Author: bugman
Date: Tue Sep 3 16:00:57 2013
New Revision: 20772
URL: http://svn.gna.org/viewcvs/relax?rev=20772&view=rev
Log:
The tutorial for adding dispersion models in the user manual has been
simplified.
Most of the text from the dispersion model addition tutorial in the
dispersion chapter of the manual
has been removed. Instead a link to the tutorial on the wiki is given as
this is a much better
place for such information
(http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax).
Modified:
branches/relax_disp/docs/latex/dispersion.tex
Modified: branches/relax_disp/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/dispersion.tex?rev=20772&r1=20771&r2=20772&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/dispersion.tex (original)
+++ branches/relax_disp/docs/latex/dispersion.tex Tue Sep 3 16:00:57 2013
@@ -1054,106 +1054,4 @@
\section{Tutorial for adding relaxation dispersion models}
\label{sect: dispersion: model tutorial}
-The following is a tutorial for adding new relaxation dispersion models for
either CPMG-type\index{relaxation dispersion!CPMG-type experiment} or
$\Ronerho$-type\index{relaxation dispersion!$\Ronerho$-type experiment}
experiments to relax. This includes both the models based on the analytical,
closed-form expressions as well as the models involving numerical solutions
of the Bloch-McConnell equations. The tutorial is designed for those who
feel adventurous enough to become a relax developer. This text derives from
the relax-devel@xxxxxxx mailing list post:
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.devel/3907}{http://article.gmane.org/gmane.science.nmr.relax.devel/3907}.
-
-The tutorial will follow the example of the addition of the `M61'
model\index{relaxation dispersion!M61 model} already present within relax,
pointing to the relevant commits for reference. To see the commit message
and the code changes in colour, click on the links found within these commit
messages. This specific case is the \citet{Meiboom61} analytic model for
2-site fast exchange equation for $\Ronerho$-type experiments.
-
-
-\subsection{Adding the model to the list}
-
-Reference commit:
\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17611}{http://article.gmane.org/gmane.science.nmr.relax.scm/17611}
-
-Firstly the model should be added to the lists of the
\module{specific\_analyses.relax\_disp.\linebreak[0]{}variables} module. The
model name is stored in a special variable which will be used throughout
relax.
-
-
-\subsection{The \uf{relax\_disp.select\_model} user function front end}
-
-Reference commit:
\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17612}{http://article.gmane.org/gmane.science.nmr.relax.scm/17612}
-
-The next step is to add the model, its description, the equations for the
analytic models, and all references to the \uf{relax\_disp.select\_model}
user function front end. When the relaxation dispersion chapter of the relax
manual is created (this will be the
\file{docs/latex/\linebreak[0]{}relax\_disp.tex} file), then the same
description should be added there as well.
-
-
-\subsection{The relax library}
-
-Reference commit:
\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17615}{http://article.gmane.org/gmane.science.nmr.relax.scm/17615}
-
-Now the dispersion function needs to be added to the relax library (in the
\module{lib.relax\_disp} package). This should be designed as a simple
Python function which takes the dispersion parameters and experimental
variables, and calculates the $\Rtwoeff$/$\Ronerho$ values. The module can
contain auxiliary functions for the calculation. Some auxiliary functions,
if not specific to relaxation dispersion, may be better placed in other
locations within the relax library.
-
-The relaxation dispersion functions in the library currently take as an
argument a data structure for the back-calculated $\Rtwoeff$/$\Ronerho$
values and populate this structure. This design is not essential if the
target function, described in the next point, handles the library function
appropriately. Just look at the files in \module{lib.dispersion} to get an
idea of the design used.
-
-The dispersion code in the relax library must be robust. This involves
identifying parameter values or combinations which would cause failures in
the mathematical operations. Numerical issues only present in software
implementation of the mathematics must be considered. Note that parameter
values of 0.0 are common within a grid search. It should be decided whether
the back-calculated $\Rtwoeff$/$\Ronerho$ value should be set to zero, to
another value, or to something large (e.g. 1e$^{100}$). For example:
-
-\begin{description}
-\item[Divisions:] Always catch zeros in the denominator with if statements,
even if you believe that this will never be encountered.
-\item[Square roots:] Make sure that the value inside is always $> 0$.
-\item[Trigonometric functions:] These should be tested for where they are
not defined or where the software implementation can no longer handle certain
values. For example try math.cosh(1000) in Python.
-\end{description}
-
-In the reference example, the M61 model\index{relaxation dispersion!M61
model} code was copied from the LM63 module and modified appropriately.
-
-
-\subsection{The target function}
-
-Reference commits:
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17616}{http://article.gmane.org/gmane.science.nmr.relax.scm/17616}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17660}{http://article.gmane.org/gmane.science.nmr.relax.scm/17660}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17661}{http://article.gmane.org/gmane.science.nmr.relax.scm/17661}
-
-The target function is used in optimisation and is a class method which
takes as a single argument the parameter vector. This list is changed by the
minimisation algorithm during optimisation. The target function should then
return a single floating point number -- the chi-squared value.
-
-Again in this example, the code for the M61\index{relaxation dispersion!M61
model} is copied from the LM63 model\index{relaxation dispersion!LM63 model}
and then modified.
-
-
-\subsection{Adding support for the parameters}
-
-Reference commit:
\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17573}{http://article.gmane.org/gmane.science.nmr.relax.scm/17573}
-
-This is needed to enable the model. This example is for the CR72
model\index{relaxation dispersion!CR72 model} implementation as the
parameters required for the M61 model\index{relaxation dispersion!M61 model}
match those of the preexisting LM63 model\index{relaxation dispersion!LM63
model}.
-
-
-\subsection{The \uf{relax\_disp.select\_model} back end}
-
-Reference commit:
\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17622}{http://article.gmane.org/gmane.science.nmr.relax.scm/17622}
-
-Now the back end of the \uf{relax\_disp.select\_model} user function for the
model can be added. This involved identifying the model and constructing the
parameter list.
-
-
-\subsection{The test suite}
-\label{sect: test suite for dispersion}
-
-Reference commits:
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17647}{http://article.gmane.org/gmane.science.nmr.relax.scm/17647}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17648}{http://article.gmane.org/gmane.science.nmr.relax.scm/17648}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17649}{http://article.gmane.org/gmane.science.nmr.relax.scm/17649}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17662}{http://article.gmane.org/gmane.science.nmr.relax.scm/17662}
-
-\href{http://article.gmane.org/gmane.science.nmr.relax.scm/17663}{http://article.gmane.org/gmane.science.nmr.relax.scm/17663}
-
-This step is normally performed first.
-This is the most important part that makes sure that the code not only works
now, but will continue working for the entire lifetime of the relax project.
-Note that if a code path is not tested, it will not considered to be a part
of relax.
-As relax is in a continuous state of evolution,
\href{http://en.wikipedia.org/wiki/Bit\_rot}{bit rot} is quite severe and the
code will likely no longer function after a year or two.
-
-The idea is that synthetic data, here for example as
Sparky\index{software!Sparky} peak lists, is created for the model and added
to the test suite directory \directory{test\_suite/shared\_data/dispersion/}.
This is then used in a system test to check that the code in relax can
reproduce the data. It is very important that the code added to the relax
library is not used to create the synthetic data!
-
-
-\subsection{Comparing to other software}
-\label{sect: dispersion software comparison}
-
-It can happen that a bug present in the \module{lib.dispersion} package code
is also replicated in the synthetic data. This is not uncommon. Therefore it
is very useful to use other software with the test data from
subsection~\ref{sect: test suite for dispersion} to see if the original
parameters can be found. A good example can be seen in the
test\_suite/shared\_data/dispersion/Hansen which contains Dr. Flemming
Hansen's CPMG data (see the \file{README} file) and the results from
different programs including NESSY\index{software!NESSY}, relax,
CPMGFit\index{software!CPMGFit}, and ShereKhan\index{software!ShereKhan}.
The comparison is in the file \file{software\_comparison}.
-
-Once the relax code is able to find identical or better results than the
dispersion softwares, then the values found in the test suite optimisation
can be locked in. The assertEqual() and assertAlmostEqual() methods can be
used to only allow the test to pass when the correct values are found.
-
-
-\subsection{Debugging}
-
-This step should not require an explanation. It goes hand-in-hand with the
steps of subsections~\ref{sect: test suite for dispersion} and~\ref{sect:
dispersion software comparison}.
+As the field of NMR relaxation dispersion has a very long history, it is not
possible to include all analytic and numeric relaxation dispersion models for
both CPMG-type\index{relaxation dispersion!CPMG-type experiment} or
$\Ronerho$-type\index{relaxation dispersion!$\Ronerho$-type experiment}
experiments in relax. However it is not too difficult to add new models for
your own needs if you have some Python, Matlab, Mathematica, or similar
scripting skills. The steps required are detailed on the
\href{http://wiki.nmr-relax.com/}{relax wiki} page for the
\href{http://wiki.nmr-relax.com/Tutorial\_for\_adding\_relaxation\_dispersion\_models\_to\_relax}{tutorial
for adding relaxation dispersion models to relax}.
r20772 - /branches/relax_disp/docs/latex/dispersion.tex