relax SVN archive

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

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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.
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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.
........

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.

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.

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.

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

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.

Merged revisions 23289-23290,23310-23312 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23289 | bugman | 2014-05-21 10:41:57 +0200 (Wed, 21 May 2014) | 6 lines

Backported the relax 3.2.0 CHANGES file changes to trunk.

The command used was:
svn merge -r23287:23288 svn+ssh://bugman@.../svn/relax/tags/3.2.0 .
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r23290 | bugman | 2014-05-21 10:43:41 +0200 (Wed, 21 May 2014) | 3 lines

Punctuation fixes throughout the CHANGES document.
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r23310 | tlinnet | 2014-05-21 17:43:47 +0200 (Wed, 21 May 2014) | 6 lines

Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.

Systemtest was renamed from test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to
reflect which model create the data and which model fits the data.
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r23311 | tlinnet | 2014-05-21 17:43:49 +0200 (Wed, 21 May 2014) | 6 lines

Modified cpmg_synthetic script to first create all time structures before doing back-calculation.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.

The numerical models need all time points which are defined in setup, to be present
when calculating.
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r23312 | tlinnet | 2014-05-21 18:00:19 +0200 (Wed, 21 May 2014) | 5 lines

Renamed systemtest to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster.

The model that creates the data has been changed to numerical model.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.
........

Merged revisions 23310-23312 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23310 | tlinnet | 2014-05-21 17:43:47 +0200 (Wed, 21 May 2014) | 6 lines

Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.

Systemtest was renamed from test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to
reflect which model create the data and which model fits the data.
........
r23311 | tlinnet | 2014-05-21 17:43:49 +0200 (Wed, 21 May 2014) | 6 lines

Modified cpmg_synthetic script to first create all time structures before doing back-calculation.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.

The numerical models need all time points which are defined in setup, to be present
when calculating.
........
r23312 | tlinnet | 2014-05-21 18:00:19 +0200 (Wed, 21 May 2014) | 5 lines

Renamed systemtest to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster.

The model that creates the data has been changed to numerical model.

bug #22017: (https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical CPMG models.
........