relax SVN archive

Fix for bug #22069 by only deleting helix and sheet data with structure.delete when it exists.

This is bug #22069 (https://gna.org/bugs/index.php?22069), the failure of the structure.delete user
function with "AttributeError: Internal instance has no attribute 'helices'".

Created the Structure.test_bug_22069_structure_delete_helix_attribute system test.

This is to catch bug #22069 (https://gna.org/bugs/index.php?22069), the failure of the
structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'".

Added 7 unit tests demonstrating edge case 'no Rex' failures of the 'NS CPMG 2-site expanded' model.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.

Such tests should be replicated for all dispersion models.

Parameter update for the 2nd rotor CaM frame order test model optimisation script.

The Euler angles for the rotation about the motional pivot have been replaced by the translation
vector and Euler angle CoM rotation parameters.

Merged revisions 23315-23319 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23315 | tlinnet | 2014-05-21 20:36:33 +0200 (Wed, 21 May 2014) | 5 lines

Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

This is to catch model B14 showing bad fitting behaviour.
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r23316 | tlinnet | 2014-05-21 20:36:36 +0200 (Wed, 21 May 2014) | 42 lines

Extremely important fix to the model B14.

This was discovered by author Andrew Baldwin of the inspection of his code in relax.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

The implementation was performed wrong for calculation of g3 and g4.
The implementations should be performed by trigonometric functions.

The model B14 was previously in a state of non-functioning.

The B14 model now shows excellent performance.

For the challenging case of data created with numerical model NS CPMG 2-site 3D:

sfrq_1 = 599.8908617*1E6
time_T2_1 = 0.06
ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60]
sfrq_2 = 499.8908617*1E6
time_T2_2 = 0.05
ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50]

r2 = 10. rad/s.
kex: 1000 rad/s
pA: 0.99
dw: 2. ppm

CR72 would fit:
----------
CR72 Ala :1@... r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000
CR72 Ala :1@... r2 499.9 GRID=10.080 MIN=9.999 SET=10.000 RELC=0.000
CR72 Ala :1@... pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000
CR72 Ala :1@... dw GRID=1.429 MIN=1.925 SET=2.000 RELC=0.039
CR72 Ala :1@... kex GRID=5714.714 MIN=1034.721 SET=1000.000 RELC=0.034

B14 fits:
-----------
B14 Ala :1@... r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000
B14 Ala :1@... r2 499.9 GRID=10.080 MIN=10.000 SET=10.000 RELC=0.000
B14 Ala :1@... pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000
B14 Ala :1@... dw GRID=1.429 MIN=2.000 SET=2.000 RELC=0.000
B14 Ala :1@... kex GRID=10000.000 MIN=1000.001 SET=1000.000 RELC=0.000
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r23317 | tlinnet | 2014-05-21 20:36:37 +0200 (Wed, 21 May 2014) | 7 lines

Parameter precision increase for systemtest Relax_disp.test_baldwin_synthetic.

The correct implementation of the trigometric functions allow for higher precision.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

Dublicate line codes was also removed.
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r23318 | tlinnet | 2014-05-21 20:36:39 +0200 (Wed, 21 May 2014) | 5 lines

Code cleanup in systemtest Relax_disp.test_baldwin_synthetic_full.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

The precision could also be increased with 1 digit.
........
r23319 | tlinnet | 2014-05-21 20:36:41 +0200 (Wed, 21 May 2014) | 5 lines

Code clean-up in systemtest Relax_disp.test_baldwin_synthetic.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

Removing many unnecessary lines of code.
........

Initialized merge tracking via "svnmerge" with revisions "1-23322" from
svn+ssh://tlinnet@.../svn/relax/trunk

Branch created from trunk to compare to the disp_speed branch.

The branch will be used to write a range of system tests that should
fail in the trunk, and now pass in the disp_speed branch.

This is to investigate:
Bug #22024 (https://gna.org/bugs/index.php?22024) Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.

Large increase in precision for the 2nd CaM frame order rotor model test data set.

The higher precision is because the number structures in the distribution is now 20 million rather
than 1,000,001 and the numpy.float128 data averaging has been used.

Huge increase in precision for the CaM frame order rotor model test data.

The higher precision is because the number structures in the distribution is now 20 million rather
than 166,666, and the numpy.float128 data averaging has been used.

Merged revisions 23315-23319 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

........
r23315 | tlinnet | 2014-05-21 20:36:33 +0200 (Wed, 21 May 2014) | 5 lines

Implemented systemtest Relax_disp.test_cpmg_synthetic_ns3d_to_b14.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

This is to catch model B14 showing bad fitting behaviour.
........
r23316 | tlinnet | 2014-05-21 20:36:36 +0200 (Wed, 21 May 2014) | 42 lines

Extremely important fix to the model B14.

This was discovered by author Andrew Baldwin of the inspection of his code in relax.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

The implementation was performed wrong for calculation of g3 and g4.
The implementations should be performed by trigonometric functions.

The model B14 was previously in a state of non-functioning.

The B14 model now shows excellent performance.

For the challenging case of data created with numerical model NS CPMG 2-site 3D:

sfrq_1 = 599.8908617*1E6
time_T2_1 = 0.06
ncycs_1 = [2, 4, 8, 10, 20, 30, 40, 60]
sfrq_2 = 499.8908617*1E6
time_T2_2 = 0.05
ncycs_2 = [2, 4, 8, 10, 30, 35, 40, 50]

r2 = 10. rad/s.
kex: 1000 rad/s
pA: 0.99
dw: 2. ppm

CR72 would fit:
----------
CR72 Ala :1@... r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000
CR72 Ala :1@... r2 499.9 GRID=10.080 MIN=9.999 SET=10.000 RELC=0.000
CR72 Ala :1@... pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000
CR72 Ala :1@... dw GRID=1.429 MIN=1.925 SET=2.000 RELC=0.039
CR72 Ala :1@... kex GRID=5714.714 MIN=1034.721 SET=1000.000 RELC=0.034

B14 fits:
-----------
B14 Ala :1@... r2 599.9 GRID=10.116 MIN=10.000 SET=10.000 RELC=0.000
B14 Ala :1@... r2 499.9 GRID=10.080 MIN=10.000 SET=10.000 RELC=0.000
B14 Ala :1@... pA GRID=0.929 MIN=0.990 SET=0.990 RELC=0.000
B14 Ala :1@... dw GRID=1.429 MIN=2.000 SET=2.000 RELC=0.000
B14 Ala :1@... kex GRID=10000.000 MIN=1000.001 SET=1000.000 RELC=0.000
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r23317 | tlinnet | 2014-05-21 20:36:37 +0200 (Wed, 21 May 2014) | 7 lines

Parameter precision increase for systemtest Relax_disp.test_baldwin_synthetic.

The correct implementation of the trigometric functions allow for higher precision.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

Dublicate line codes was also removed.
........
r23318 | tlinnet | 2014-05-21 20:36:39 +0200 (Wed, 21 May 2014) | 5 lines

Code cleanup in systemtest Relax_disp.test_baldwin_synthetic_full.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

The precision could also be increased with 1 digit.
........
r23319 | tlinnet | 2014-05-21 20:36:41 +0200 (Wed, 21 May 2014) | 5 lines

Code clean-up in systemtest Relax_disp.test_baldwin_synthetic.

bug #22021: (https://gna.org/bugs/?22021) Model B14 shows bad fitting to data.

Removing many unnecessary lines of code.
........