relax SVN archive

Fix of bug where self.relax.data.select_sim was treated as a list

See bug #5977 and followup discussion on the relax_devel list:
https://gna.org/bugs/?func=detailitem&item_id=5977
https://mail.gna.org/public/relax-devel/2006-05/msg00007.html

A number of improvements to the manual.

The relaxation curve-fitting chapter now has a mini-title to improve the header.

The file 'relax.bst' has been added. This is a bibliography style file which has been modified from
the `apalike' file. This significantly improves the bibliography layout.

The 'Values, gradients, and Hessians' chapter has been expanded. A section describing the four
parameter combinations has been added. Another section describing the construction of the value,
gradient, and Hessian has been added as well. This section contains the Hessian kite diagram and
the gradient construction diagram. A number of other fixes have been made to the chapter.

The bibtex bibliography file has been significantly expanded for future referencing.

Added a forth round of LaTeX compilation to improve the referencing.

Proposed fix of Monte Carlo setup bugs for 'diff' type simulations

Proposed fix of bug #5977 at
https://gna.org/bugs/index.php?func=detailitem&item_id=5977

Editing of the 'Values, gradients, and Hessians' chapter of the manual.

Modifications to the notation used in the generic model-free equations, gradients, and Hessians.

The geometric parameters {Diso, Da, Dr} of the ellipsoid, {Diso, Da} of the spheroid, and {Diso} of
the sphere have been changed from the Dj and Dk notation to the new set theory notation Gj and Gk.
This is because the geometric parameter set is denoted by the symbol G in Gothic font.

The summation notation has also been changed. Instead of the summation index i ranging from m to n
it now ranges from -k to k.

A number of large additions to the relax manual.

In the development chapter a section called the 'The core design of relax' has been added. This
section has a diagram of the internal design of relax and text describing all the parts.

The 'Values, gradients, and Hessians' chapter has been completed. All the first and second partial
derivatives of the weights and correlation times of the ellipsoid, spheroid, and sphere have been
added (as well as the original equations). The equations, gradients, and Hessians of the dot
products used in the weights of the ellipsoid and spheroid have been added. Importantly, the
model-free equations and the first and second partial derivatives which create the gradients and
Hessians have been added. These equations include the derivatives of the original model-free
formula of Lipari and Szabo (1982a,b) with the parameters {S2, te}, the derivatives of the extended
model-free formula of Clore (1990) with the parameters {S2, S2f, tf, ts}, and the derivatives of an
alternative set of extended parameters {S2f, S2s, tf, ts}.

Modified the Sconstruct manual cleaning target to remove the 'relax.out' file.

Split the Sparky and XEasy peak intensity reading functions to allow the easy addition of new types.

Added the model m0 to the sample scripts.

Editing of all chapters of the manual and a few large changes.

The data analysis chapter has been split into four. The new chapters include the NOE chapter, the
relaxation curve-fitting chapter, the model-free chapter, and the reduced spectral density mapping
chapter.

The start of the 'Value, gradient, and Hessian' chapter has been moved into the new model-free
chapter under the section 'Theory'. The material moved includes the chi-squared equation, the
relaxation equations, the transformed relaxation equations, the model-free spectral density
functions, and the Brownian rotational diffusion equations.

Many more places in the text have been indexed.

The text of all chapters has been proofed.