian calls: 0 Warning: None Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.48999999e-01]) Function value: 2.3477234248531005e-18 Iterations: 198 Function calls: 757 Gradient calls: 757 Hessian calls: 0 Warning: None Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 452, in test_opt_constr_cd_mt_S2_0_970_te_2048_Rex_0_149 self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, h_count, warning) File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047, in value_test self.assertEqual(spin.f_count, f_count, msg=mesg) AssertionError: Optimisation failure. System: Darwin Release: 9.5.0 Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC Win32 version: Distribution: Architecture: 32bit Machine: Power Macintosh Processor: powerpc Python version: 2.5.2 numpy version: 1.1.1 s2: 0.9700000000219674 te: 2048.0000015341870 rex: 0.14899999946977982 chi2: 2.3477234248531005e-18 iter: 198 f_count: 757 g_count: 757 h_count: 0 warning: None ====================================================================== FAIL: Constrained Newton opt, GMW Hessian mod, backtracking line search {S2=0.970, te=2048, Rex=0.149} ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 ALA None None relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, file='r1.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, file='r2.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, file='noe.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out' for reading. relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0, file='r1.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0, file='r2.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0, file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None, fixed=True) relax> value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None) relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None) relax> value.set(val='15N', param='heteronucleus', spin_id=None) relax> value.set(val='1H', param='proton', spin_id=None) relax> model_free.select_model(model='m4', spin_id=None) relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None) relax> minimise(*args=('newton', 'gmw', 'back'), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1) Only the model-free parameters for single spins will be used. Fitting to spin ':2&:ALA' ~~~~~~~~~~~~~~~~~~~~~~~~ Method of Multipliers ~~~~~~~~~~~~~~~~~~~~ k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Parameter values: array([ 0.90905499, 74.36909171, 1.22310096]) Function value: -1447.7789206948949 Iterations: 4 Function calls: 9 Gradient calls: 5 Hessian calls: 4 Warning: None k: 1 xk: array([ 0.90905499, 74.36909171, 1.22310096]) fk: 48.121433050621448 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 0.90905499, 74.36909171, 1.22310096]) fk: 46.071609923379611 Parameter values: array([ 9.69999986e-01, 2.04799695e+03, 1.49000257e-01]) Function value: -2.0498231272384211 Iterations: 11 Function calls: 37 Gradient calls: 12 Hessian calls: 11 Warning: None k: 2 xk: array([ 9.69999986e-01, 2.04799695e+03, 1.49000257e-01]) fk: 3.414668279588586e-12 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.69999986e-01, 2.04799695e+03, 1.49000257e-01]) fk: 3.414668279588586e-12 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 1.2385186715645527e-22 Iterations: 1 Function calls: 3 Gradient calls: 2 Hessian calls: 1 Warning: None k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.2385186715645527e-22 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 1.2385186715645527e-22 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 5.7085251917483392e-28 Iterations: 1 Function calls: 3 Gradient calls: 2 Hessian calls: 1 Warning: None k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 5.7085251917483392e-28 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: Backtracking line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 5.7085251917483392e-28 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 5.7085251917483392e-28 Iterations: 1 Function calls: 42 Gradient calls: 2 Hessian calls: 1 Warning: None Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 5.7085251917483392e-28 Iterations: 18 Function calls: 94 Gradient calls: 23 Hessian calls: 18 Warning: None Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 499, in test_opt_constr_newton_gmw_back_S2_0_970_te_2048_Rex_0_149 self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, h_count, warning) File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047, in value_test self.assertEqual(spin.f_count, f_count, msg=mesg) AssertionError: Optimisation failure. System: Darwin Release: 9.5.0 Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC Win32 version: Distribution: Architecture: 32bit Machine: Power Macintosh Processor: powerpc Python version: 2.5.2 numpy version: 1.1.1 s2: 0.9699999999999993 te: 2048.0000000000427 rex: 0.14900000000002098 chi2: 5.7085251917483392e-28 iter: 18 f_count: 94 g_count: 23 h_count: 18 warning: None ====================================================================== FAIL: Constrained Newton opt, GMW Hessian mod, More and Thuente line search {S2=0.970, te=2048, Rex=0.149} ---------------------------------------------------------------------- relax> pipe.create(pipe_name='mf', pipe_type='mf') relax> sequence.read(file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. Mol_name Res_num Res_name Spin_num Spin_name None 1 GLY None None None 2 ALA None None relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, file='r1.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, file='r2.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, file='noe.600.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out' for reading. relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0, file='r1.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out' for reading. relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0, file='r2.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out' for reading. relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0, file='noe.500.out', dir='/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149', mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) Opening the file '/sw/lib/relax-py25/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out' for reading. relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None, fixed=True) relax> value.set(val=1.0200000000000001e-10, param='bond_length', spin_id=None) relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None) relax> value.set(val='15N', param='heteronucleus', spin_id=None) relax> value.set(val='1H', param='proton', spin_id=None) relax> model_free.select_model(model='m4', spin_id=None) relax> value.set(val=[1.0, 0.0, 0.0], param=['S2', 'te', 'Rex'], spin_id=None) relax> minimise(*args=('newton', 'gmw', 'mt'), func_tol=1e-25, max_iterations=10000000, constraints=True, scaling=True, verbosity=1) Only the model-free parameters for single spins will be used. Fitting to spin ':2&:ALA' ~~~~~~~~~~~~~~~~~~~~~~~~ Method of Multipliers ~~~~~~~~~~~~~~~~~~~~ k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 1., 0., 0.]) fk: 3.9844117908982288 Parameter values: array([ 0.90905499, 74.36909171, 1.22310096]) Function value: -1447.7789206948949 Iterations: 4 Function calls: 9 Gradient calls: 9 Hessian calls: 4 Warning: None k: 1 xk: array([ 0.90905499, 74.36909171, 1.22310096]) fk: 48.121433050621448 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 0.90905499, 74.36909171, 1.22310096]) fk: 46.071609923379611 Parameter values: array([ 9.69999996e-01, 2.04799919e+03, 1.49000073e-01]) Function value: -2.0498231272415968 Iterations: 15 Function calls: 73 Gradient calls: 73 Hessian calls: 15 Warning: None k: 2 xk: array([ 9.69999996e-01, 2.04799919e+03, 1.49000073e-01]) fk: 2.3886846326646765e-13 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.69999996e-01, 2.04799919e+03, 1.49000073e-01]) fk: 2.3886846326646765e-13 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 6.1070040854035286e-25 Iterations: 1 Function calls: 3 Gradient calls: 3 Hessian calls: 1 Warning: None k: 3 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 6.1070040854035286e-25 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 6.1070040854035286e-25 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 6.8756889983348349e-28 Iterations: 1 Function calls: 3 Gradient calls: 3 Hessian calls: 1 Warning: None k: 4 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 6.8756889983348349e-28 Entering sub-algorithm. Newton minimisation ~~~~~~~~~~~~~~~~~~~ Line search: More and Thuente line search. Hessian modification: The Gill, Murray, and Wright modified Cholesky algorithm. k: 0 xk: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) fk: 6.8756889983348349e-28 Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 6.8756889983348349e-28 Iterations: 1 Function calls: 72 Gradient calls: 72 Hessian calls: 1 Warning: None Parameter values: array([ 9.70000000e-01, 2.04800000e+03, 1.49000000e-01]) Function value: 6.8756889983348349e-28 Iterations: 22 Function calls: 160 Gradient calls: 160 Hessian calls: 22 Warning: None Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 554, in test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149 self.value_test(spin, select, s2, te, rex, chi2, iter, f_count, g_count, h_count, warning) File "/sw/lib/relax-py25/test_suite/system_tests/model_free.py", line 1047, in value_test self.assertEqual(spin.f_count, f_count, msg=mesg) AssertionError: Optimisation failure. System: Darwin Release: 9.5.0 Version: Darwin Kernel Version 9.5.0: Wed Sep 3 11:31:44 PDT 2008; root:xnu-1228.7.58~1/RELEASE_PPC Win32 version: Distribution: Architecture: 32bit Machine: Power Macintosh Processor: powerpc Python version: 2.5.2 numpy version: 1.1.1 s2: 0.9699999999999993 te: 2048.0000000000409 rex: 0.14900000000002178 chi2: 6.8756889983348349e-28 iter: 22 f_count: 160 g_count: 160 h_count: 22 warning: None ---------------------------------------------------------------------- Ran 59 tests in 154.110s FAILED (failures=6, errors=1) ############## # Unit tests # ############## testing units... ---------------- /sw/lib/relax-py25/test_suite/unit_tests ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................F............F.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ====================================================================== FAIL: Test the Internal.atom_loop() method with the '@163' spin selection. ---------------------------------------------------------------------- Opening the file '/sw/lib/relax-py25/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb' for reading. Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/unit_tests/_generic_fns/_structure/test_internal.py", line 197, in test_atom_loop_spin_selection2 self.assertEqual(pos.tostring(), '\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0') AssertionError: '@$\x1c(\xf5\xc2\x8f\\\xc0\x05\xeb\x85\x1e\xb8Q\xec\xc0*b\xd0\xe5`A\x89' != '\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0' ====================================================================== FAIL: Test the Scientific_data.atom_loop() method with the '@163' spin selection. ---------------------------------------------------------------------- Traceback (most recent call last): File "/sw/lib/relax-py25/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py", line 297, in test_atom_loop_spin_selection2 self.assertEqual(pos.tostring(), '\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0') AssertionError: '@$\x1c(\xf5\xc2\x8f\\\xc0\x05\xeb\x85\x1e\xb8Q\xec\xc0*b\xd0\xe5`A\x89' != '\\\x8f\xc2\xf5(\x1c$@\xecQ\xb8\x1e\x85\xeb\x05\xc0\x89A`\xe5\xd0b*\xc0' ---------------------------------------------------------------------- Ran 1046 tests in 27.144s FAILED (failures=2) ################################### # Summary of the relax test suite # ################################### System/functional tests ............................................................. [ Failed ] Unit tests .......................................................................... [ Failed ] Synopsis ............................................................................ [ Failed ]