Author: bugman
Date: Mon Oct 12 11:41:27 2015
New Revision: 28027
URL: http://svn.gna.org/viewcvs/relax?rev=28027&view=rev
Log:
Ported r28025 from trunk to allow the HTML manual to be compiled.
The command used was:
svn merge -r28025:28026 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk/ .
.....
r28026 | bugman | 2015-10-12 11:39:20 +0200 (Mon, 12 Oct 2015) | 7 lines
Changed paths:
M /trunk/docs/latex/frame_order/models.tex
M /trunk/docs/latex/frame_order/pcs_numerical_integration.tex
M /trunk/docs/latex/relax.tex
Removed the newparagraph and newsubparagraph definitions from the LaTeX
manual.
These were causing conflicts with latex2html, preventing the HTML version
of the manual at
http://www.nmr-relax.com/manual/index.html from being compiled. These
definitions are unnecessary
for the current set up of the sectioning in the manual.
.....
Modified:
tags/4.0.0/docs/latex/frame_order/models.tex
tags/4.0.0/docs/latex/frame_order/pcs_numerical_integration.tex
tags/4.0.0/docs/latex/relax.tex
Modified: tags/4.0.0/docs/latex/frame_order/models.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.0/docs/latex/frame_order/models.tex?rev=28027&r1=28026&r2=28027&view=diff
==============================================================================
--- tags/4.0.0/docs/latex/frame_order/models.tex (original)
+++ tags/4.0.0/docs/latex/frame_order/models.tex Mon Oct 12 11:41:27
2015
@@ -88,7 +88,7 @@
where surface normalisation factor is 1.
-\newparagraph{Rigid \nth{1} degree frame order}
+\paragraph{Rigid \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is the identity
matrix
\begin{subequations} \label{eq: rigid 1st degree frame order matrix}
@@ -103,7 +103,7 @@
\end{subequations}
-\newparagraph{Rigid \nth{2} degree frame order}
+\paragraph{Rigid \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 is the identity
matrix
\begin{subequations} \label{eq: rigid 2nd degree frame order matrix}
@@ -254,7 +254,7 @@
\end{subequations}
-\newparagraph{Rotor \nth{1} degree frame order}
+\paragraph{Rotor \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: rotor 1st degree frame order matrix}
@@ -270,7 +270,7 @@
\end{subequations}
-\newparagraph{Rotor \nth{2} degree frame order}
+\paragraph{Rotor \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 is
\begin{subequations}
@@ -320,7 +320,7 @@
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Rotor frame
order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Rotor frame
order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: rotor 1st degree frame
order matrix} and~\ref{eq: rotor 2nd degree frame order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -413,7 +413,7 @@
\end{subequations}
-\newparagraph{Free rotor \nth{1} degree frame order}
+\paragraph{Free rotor \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: free rotor 1st degree frame order matrix}
@@ -429,7 +429,7 @@
\end{subequations}
-\newparagraph{Free rotor \nth{2} degree frame order}
+\paragraph{Free rotor \nth{2} degree frame order}
The frame order matrix in Kronecker product notation is fixed as
\begin{equation} \label{eq: free rotor 2nd degree frame order matrix}
@@ -448,7 +448,7 @@
\end{equation}
-\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor
frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Free rotor
frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: free rotor 1st degree
frame order matrix} and~\ref{eq: free rotor 2nd degree frame order matrix}
above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -596,7 +596,7 @@
\end{subequations}
-\newparagraph{Isotropic cone \nth{1} degree frame order}
+\paragraph{Isotropic cone \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: iso cone 1st degree frame order matrix}
@@ -612,7 +612,7 @@
\end{subequations}
-\newparagraph{Isotropic cone \nth{2} degree frame order}
+\paragraph{Isotropic cone \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations} \label{eq: iso cone 2nd degree frame order matrix}
@@ -642,7 +642,7 @@
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Isotropic
cone frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Isotropic cone
frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: iso cone 1st degree frame
order matrix} and~\ref{eq: iso cone 2nd degree frame order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -736,7 +736,7 @@
\end{subequations}
-\newparagraph{Torsionless isotropic cone \nth{1} degree frame order}
+\paragraph{Torsionless isotropic cone \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: iso cone, torsionless 1st degree frame order
matrix}
@@ -752,7 +752,7 @@
\end{subequations}
-\newparagraph{Torsionless isotropic cone \nth{2} degree frame order}
+\paragraph{Torsionless isotropic cone \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations}
@@ -808,7 +808,7 @@
\end{align}
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Torsionless
isotropic cone frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Torsionless
isotropic cone frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: iso cone, torsionless 1st
degree frame order matrix} and~\ref{eq: iso cone, torsionless 2nd degree
frame order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -902,7 +902,7 @@
\end{subequations}
-\newparagraph{Free rotor isotropic cone \nth{1} degree frame order}
+\paragraph{Free rotor isotropic cone \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: iso cone, free rotor 1st degree frame order
matrix}
@@ -918,7 +918,7 @@
\end{subequations}
-\newparagraph{Free rotor isotropic cone \nth{2} degree frame order}
+\paragraph{Free rotor isotropic cone \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
@@ -949,7 +949,7 @@
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor
isotropic cone frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Free rotor
isotropic cone frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: iso cone, free rotor 1st
degree frame order matrix} and~\ref{eq: iso cone, free rotor 2nd degree frame
order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -1237,7 +1237,7 @@
\end{align}
\end{subequations}
-\newparagraph{Pseudo-ellipse \nth{1} degree frame order}
+\paragraph{Pseudo-ellipse \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 consists of the
following elements
\begin{subequations} \label{eq: pseudo-ellipse 1st degree frame order matrix}
@@ -1264,7 +1264,7 @@
As the trigonometric functions of $\conethetamax$ cannot be integrated,
these components must be numerically integrated.
-\newparagraph{Pseudo-ellipse \nth{2} degree frame order}
+\paragraph{Pseudo-ellipse \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations} \label{eq: pseudo-ellipse 2nd degree frame order matrix}
@@ -1442,7 +1442,7 @@
All other frame order matrix elements can be numerically shown to be zero.
-\newsubparagraph[Frame order matrix simulation and
calculation]{Pseudo-ellipse frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Pseudo-ellipse
frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: pseudo-ellipse 1st degree
frame order matrix} and~\ref{eq: pseudo-ellipse 2nd degree frame order
matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -1588,7 +1588,7 @@
\end{subequations}
-\newparagraph{Torsionless pseudo-ellipse \nth{1} degree frame order}
+\paragraph{Torsionless pseudo-ellipse \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 consists of the
following elements
\begin{subequations} \label{eq: pseudo-ellipse, torsionless 1st degree frame
order matrix}
@@ -1615,7 +1615,7 @@
As the trigonometric functions of $\conethetamax$ cannot be symbolically
integrated, these components must be numerically integrated.
-\newparagraph{Torsionless pseudo-ellipse \nth{2} degree frame order}
+\paragraph{Torsionless pseudo-ellipse \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations} \label{eq: pseudo-ellipse, torsionless 2nd degree frame
order matrix}
@@ -1742,7 +1742,7 @@
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Torsionless
pseudo-ellipse frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Torsionless
pseudo-ellipse frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: pseudo-ellipse,
torsionless 1st degree frame order matrix} and~\ref{eq: pseudo-ellipse,
torsionless 2nd degree frame order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -1878,7 +1878,7 @@
\end{subequations}
-\newparagraph{Free rotor pseudo-ellipse \nth{1} degree frame order}
+\paragraph{Free rotor pseudo-ellipse \nth{1} degree frame order}
The \nth{1} degree frame order matrix with tensor rank-2 is
\begin{subequations} \label{eq: pseudo-ellipse, free rotor 1st degree frame
order matrix}
@@ -1897,7 +1897,7 @@
\end{subequations}
-\newparagraph{Free rotor pseudo-ellipse \nth{2} degree frame order}
+\paragraph{Free rotor pseudo-ellipse \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations} \label{eq: pseudo-ellipse, free rotor 2nd degree frame
order matrix}
@@ -2001,7 +2001,7 @@
\end{subequations}
-\newsubparagraph[Frame order matrix simulation and calculation]{Free rotor
pseudo-ellipse frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Free rotor
pseudo-ellipse frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: pseudo-ellipse, free
rotor 1st degree frame order matrix} and~\ref{eq: pseudo-ellipse, free rotor
2nd degree frame order matrix} above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
@@ -2180,7 +2180,7 @@
\end{subequations}
-\newparagraph{Double rotor \nth{1} degree frame order}
+\paragraph{Double rotor \nth{1} degree frame order}
The un-normalised \nth{1} degress frame order matrix with tensor rank-2 is
\begin{subequations}
@@ -2206,7 +2206,7 @@
\end{pmatrix}.
\end{equation}
-\newparagraph{Double rotor \nth{2} degree frame order}
+\paragraph{Double rotor \nth{2} degree frame order}
The \nth{2} degree frame order matrix with tensor rank-4 consists of the
following elements, using Kronecker product double indices from 0 to 8
\begin{subequations} \label{eq: double rotor 2nd degree frame order matrix}
@@ -2237,7 +2237,7 @@
-\newsubparagraph[Frame order matrix simulation and calculation]{Double rotor
frame order matrix simulation and calculation}
+\subparagraph[Frame order matrix simulation and calculation]{Double rotor
frame order matrix simulation and calculation}
The frame order matrix element simulation script from Section~\ref{sect:
frame order simulation}, page~\pageref{sect: frame order simulation} was used
to compare the implementation of equations~\ref{eq: double rotor 1st degree
frame order matrix} and~\ref{eq: double rotor 2nd degree frame order matrix}
above.
Frame order matrix $\FOone$ and $\FOtwo$ values were both simulated and
calculated, both within and out of the motional eigenframe.
Modified: tags/4.0.0/docs/latex/frame_order/pcs_numerical_integration.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.0/docs/latex/frame_order/pcs_numerical_integration.tex?rev=28027&r1=28026&r2=28027&view=diff
==============================================================================
--- tags/4.0.0/docs/latex/frame_order/pcs_numerical_integration.tex
(original)
+++ tags/4.0.0/docs/latex/frame_order/pcs_numerical_integration.tex Mon
Oct 12 11:41:27 2015
@@ -138,7 +138,7 @@
The modelling of the $\sigma$ torsion angle gives a number of categories of
related models, those with no torsion, those with restricted torsion, and the
free rotors.
-\newparagraph{No torsion}
+\paragraph{No torsion}
When $\sigma = 0$, the following models are defined:
\begin{itemize}
@@ -148,7 +148,7 @@
\end{itemize}
-\newparagraph{Restricted torsion}
+\paragraph{Restricted torsion}
When $0 < \sigma < \pi$, the following models are defined:
\begin{itemize}
@@ -158,7 +158,7 @@
\end{itemize}
-\newparagraph{Free rotors}
+\paragraph{Free rotors}
When $\sigma = \pi$, i.e.\ there is no torsional restriction, the following
models are defined:
\begin{itemize}
@@ -168,7 +168,7 @@
\end{itemize}
-\newparagraph{Multiple torsion angles}
+\paragraph{Multiple torsion angles}
This covers a single model -- the double rotor.
@@ -179,7 +179,7 @@
There are three major parameter categories -- the average domain position,
the eigenframe of the motion, and the amplitude of the motion.
-\newparagraph{Average domain position}
+\paragraph{Average domain position}
Let the translational parameters be
\begin{equation}
@@ -200,7 +200,7 @@
\end{subequations}
-\newparagraph{The motional eigenframe}
+\paragraph{The motional eigenframe}
This consists of either the full eigenframe or a single axis, combined with
the pivot point(s) defining the origin of the frame(s) within the PDB space.
The eigenframe parameters themselves are
@@ -221,7 +221,7 @@
\end{subequations}
-\newparagraph{The rigid body ordering}
+\paragraph{The rigid body ordering}
The parameters of order are
\begin{equation}
Modified: tags/4.0.0/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.0/docs/latex/relax.tex?rev=28027&r1=28026&r2=28027&view=diff
==============================================================================
--- tags/4.0.0/docs/latex/relax.tex (original)
+++ tags/4.0.0/docs/latex/relax.tex Mon Oct 12 11:41:27 2015
@@ -28,18 +28,6 @@
% Better Table of contents (Toc), List of figures (Lof), and List of tables
(Lot).
\usepackage{tocloft}
-
-% Paragraph section formatting.
-\newcommand{\newparagraph}[2][]{
- \ifthenelse { \equal {#1} {} }
- { \paragraph{#2}\mbox{} \\}
- { \paragraph[#1]{#2}\mbox{} \\ }
-}
-\newcommand{\newsubparagraph}[2][]{
- \ifthenelse { \equal {#1} {} }
- { \subparagraph{#2}\mbox{} \\}
- { \subparagraph[#1]{#2}\mbox{} \\ }
-}
% Hyperlinks.
\usepackage[pdftitle={The relax manual}]{hyperref}
r28027 - in /tags/4.0.0/docs/latex: frame_order/models.tex frame_order/pcs_numerical_integration.tex relax.tex