Author: bugman
Date: Sun Oct 27 17:55:18 2013
New Revision: 21252
URL: http://svn.gna.org/viewcvs/relax?rev=21252&view=rev
Log:
Changed the definition of tex thanks to feedback from Nikolai Skrynnikov.
This was previously defined as tex = 1/(2kex) to be compatible with CPMGFit,
but has now been
changed to tex = 1/kex.
Modified:
branches/relax_disp/docs/latex/dispersion_params.tex
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/optimisation.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
Modified: branches/relax_disp/docs/latex/dispersion_params.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion_params.tex?rev=21252&r1=21251&r2=21252&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion_params.tex (original)
+++ branches/relax_disp/docs/latex/dispersion_params.tex Sun Oct 27 17:55:18
2013
@@ -35,12 +35,12 @@
$\theta$ & $\arctan \left( \frac{\omegaone}{\aveoffset} \right)$
& Rotating frame tilt angle & rad \\
$\kAB$ & $\pB\kex$ & The forward exchange
rate from state A to state B & rad.s$^{-1}$ \\
$\kBA$ & $\pA\kex$ & The reverse exchange
rate from state B to state A & rad.s$^{-1}$ \\
-$\kex$ & $1 / (2 \tex)$ & Chemical exchange rate
constant & rad.s$^{-1}$ \\
+$\kex$ & $1 / \tex$ & Chemical exchange rate
constant & rad.s$^{-1}$ \\
$\kexB$ & $\kAB + \kBA$ & Chemical exchange rate
constant between sites A and B & rad.s$^{-1}$ \\
$\kexC$ & $\kAC + \kCA$ & Chemical exchange rate
constant between sites A and C & rad.s$^{-1}$ \\
$\kB$ & $\approx \kexB$ & Approximate chemical
exchange rate constant between sites A and B & rad.s$^{-1}$ \\
$\kC$ & $\approx \kexC$ & Approximate chemical
exchange rate constant between sites A and C & rad.s$^{-1}$ \\
-$\tex$ & $1 / (2 \kex)$ & Time of exchange
& s.rad$^{-1}$ \\
+$\tex$ & $1 / \kex$ & Time of exchange
& s.rad$^{-1}$ \\
$\pA$ & - & Population of state A
& - \\
$\pB$ & - & Population of state B
& - \\
$\dw$ & - & Chemical shift
difference between the two states & rad.s$^{-1}$
(stored as ppm) \\
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=21252&r1=21251&r2=21252&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Sun Oct 27
17:55:18 2013
@@ -94,7 +94,7 @@
self.PARAMS.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.PARAMS.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.PARAMS.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.PARAMS.add('tex', scope='spin', default=1.0/20000.0, desc='The
time of exchange (tex = 1/(2kex))', set='params', py_type=float,
grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True)
+ self.PARAMS.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.PARAMS.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.PARAMS.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.PARAMS.add('params', scope='spin', desc='The model parameters',
py_type=list)
@@ -849,7 +849,7 @@
_table.add_row(["Exchange rate (rad/s)", "'kex'", "10000.0"])
_table.add_row(["Exchange rate between sites A and B (rad/s)", "'kB'",
"10000.0"])
_table.add_row(["Exchange rate between sites A and C (rad/s)", "'kC'",
"10000.0"])
- _table.add_row(["Time of exchange (s/rad)", "'tex'", "1.0/20000.0"])
+ _table.add_row(["Time of exchange (s/rad)", "'tex'", "1.0/10000.0"])
_table.add_row(["Exchange rate from state A to state B (rad/s)",
"'k_AB'", "10000.0"])
_table.add_row(["Exchange rate from state B to state A (rad/s)",
"'k_BA'", "10000.0"])
default_value_doc.add_table(_table.label)
Modified: branches/relax_disp/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/optimisation.py?rev=21252&r1=21251&r2=21252&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Sun Oct
27 17:55:18 2013
@@ -143,8 +143,8 @@
# Time of exchange.
elif param_name in ['tex']:
- lower.append(1/200000.0)
- upper.append(0.5)
+ lower.append(1/100000.0)
+ upper.append(1.0)
# Pre-set parameters.
for param_name, param_index, spin_index, frq_index in
loop_parameters(spins=spins, model_type=cdp.model_type):
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=21252&r1=21251&r2=21252&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Sun Oct 27
17:55:18 2013
@@ -720,7 +720,7 @@
# The kex to tex conversion.
if param_name == 'kex':
- tex = 1.0 / (2.0 * value)
+ tex = 1.0 / value
set_value(value=tex, key=key, spins=spins, sim_index=sim_index,
param_name='tex', spin_index=spin_index, frq_index=frq_index)
# The kex to k_AB and k_BA conversion.
@@ -736,7 +736,7 @@
# The tex to kex conversion.
if param_name == 'tex':
- kex = 1.0 / (2.0 * value)
+ kex = 1.0 / value
set_value(value=kex, key=key, spins=spins, sim_index=sim_index,
param_name='kex', spin_index=spin_index, frq_index=frq_index)
r21252 - in /branches/relax_disp: docs/latex/ specific_analyses/relax_disp/