Author: bugman
Date: Wed Jun 12 11:58:44 2013
New Revision: 20073
URL: http://svn.gna.org/viewcvs/relax?rev=20073&view=rev
Log:
Editing of the tutorial for adding dispersion models in the relax manual.
Modified:
branches/relax_disp/docs/latex/relax_disp.tex
Modified: branches/relax_disp/docs/latex/relax_disp.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax_disp.tex?rev=20073&r1=20072&r2=20073&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax_disp.tex (original)
+++ branches/relax_disp/docs/latex/relax_disp.tex Wed Jun 12 11:58:44 2013
@@ -61,23 +61,23 @@
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
specific\_analyses.relax\_disp.variables module. The model name is stored in
a special variable which will be used throughout relax.
+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 relax\_disp.select\_model user function front end}
+\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 relax\_disp.select\_model user
function front end. When the relaxation dispersion chapter of the relax
manual is created (this will be the docs/latex/relax\_disp.tex file), then
the same description should be added there as well.
+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
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.
+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 lib.dispersion to get an idea of
the design used.
+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:
@@ -100,7 +100,7 @@
\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.
+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.
@@ -112,11 +112,11 @@
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 relax\_disp.select\_model back end}
+\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 relax\_disp.select\_model user function for the
model can be added. This involved identifying the model and constructing the
parameter list.
+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}
@@ -134,19 +134,19 @@
\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 as step number 1. 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.
+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.
-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 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!
+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 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 step 7 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 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 `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}.
+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}.
r20073 - /branches/relax_disp/docs/latex/relax_disp.tex