Author: bugman
Date: Sun Dec 8 12:32:35 2013
New Revision: 21866
URL: http://svn.gna.org/viewcvs/relax?rev=21866&view=rev
Log:
The 'LM63' and 'LM63 3-site' models are now classified as nested in the
dispersion auto-analysis.
The grid search for the 'LM63 3-site' model is therefore skipped and the
starting parameters for
optimisation are set to those of the optimised 'LM63' model.
Modified:
trunk/auto_analyses/relax_disp.py
trunk/docs/latex/dispersion.tex
Modified: trunk/auto_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=21866&r1=21865&r2=21866&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp.py (original)
+++ trunk/auto_analyses/relax_disp.py Sun Dec 8 12:32:35 2013
@@ -233,6 +233,8 @@
# The simpler model.
nested_pipe = None
+ if model == MODEL_LM63_3SITE and MODEL_LM63 in self.models:
+ nested_pipe = MODEL_LM63
if model == MODEL_CR72_FULL and MODEL_CR72 in self.models:
nested_pipe = MODEL_CR72
if model == MODEL_MMQ_CR72 and MODEL_CR72 in self.models:
@@ -285,6 +287,13 @@
else:
setattr(spin, 'r2', deepcopy(nested_spin.r2))
+ # The LM63 3-site model parameters.
+ if model == MODEL_LM63_3SITE:
+ setattr(spin, 'phi_ex_B', deepcopy(nested_spin.phi_ex))
+ setattr(spin, 'phi_ex_C', deepcopy(nested_spin.phi_ex))
+ setattr(spin, 'kB', deepcopy(nested_spin.kex))
+ setattr(spin, 'kC', deepcopy(nested_spin.kex))
+
# All other spin parameters.
for param in spin.params:
if param in ['r2', 'r2a', 'r2b']:
@@ -292,6 +301,10 @@
# The parameter does not exist.
if not hasattr(nested_spin, param):
+ continue
+
+ # Skip the LM63 3-site model parameters
+ if model == MODEL_LM63_3SITE and param in ['phi_ex', 'kex']:
continue
# Copy the parameter.
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21866&r1=21865&r2=21866&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Sun Dec 8 12:32:35 2013
@@ -1133,7 +1133,7 @@
\item[Grid search avoidance:] A number of tricks are used to speed up
optimisation by skipping or decreasing the size of the initial grid search:
\begin{description}
\item[Pre-run directory:] If a pre-run directory is supplied -- a separate
directory containing the dispersion auto-analysis results from a previous run
-- the optimised parameters from these previous results will be used as the
starting point for optimisation rather than performing a grid search. This
is used in a clustered analysis whereby the pre-run directory contains
results from a non-clustered analysis. This is essential for when large spin
clusters are specified, as a grid search becomes prohibitively expensive with
clusters of three or more spins. At some point a RelaxError will occur
because the grid search is impossibly large. For the cluster specific
parameters, i.e.\ the populations of the states and the exchange parameters,
an average value will be used as the starting point. For all other
parameters, the $\Rtwozero$ values for each spin and magnetic field, as well
as the parameters related to the chemical shift difference $\dw$, the
optimised values of the previous run will be directly copied.
-\item[Model nesting:] If two models are nested, then the parameters of the
simpler will be used as the starting point for optimisation of the more
complex. The currently supported nested model pairs are `CR72' and `CR72
full', `CR72' and `MMQ CR72', `NS CPMG 2-site 3D' and `NS CPMG 2-site 3D
full', and `NS CPMG 2-site star' and `NS CPMG 2-site star full'. In these
cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter values are set to the
simpler model $\Rtwozero$ value and the grid search is bypassed.
+\item[Model nesting:] If two models are nested, then the parameters of the
simpler will be used as the starting point for optimisation of the more
complex. The currently supported nested model pairs are `LM63' and `LM63
3-site', `CR72' and `CR72 full', `CR72' and `MMQ CR72', `NS CPMG 2-site 3D'
and `NS CPMG 2-site 3D full', and `NS CPMG 2-site star' and `NS CPMG 2-site
star full'. In these cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter
values are set to the simpler model $\Rtwozero$ value and the grid search is
bypassed.
\item[Model equivalence:] When two models are equivalent, the optimised
parameters of one model can be used as the starting point of the other rather
than performing a grid search. This is used in the auto-analysis for
avoiding the grid search in the numeric models. The optimised `CR72' model
is used for the `NS CPMG 2-site expanded', `NS CPMG 2-site 3D', and `NS CPMG
2-site star' models. The optimised `MMQ CR72' model is used for the `NS MMQ
2-site' model. And the `MP05' model is used for the `NS R1rho 2-site' model.
\end{description}
\item[Interruption:] The optimisation procedure of the auto-analysis can
read saved results files if a previous calculation was interrupted.
r21866 - in /trunk: auto_analyses/relax_disp.py docs/latex/dispersion.tex