Author: bugman
Date: Fri May 23 10:06:32 2014
New Revision: 23368
URL: http://svn.gna.org/viewcvs/relax?rev=23368&view=rev
Log:
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.
Modified:
trunk/specific_analyses/relax_disp/parameter_object.py
Modified: trunk/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameter_object.py?rev=23368&r1=23367&r2=23368&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/parameter_object.py (original)
+++ trunk/specific_analyses/relax_disp/parameter_object.py Fri May 23
10:06:32 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)
r23368 - /trunk/specific_analyses/relax_disp/parameter_object.py