Author: tlinnet
Date: Wed May 28 16:49:06 2014
New Revision: 23530
URL: http://svn.gna.org/viewcvs/relax?rev=23530&view=rev
Log:
Added all the default values for the lower/upper bounds which is set for the
parameters in the grid search.
This is added in the collected table of
specific_analysis/relax_disp/parameter_object.py.
The values were extracted from: specific_analysis/relax_disp/optimisation.py
in grid_search_setup().
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of
dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
In any function, these default values can get accessed by:
from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_upper('pA')
This provides a good look-up table, when stress testing the different
lib/dispersion/* functions.
Modified:
branches/disp_speed/specific_analyses/relax_disp/parameter_object.py
Modified: branches/disp_speed/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/specific_analyses/relax_disp/parameter_object.py?rev=23530&r1=23529&r2=23530&view=diff
==============================================================================
--- branches/disp_speed/specific_analyses/relax_disp/parameter_object.py
(original)
+++ branches/disp_speed/specific_analyses/relax_disp/parameter_object.py
Wed May 28 16:49:06 2014
@@ -58,34 +58,34 @@
self._add('i0', scope='spin', default=10000.0, desc='The initial
intensity', py_type=dict, set='params', grace_string='\\qI\\s0\\Q', err=True,
sim=True)
# Add the parameters of all dispersion models.
- 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('r2', scope='spin', default=10.0, grid_lower=5.0,
grid_upper=20.0, 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, grid_lower=5.0,
grid_upper=20.0, 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, grid_lower=5.0,
grid_upper=20.0, 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=0.90, grid_lower=0.5,
grid_upper=1.0, 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('pB', scope='spin', default=0.5, grid_lower=0.0,
grid_upper=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=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('phi_ex', scope='spin', default=5.0, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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=1.0, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=10.0, 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, grid_lower=0.0,
grid_upper=3.0, 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, grid_lower=0.0,
grid_upper=3.0, 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, grid_lower=0.0,
grid_upper=3.0, 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, grid_lower=0.0,
grid_upper=3.0, 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, grid_lower=1.0,
grid_upper=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=1000.0, grid_lower=1.0,
grid_upper=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=1000.0, grid_lower=1.0,
grid_upper=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=1000.0, grid_lower=1.0,
grid_upper=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=1000.0, grid_lower=1.0,
grid_upper=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=1000.0, grid_lower=1.0,
grid_upper=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=1.0/1000.0,
grid_lower=1/10000.0, grid_upper=1.0, 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=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_AB', scope='spin', default=1000.0, grid_lower=1.0,
grid_upper=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=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.
r23530 - /branches/disp_speed/specific_analyses/relax_disp/parameter_object.py