Author: bugman
Date: Fri May 23 10:29:49 2014
New Revision: 23371
URL: http://svn.gna.org/viewcvs/relax?rev=23371&view=rev
Log:
Merged revisions 23368-23370 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23368 | bugman | 2014-05-23 10:06:32 +0200 (Fri, 23 May 2014) | 11 lines
Changed most default dispersion parameter values to avoid edge cases where
there is no exchange.
The dw parameters were all 0.0 and kex 1e5, both of which result in no
exchange. If this is ever
used for an optimisation starting point - which it never should, apart from
development, test suite,
and debugging purposes - then the optimisation algorithm will have a very
hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while
still staying far away
from the no exchange condition of pA = 1.0.
This follows from
http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
........
r23369 | bugman | 2014-05-23 10:10:46 +0200 (Fri, 23 May 2014) | 10 lines
Fixes for 3 dispersion system tests for the change in default parameter
values.
The default values are used in the auto-analysis in the test suite to avoid
the grid search. The
changed values affected the optimisation of two spins from Flemming
Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of
no exchange and residue
70 used as an example where data is only available at one field. The
system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it
was directly checking these
default values.
........
r23370 | bugman | 2014-05-23 10:18:37 +0200 (Fri, 23 May 2014) | 7 lines
Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.
This uses the default parameter values to start the optimisation, therefore
the recent change away
from edge case 'no Rex' values allows the parameter values stored in
ds.dx_clust_val to be correctly
optimised.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri May 23 10:29:49 2014
@@ -1 +1 @@
-/trunk:1-23366
+/trunk:1-23370
Modified:
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py?rev=23371&r1=23370&r2=23371&view=diff
==============================================================================
---
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
(original)
+++
branches/frame_order_cleanup/specific_analyses/relax_disp/parameter_object.py
Fri May 23 10:29:49 2014
@@ -61,32 +61,32 @@
self._add('r2', scope='spin', default=10.0, desc='The transversal
relaxation rate', set='params', py_type=dict, grace_string='\\qR\\s2\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
self._add('r2a', scope='spin', default=10.0, desc='The transversal
relaxation rate for state A in the absence of exchange', set='params',
py_type=dict, grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True,
sim=True)
self._add('r2b', scope='spin', default=10.0, desc='The transversal
relaxation rate for state B in the absence of exchange', set='params',
py_type=dict, grace_string='\\qR\\s2,B\\N\\Q (rad.s\\S-1\\N)', err=True,
sim=True)
- self._add('pA', scope='spin', default=0.5, desc='The population for
state A', set='params', py_type=float, grace_string='\\qp\\sA\\N\\Q',
err=True, sim=True)
+ self._add('pA', scope='spin', default=0.90, desc='The population for
state A', set='params', py_type=float, grace_string='\\qp\\sA\\N\\Q',
err=True, sim=True)
self._add('pB', scope='spin', default=0.5, desc='The population for
state B', set='params', py_type=float, grace_string='\\qp\\sB\\N\\Q',
err=True, sim=True)
self._add('pC', scope='spin', default=0.5, desc='The population for
state C', set='params', py_type=float, grace_string='\\qp\\sC\\N\\Q',
err=True, sim=True)
self._add('phi_ex', scope='spin', default=5.0, desc='The phi_ex =
pA.pB.dw**2 value (ppm^2)', set='params', py_type=float,
grace_string='\\xF\\B\\sex\\N = \\q p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q
(ppm\\S2\\N)', err=True, sim=True)
self._add('phi_ex_B', scope='spin', default=5.0, desc='The fast
exchange factor between sites A and B (ppm^2)', set='params', py_type=float,
grace_string='\\xF\\B\\sex,B\\N (ppm\\S2\\N)', err=True, sim=True)
self._add('phi_ex_C', scope='spin', default=5.0, desc='The fast
exchange factor between sites A and C (ppm^2)', set='params', py_type=float,
grace_string='\\xF\\B\\sex,C\\N (ppm\\S2\\N)', err=True, sim=True)
self._add('padw2', scope='spin', default=1.0, desc='The pA.dw**2
value (ppm^2)', set='params', py_type=float,
grace_string='\\qp\\sA\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True,
sim=True)
- self._add('dw', scope='spin', default=0.0, desc='The chemical shift
difference between states A and B (in ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\Q (ppm)', err=True, sim=True)
- self._add('dw_AB', scope='spin', default=0.0, desc='The chemical
shift difference between states A and B for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAB\\N (ppm)',
err=True, sim=True)
- self._add('dw_AC', scope='spin', default=0.0, desc='The chemical
shift difference between states A and C for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAC\\N (ppm)',
err=True, sim=True)
- self._add('dw_BC', scope='spin', default=0.0, desc='The chemical
shift difference between states B and C for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SBC\\N (ppm)',
err=True, sim=True)
- self._add('dwH', scope='spin', default=0.0, desc='The proton
chemical shift difference between states A and B (in ppm)', set='params',
py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q (ppm)', err=True, sim=True)
- self._add('dwH_AB', scope='spin', default=0.0, desc='The proton
chemical shift difference between states A and B for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAB\\N (ppm)', err=True, sim=True)
- self._add('dwH_AC', scope='spin', default=0.0, desc='The proton
chemical shift difference between states A and C for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAC\\N (ppm)', err=True, sim=True)
- self._add('dwH_BC', scope='spin', default=0.0, desc='The proton
chemical shift difference between states B and C for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SBC\\N (ppm)', err=True, sim=True)
- self._add('kex', scope='spin', default=10000.0, desc='The exchange
rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
- self._add('kex_AB', scope='spin', default=10000.0, desc='The
exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB +
k_BA (rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SAB\\N (rad.s\\S-1\\N)', err=True, sim=True)
- self._add('kex_AC', scope='spin', default=10000.0, desc='The
exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC +
k_CA (rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SAC\\N (rad.s\\S-1\\N)', err=True, sim=True)
- self._add('kex_BC', scope='spin', default=10000.0, desc='The
exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC +
k_CB (rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SBC\\N (rad.s\\S-1\\N)', err=True, sim=True)
- self._add('kB', scope='spin', default=10000.0, desc='Approximate
chemical exchange rate constant between sites A and B (rad.s^-1)',
set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
- self._add('kC', scope='spin', default=10000.0, desc='Approximate
chemical exchange rate constant between sites A and C (rad.s^-1)',
set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
- self._add('tex', scope='spin', default=1.0/10000.0, desc='The time
of exchange (tex = 1/kex)', set='params', py_type=float,
grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True)
+ self._add('dw', scope='spin', default=1.0, desc='The chemical shift
difference between states A and B (in ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\Q (ppm)', err=True, sim=True)
+ self._add('dw_AB', scope='spin', default=1.0, desc='The chemical
shift difference between states A and B for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAB\\N (ppm)',
err=True, sim=True)
+ self._add('dw_AC', scope='spin', default=1.0, desc='The chemical
shift difference between states A and C for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAC\\N (ppm)',
err=True, sim=True)
+ self._add('dw_BC', scope='spin', default=1.0, desc='The chemical
shift difference between states B and C for 3-site exchange (in ppm)',
set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SBC\\N (ppm)',
err=True, sim=True)
+ self._add('dwH', scope='spin', default=1.0, desc='The proton
chemical shift difference between states A and B (in ppm)', set='params',
py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q (ppm)', err=True, sim=True)
+ self._add('dwH_AB', scope='spin', default=1.0, desc='The proton
chemical shift difference between states A and B for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAB\\N (ppm)', err=True, sim=True)
+ self._add('dwH_AC', scope='spin', default=1.0, desc='The proton
chemical shift difference between states A and C for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAC\\N (ppm)', err=True, sim=True)
+ self._add('dwH_BC', scope='spin', default=1.0, desc='The proton
chemical shift difference between states B and C for 3-site exchange (in
ppm)', set='params', py_type=float,
grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SBC\\N (ppm)', err=True, sim=True)
+ self._add('kex', scope='spin', default=1000.0, desc='The exchange
rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q
(rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('kex_AB', scope='spin', default=1000.0, desc='The exchange
rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA
(rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SAB\\N (rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('kex_AC', scope='spin', default=1000.0, desc='The exchange
rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA
(rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SAC\\N (rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('kex_BC', scope='spin', default=1000.0, desc='The exchange
rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB
(rad.s^-1)', set='params', py_type=float,
grace_string='\\qk\\sex\\N\\Q\\SBC\\N (rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('kB', scope='spin', default=1000.0, desc='Approximate
chemical exchange rate constant between sites A and B (rad.s^-1)',
set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
+ self._add('kC', scope='spin', default=1000.0, desc='Approximate
chemical exchange rate constant between sites A and C (rad.s^-1)',
set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q (rad.s\\S-1\\N)',
err=True, sim=True)
+ self._add('tex', scope='spin', default=1.0/1000.0, desc='The time of
exchange (tex = 1/kex)', set='params', py_type=float,
grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True)
self._add('theta', scope='spin', desc='Rotating frame tilt angle : (
theta = arctan(w_1 / Omega) ) (rad)', grace_string='Rotating frame tilt angle
(rad)', py_type=dict, set='all', err=False, sim=False)
self._add('w_eff', scope='spin', desc='Effective field in rotating
frame : ( w_eff = sqrt(Omega^2 + w_1^2) ) (rad.s^-1)',
grace_string='Effective field in rotating frame (rad.s\\S-1\\N)',
py_type=dict, set='all', err=False, sim=False)
- self._add('k_AB', scope='spin', default=10000.0, desc='The exchange
rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
- self._add('k_BA', scope='spin', default=10000.0, desc='The exchange
rate from state B to state A', set='params', py_type=float,
grace_string='\\qk\\sBA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('k_AB', scope='spin', default=1000.0, desc='The exchange
rate from state A to state B', set='params', py_type=float,
grace_string='\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
+ self._add('k_BA', scope='spin', default=1000.0, desc='The exchange
rate from state B to state A', set='params', py_type=float,
grace_string='\\qk\\sBA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True)
# Add the minimisation data.
self._add_min_data(min_stats_global=False, min_stats_spin=True)
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=23371&r1=23370&r2=23371&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py Fri
May 23 10:29:49 2014
@@ -1475,7 +1475,7 @@
print("\nChecking the dx point point file.")
res_file = [
'0.8 3.92 0.39964 1'+"\n",
- '4e-05 0.08 3.8 1'+"\n",
+ '0.76981 3.9169 0.41353 1'+"\n",
]
file = open(point_point, 'r')
lines = file.readlines()
@@ -1887,18 +1887,18 @@
print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw))
print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex))
print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
- self.assertAlmostEqual(spin70.r2[r20_key1], 6.95820070286795, 3)
- self.assertAlmostEqual(spin70.r2[r20_key2], 9.39657836325177, 3)
- self.assertAlmostEqual(spin70.pA, 0.989701009272583, 3)
- self.assertAlmostEqual(spin70.dw, 5.67326272877785, 3)
- self.assertAlmostEqual(spin70.kex/10000, 1713.54848022381/10000, 3)
- self.assertAlmostEqual(spin70.chi2, 52.5106852884892, 3)
- self.assertAlmostEqual(spin71.r2[r20_key1], 4.99887619838854, 3)
- self.assertAlmostEqual(spin71.r2[r20_key2], 6.89817579107423, 3)
- self.assertAlmostEqual(spin71.pA, 0.986695947044873, 3)
- self.assertAlmostEqual(spin71.dw, 2.09130944488215, 3)
- self.assertAlmostEqual(spin71.kex/10000, 2438.42961328059/10000, 3)
- self.assertAlmostEqual(spin71.chi2, 15.1644963157243, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key1], 6.95815351460902, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key2], 9.39649535771294, 3)
+ self.assertAlmostEqual(spin70.pA, 0.989701014493195, 3)
+ self.assertAlmostEqual(spin70.dw, 5.67314464776128, 3)
+ self.assertAlmostEqual(spin70.kex/10000, 1713.65380495429/10000, 3)
+ self.assertAlmostEqual(spin70.chi2, 52.5106880917473, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key1], 4.99889337382435, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key2], 6.89822887466673, 3)
+ self.assertAlmostEqual(spin71.pA, 0.986709050819695, 3)
+ self.assertAlmostEqual(spin71.dw, 2.09238266766502, 3)
+ self.assertAlmostEqual(spin71.kex/10000, 2438.27019901422/10000, 3)
+ self.assertAlmostEqual(spin71.chi2, 15.1644906963987, 3)
# The final data pipe checks.
self.interpreter.pipe.switch(pipe_name='final - relax_disp')
@@ -2048,23 +2048,23 @@
print("%-20s %20.15g %20.15g %20.15g" % ("dw", spin4.dw, spin70.dw,
spin71.dw))
print("%-20s %20.15g %20.15g %20.15g" % ("kex", spin4.kex,
spin70.kex, spin71.kex))
print("%-20s %20.15g %20.15g %20.15g\n" % ("chi2", spin4.chi2,
spin70.chi2, spin71.chi2))
- self.assertAlmostEqual(spin4.r2[r20_key1], 1.58622828626709, 2)
- self.assertAlmostEqual(spin4.r2[r20_key2], 1.58592122315687, 3)
- self.assertAlmostEqual(spin4.pA, 0.51276361588332, 3)
- self.assertAlmostEqual(spin4.dw, 0.0677279657953332, 3)
- self.assertAlmostEqual(spin4.kex/10000, 2448.82586714642/10000, 3)
- self.assertAlmostEqual(spin4.chi2, 20.4855900585583, 3)
- self.assertAlmostEqual(spin70.r2[r20_key1], 6.97252087724882, 3)
- self.assertAlmostEqual(spin70.r2[r20_key2], 9.40960089079409, 3)
- self.assertAlmostEqual(spin70.pA, 0.989857038532724, 3)
- self.assertAlmostEqual(spin70.dw, 5.60897947735102, 3)
- self.assertAlmostEqual(spin70.kex/10000, 1752.98845226051/10000, 3)
- self.assertAlmostEqual(spin70.chi2, 53.8382162820491, 3)
- self.assertAlmostEqual(spin71.r2[r20_key1], 4.98111206240747, 3)
- self.assertAlmostEqual(spin71.pA, 0.996607989009612, 3)
- self.assertAlmostEqual(spin71.dw, 4.34436483888832, 3)
- self.assertAlmostEqual(spin71.kex/10000, 1936.74679136572/10000, 3)
- self.assertAlmostEqual(spin71.chi2, 5.5170374277749, 3)
+ self.assertAlmostEqual(spin4.r2[r20_key1], 1.60462456409508, 2)
+ self.assertAlmostEqual(spin4.r2[r20_key2], 1.63221781206148, 3)
+ self.assertAlmostEqual(spin4.pA, 0.899911303159742, 3)
+ self.assertAlmostEqual(spin4.dw, 0.000048303116437, 3)
+ self.assertAlmostEqual(spin4.kex/10000, 0.0796851577904277/10000, 3)
+ self.assertAlmostEqual(spin4.chi2, 26.7356693257612, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key1], 6.97235130701478, 3)
+ self.assertAlmostEqual(spin70.r2[r20_key2], 9.40988386796136, 3)
+ self.assertAlmostEqual(spin70.pA, 0.989856745034836, 3)
+ self.assertAlmostEqual(spin70.dw, 5.60878828496508, 3)
+ self.assertAlmostEqual(spin70.kex/10000, 1752.93345983946/10000, 3)
+ self.assertAlmostEqual(spin70.chi2, 53.8382172686916, 3)
+ self.assertAlmostEqual(spin71.r2[r20_key1], 4.98111647969012, 3)
+ self.assertAlmostEqual(spin71.pA, 0.996608013844177, 3)
+ self.assertAlmostEqual(spin71.dw, 4.34425685338434, 3)
+ self.assertAlmostEqual(spin71.kex/10000, 1937.21776309767/10000, 3)
+ self.assertAlmostEqual(spin71.chi2, 5.51703749012473, 3)
def test_hansen_cpmg_data_to_cr72(self):
@@ -4529,9 +4529,9 @@
# Testing the r2 values.
self.assertEqual(spin.r2[r20_key_600], 10.00)
self.assertEqual(spin.r2[r20_key_500], 10.00)
- self.assertEqual(spin.pA, 0.5)
- self.assertEqual(spin.dw, 0.0)
- self.assertEqual(spin.kex, 10000.0)
+ self.assertEqual(spin.pA, 0.9)
+ self.assertEqual(spin.dw, 1.0)
+ self.assertEqual(spin.kex, 1000.0)
print("###########################################")
print("Trying GRID SEARCH for standard R2eff values")
r23371 - in /branches/frame_order_cleanup: ./ specific_analyses/relax_disp/ test_suite/system_tests/