minor updates and spelling corrections

BD/BD.tex

@@ -26,7 +26,7 @@
 \item  {\bf STRATEGIC FIT} % - to UKAEA mission
 
 {\bf National}: The \exc \ project is of national importance to UK government
-(represented by the BEIS dept.)  to demonstrate
+(represented initially by the BEIS and subsequently the DESNZ dept.)  to demonstrate
 how to produce software that can exploit all the latest, most powerful hardware
 for scientific computation.  The Fusion Modelling System~(FMS) is one
 of \exc 's principal use cases, for which project \nep \ will explore efficient development of

DDF/basic_objects.tex

@@ -1,6 +1,6 @@
 \textbf{Notes} Procedures denoted in boldface, as separate sections.\\
 \emph{n-D} does not include time\\
-Refs \cite{sciplan} in exc.bib
+\cite{sciplan} in exc.bib
 
 \subsection{Base classes}\label{sec:base-classes}
 The proposed base classes for \nep\ are listed below and shown graphically in \Fig{baseclasses}.

DDF/desipatt.tex

@@ -1,5 +1,5 @@
 The design patterns likely to be most relevant to \nep \ are described
-in refs~\cite{y2re332,y2re333}.
+in~\cite{y2re332,y2re333}.
 
 The PUPPETEER pattern appears to be
 exclusive to the works of Rouson~et~al, hence is described further here.

DDF/functions.tex

@@ -55,7 +55,7 @@ \subsection{Solution}\label{sec:solution}
 \item
   Outer loop over time
 \item
-  Inner loop over solvera
+  Inner loop over solver
 
   \begin{itemize}
   \item
@@ -95,7 +95,7 @@ \subsection{Solution}\label{sec:solution}
   \item
     Gyro-averaging
   \item
-    Sparse models for Data Assimilation (SINDy)
+    Sparse models for Data Assimilation (via SINDy)
   \item
     Gaussian Process
   \item

DJF/general.tex

@@ -4,7 +4,7 @@
 special coding at boundaries, the educational material for finite difference
 modellers explains why this approach is unsatisfactory, and the same objection
 also applies to AMR type meshes, although in view of the unexpected success of AMR
-in fluid and PIC codes, it was carefully discussed as detailed in ref~\cite{y1re211}. The
+in fluid and PIC codes, it was carefully discussed as detailed in~\cite{y1re211}. The
 most serious objection appeared to be the need to represent plasma diffusion
 which is strongly anisotropic due to an applied magnetic field. (Moreover,
 if hanging nodes are allowed in the FEM, then AMR behaviour may be reproduced by FEM codes,

MGT/MGT_intro.tex

@@ -4,7 +4,7 @@
 presents guidance concerning the mechanics of an opensource development
 by a community distributed  across different sites and organisations,
 intended to produce software intended for widespread long-term usage.
-Parts of ref~\cite{y3re314} relate more to 
+Parts of~\cite{y3re314} relate more to 
 the technical specification~(TS) and are reproduced in \Sec{TS_sw_response},
 another part concerns operational aspects~(OP), see \Sec{OP_MGT}.
 Its recommendations are broadly consistent with those laid out by Bungarth \&
@@ -14,9 +14,9 @@
 and does not cover code coupling, both of which topics are discussed in the open literature,
 see in particular Lawrence~et~al~\cite{La18Cros} for HPC software engineering and
 Belete~et~al~\cite{Be17over} for code coupling,
-also see other \nep \ reports, particularly refs~\cite{y2re312,y2re333,y3re72}.
+also see other \nep \ reports, particularly~\cite{y2re312,y2re333,y3re72}.
 
-Ref~\cite{y3re314} assumes that all the community has signed up to a ``Charter"
+\cite{y3re314} assumes that all the community has signed up to a ``Charter"
 which for \nep \ appeared as report~\cite{charter}, reproduced in \Sec{charter}.
 The guidance\cite{y3re314}  includes  important issues that need to be agreed as early as possible.
 %drawing on the ``Development Plan" document~\cite{y2d34} and on
@@ -33,7 +33,7 @@
 %This note relates most closely to the third case.
 The guidance document\cite{y3re314} also seeks not merely to prescribe, but to
 give compelling arguments for the choices made in respect of guidelines.
-Acknowledging the possibility of diagreements, it states that efforts will be made to ensure
+Acknowledging the possibility of disagreements, it states that efforts will be made to ensure
 consensus or at least agreement between the two most affected project partners
 on any decisions taken. However, in the event of continuing disagreement, the technical
 leader or `Lead' for the project will ultimately decide on the basis of technical

MGT/charter.tex

@@ -76,4 +76,4 @@
 3-clause BSD for core/foundational infrastructure~\cite{bsd3clause}). Government 
 Digital Service guidance (to which the project subscribes), discussing 
 the benefits of open versus closed technology/software/data can be found 
-in refs~\cite{os,os2}.
+in~\cite{os,os2}.

MGT/dudson.tex

@@ -31,7 +31,7 @@ \subsection{Meetings and Workshops} \label{sec:meet}
 \item Documentation infrastructure, ie.\ as a website
 \item A repository for long-term storage of large files, records of
 meetings, presentations etc. (eg.\ Google shared drive)
-\item A chat/messaging service such as Slack, to facilitate interactions
+\item A chat/messaging service such as Slack or Zulip, to facilitate interactions
 between developers
 \end{enumerate}
 As these are established, a series of training workshops should be
@@ -152,7 +152,7 @@ \subsection{Development workflow} \label{sec:develop}
 through a pull request mechanism which ensures peer review and testing. Bug fixes
 and feature development are done in separate branches, either in the same
 repository, or in forked repositories. When someone encounters a bug, or wishes to
-develop a new feature, the recommended approach ise:
+develop a new feature, the recommended approach is:
 
 \begin{enumerate}
 \item An issue is opened, describing the bug or feature request or proposal. This

OP/DevMan.tex

@@ -11,7 +11,7 @@
 
 Separate the subject from body with a blank line and limit the subject line to 50 characterss
 
-Importance of Slack
+Importance of Slack or Zulip
 
 producing FMS reports collaboratively using git and mostly LaTeX some markdown,
 markdown is not a standard, except very minimally, so I would demand compatibility with pandoc.

OP/UMan.tex

@@ -5,7 +5,7 @@
 recipient can immediately execute in a browser
 \newsectionnobreak{Feedback and Communication}{sec:feedback}
 \begin{itemize}
-\item Matrix chat - Slack?
+\item Matrix chat - Slack or Zulip?
 \item Discourse group
 \item Mailing list
 \item Suggestion box

OP/objdisc.tex

@@ -1,6 +1,6 @@
 \begin{table}[h]
 \begin{center}
-\caption{Key Strategies for Object Identification. After Table~5.1 from ref~\cite{douglass},
+\caption{Key Strategies for Object Identification. After Table~5.1 from~\cite{douglass},
 slightly amended.
 All the strategies except the last, are concerned with identifying the objects listed.
 \label{tab:objdisc}}

OP/opmgt.tex

@@ -19,7 +19,7 @@ \subsection{Documentation} \label{sec:doc}
 include elements such as equations, code blocks, graphs and figures.
 It should also be easily convertible to other formats, and in
 particular online documentation. \LaTeX \ as used to produce the current document
-can be easily converted to .html as explained in ref~\cite{y2d34} provided
+can be easily converted to .html as explained in~\cite{y2d34} provided
 the restrictions (as to accepted packages) noted in the reference are observed.
 \end{itemize}
 

PN/PN.tex

@@ -34,7 +34,8 @@ \subsection{Benefits of community membership}
 In addition members will also gain
 \begin{itemize}
 \item Access to reports as the community produces them, in the access-controlled github site~\cite{xpndocswebsite},
-subdirectories {\tt reports} and {\tt reports/ukaea\_reports}.
+subdirectories {\tt reports} and {\tt reports/ukaea\_reports}. (\cite{neptunesearchwebsite} is  a searchable public github site
+containing most of the material.)
 These directories already include educational material on
 \begin{itemize}
 \item Finite elements
@@ -43,16 +44,17 @@ \subsection{Benefits of community membership}
 \item Uncertainty Quantification
 \item Aspects of software engineering, such as design patterns
 \end{itemize}
-\item Rights to attend workshops and shape the \nep\ software, announced in the Slack channel.
+\item Rights to attend workshops and shape the \nep\ software, announced in the Slack or Zulip channel.
 \item Right to attend project lectures on work performed by the community, and on
-relevant background material such as the spectral/hp element method, announced in the Slack channel.
+relevant background material such as the spectral/hp element method, announced in the Slack or Zulip channel.
 \item The {\tt tex} subdirectory~\cite{xpntexwebsite} contains bibtex databases to aid report writing in subdirectory {\tt bib} and graphics suitable for producing presentations
 in subdirectories {\tt pics} and {\tt png}.
 \end{itemize}
 The Slack channel is `\#excalibur-neptune'. (The Slack communication
 software is downloadable from \url{https://slack.com/}).
+It is anticipated that Slack will ultimately replaced by an Opensource option such as Zulip.
 
-(Note that access to most \nep \ reports is restricted to community members.)
+(Note that access to some \nep \ reports is restricted to community members.)
 
 \subsection{Convention on use of IETF Keywords (not yet enforced)}
 The RFC2119 subset of the Internet Engineering Task Force~(IETF) keywords~\cite{rfc2119}

RB/edgeprop.tex

@@ -12,7 +12,7 @@
 Unless stated otherwise, the derived length, timescales and speeds are derived from
 formulae and graphs in Wesson's book~\cite[Chap 10]{wesson}.
 The derived quantities have been checked against SI formulae
-in ref~\cite[Table 2.2]{miyamoto}, and also compared with those
+in~\cite[Table 2.2]{miyamoto}, and also compared with those
 listed in~\cite[Appendix]{Xu10Inte}. It is worth noting that although
 the latter table describes the SOL of JET (and in addition its separatrix and pedestal),
 JET values are typically within a factor of~$2$ of those for MAST, hence similar
@@ -77,8 +77,8 @@ \subsection{Applicability of Fluid Models}\label{sec:applmhd}
 although MHD treats a faster timescale, it is valid on longer timescales, provided
 relevant smaller/slower terms are retained.)
 Moreover, SOL timescales involving filaments are fast, witnessed by the fact that
-the ion gyro-frequency is used as normalisation for electrostatic models in
-ref~\cite{Mi12Simu}, which from \Sec{props} is a not too dissimilar timescale~$10^{-7}\,s$
+the ion gyro-frequency is used as normalisation for electrostatic models in~\cite{Mi12Simu},
+which from \Sec{props} is a not too dissimilar timescale~$10^{-7}\,s$
 to the Alfven timescale based on the poloidal field~($1$\,cm/$10^6 \approx 10^{-8}$\,s).
 Later, Freidberg~\cite{freidberg}
 showed that, at least in directions perpendicular to~${\bf B}$, the dynamical MHD equation
@@ -99,8 +99,8 @@ \subsection{Applicability of Fluid Models}\label{sec:applmhd}
 
 \subsection{Effect of Neutrals}\label{sec:neuts}
 Formulae for a weakly ionised plasma are given in the Plasma Formulary~\cite{NRLpf07}.
-The collision cross-sections for electrons and ions respectively from
-ref~\cite{Ha91hydr} are $\sigma_s^{e|0}= 10^{-19}$\,$m^2$ and
+The collision cross-sections for electrons and ions respectively from~\cite{Ha91hydr}
+are $\sigma_s^{e|0}= 10^{-19}$\,$m^2$ and
 $\sigma_s^{i|0}= 4 \times 10^{-19}$\,$m^2$.
 Hence, the collision frequencies for electrons and ions respectively are
 \begin{equation}
@@ -127,7 +127,7 @@ \subsection{Effect of Neutrals}\label{sec:neuts}
 \eta_{e {\sf n}\parallel} =4 \frac{{\sf n}}{n},\;\;\;
 \eta_{i {\sf n}\parallel} =0.5 \frac{{\sf n}}{n}
 \end{equation}
-The implication from the formulae in ref~\cite{Le06emer} is that 
+The implication from the formulae in~\cite{Le06emer} is that 
 the value for $\eta_{e \parallel}$ combines additively with the usual
 Spitzer value in a more
 highly ionised plasma. Assuming ${\sf n} \approx n$, however the correction

README.md

@@ -18,6 +18,7 @@ If you want to generate just the pdf version of the website then you perform the
 ```
 bash buildwebsite-local.sh PDF
 ```
+and the PDF appears as ./public/main.pdf
 
 ##  Partial PDF and HTML generation
 If you want to generate just the HTML and PDF of some tex, and not the whole website, then you perform the following command (where proxyapps/proxyapps is replaced with the relative path to the tex file you want to convert to PDF and HTML)

REF/acro.tex

@@ -59,6 +59,7 @@
 DDD & Document-Driven Design \\
 DE & Differential equation \\
 DEIM & Discrete Empirical Interpolation Method \\
+DESNZ & Department for Energy Security and Net Zero  \\
 DFT & Discrete Fourier Transform \\
 DiMDc  & Dynamic mode decomposition with control \\
 DL  & Deep learning \\
@@ -246,7 +247,7 @@
 SDLC & Software Development Life Cycle \\
 SGD  & Stochastic gradient descent \\
 SIAM & Society for Industrial and Applied Mathematics \\
-SINDy  & Sparse identification of nonlinear dynamics \\
+SINDy  & Sparse identification of nonlinear dynamical systems \\
 SISO  & Single input, single output \\
 SLA & Service-level Agreement \\
 SLE & Software Language Extensions \\
@@ -260,6 +261,7 @@
 SOL & Scrape-Off Layer \\
 SOLEDGE & name of edge modelling code \\
 SOLPS & name of edge modelling code combines B2 and EIRENE\\
+SpH & Spatial Hybridisation \\
 SPH & Smoothed Particle Hydrodynamics \\
 SRC  & Sparse representation for classification \\
 SRO & Senior Responsible Owner role in UK  government project delivery \\

REF/symb.tex

@@ -58,7 +58,7 @@
 ${\bf v}_\textrm{diff}$ & `diffusive' perpendicular fluid velocity component  &  $m s^{-1}$ \\
 ${\bf x}=\left(x_1,x_2,\dots,x_d\right)$ & is a $d$-dimensional vector  & \\
 ${\bf x}$ & position  &  $m$ \\
-$b_n$ & `b-factors'~ref~\cite[slide 21]{omullane} & \\
+$b_n$ & `b-factors'~\cite[slide 21]{omullane} & \\
 $\boldsymbol{\xi}(\theta)$ & multi-dimensional random variable with a specific probability distribution as a function of the random parameter~$0\leq\theta\leq 1$ & \\
 $\boldsymbol{B}$ &  (K+S) Basis matrix & \\
 $\boldsymbol{D}_{\xi}$ &  (K+S) Elemental derivative matrix with respect to $\xi$ & \\
@@ -155,7 +155,7 @@
 $i$ & as suffix generic label & \\
 $I$ & as suffix labels Monte-Carlo interactions & \\
 $I_\phi$ & $\phi-$ or toroidal component of plasma current & $A$ \\
-$I_H$ & Hydrogen reionisation potential as defined in ref~\cite{Ha13Benc} & $eV$ \\
+$I_H$ & Hydrogen reionisation potential as defined in~\cite{Ha13Benc} & $eV$ \\
 $i,j,k$ &  (K+S) General summation indices & \\
 $^I\mathcal{F}_{i\sigma}$ & coefficient of ionisation for the transition from metastable state~$\sigma$ to regular excited state~$i$ & \\
 $\in$ &  (Sets) Is a member of; belongs to & \\
@@ -338,7 +338,7 @@
 $q_\alpha$ & charge on a particle of species~$\alpha$ & $C$ \\
 $q_e$ & charge on an electron, negative by convention & $C$ \\
 $Q(f_\alpha, f_\beta)$ & Boltzmann collision operator  & $m^{-6} s^2$ \\
-$Q_H$ & cooling rate due to excitation as defined in ref~\cite{Ha13Benc}  & $K m^{-3} s^{-1}$ \\
+$Q_H$ & cooling rate due to excitation as defined in~\cite{Ha13Benc}  & $K m^{-3} s^{-1}$ \\
 $q_i$ & charge on an ion  & $C$ \\
 $q_{\|e}$ & electron energy flux along fieldline & $J m^{-2} s^{-1}$ \\
 $q_{\|i}$ & ion energy flux along fieldline & $J m^{-2} s^{-1}$ \\

TS/mgt.tex

@@ -100,7 +100,7 @@ \subsection{Code style} \label{sec:style}
 recommend the following one for coders who wish to do so.
 
 For C++, based on the recommendations of the book ``Professional C++" (eg.\
-ref~\cite[\S\,7]{solterkleper}, the following prefix strings should be employed:
+\cite[\S\,7]{solterkleper}, the following prefix strings should be employed:
 `m\_' for  member (particularly useful for indicating scope),
 `p\_' for pointer, `s\_' for static, `k\_' for constant,
 `f\_' for flag (Boolean value),

TS/naming.tex

@@ -21,7 +21,7 @@ \subsubsection{Two character variables}\label{sec:two-character-variables}
 
 Each keyboard character will be represented by one or two lowercase
 letters, normally those which form the first two letters of its name,
-ommitting `o', thus :
+omitting `o', thus :
 
 \begin{itemize}
 \item `a' will represent `a'

TS/nonfunc.tex

@@ -24,8 +24,8 @@ \subsection{General Considerations}\label{sec:TS_considers}
 further into packages which might contain in turn $10$-$50$ modules. 
 As a way of providing further indication to developers,
 it is helpful to talk of packages as being arranged into layers, as discussed
-in ref~\cite[\S\S\,2.4,3.2]{y2re333}, see \Fig{hierarchygroup}.
-Then, as prefigured in ref~\cite[Annex~A]{y2re333}, it should be  possible to encapsulate
+in~\cite[\S\S\,2.4,3.2]{y2re333}, see \Fig{hierarchygroup}.
+Then, as prefigured in~\cite[Annex~A]{y2re333}, it should be  possible to encapsulate
 the necessary complexity in one, albeit large diagram.
 \begin{figure}
 \centerline{\includegraphics[width=0.7\textwidth]{./png/hierarchygroup.png}}
@@ -36,14 +36,14 @@ \subsection{General Considerations}\label{sec:TS_considers}
 
 \subsection{Considerations for Scientific Software}\label{sec:TS_scistruct}
 \subsubsection{Structural Considerations}\label{sec:TS_structure}
-In both refs~\cite{y1re331,y2re332}, a figure from Dubey~et~al~\cite{Du16Idea} is reproduced
+In both~\cite{y1re331,y2re332}, a figure from Dubey~et~al~\cite{Du16Idea} is reproduced
 that illustrates how scientific software may be developed by beginning with an ``infrastructure"
 capability into which initially exploratory scientific software is integrated as its worth
 is established. Unfortunately for \nep, it is not clear initially what  aspects  of the infrastructure
 will be durable and stable, although once the software is more mature, Dubey~et~al's methodology
 appears attractive.
 
-The literature referenced in ref~\cite{y2re333}
+The literature referenced in~\cite{y2re333}
 indicates that scientific software should be produced by aggregation, but is less
 helpful as to what is to be aggregated, ie.\  the modular decomposition as to what should
 constitute a single module etc.
@@ -73,7 +73,7 @@ \subsubsection{Interactions between Modules}\label{sec:TS_modulint}
 use of  a directed, acyclic graph~(DAG) structure might be thought mandatory,
 particularly to  process the input
 data in order to specify coherently the construction of the elements of the solution matrix.
-However, as prefigured in ref~\cite{y2re333} for the gyrokinetics code \F{GS2},
+However, as prefigured in~\cite{y2re333} for the gyrokinetics code \F{GS2},
 the tightly coupled nature of the central edge
 physics problem  means that input is more about gathering \emph{all} the data, for only at that point
 can fields be computed and only after that may matrix coefficients be computed.
@@ -103,7 +103,7 @@ \subsubsection{Notation}
 %requires only one copy of a class's attributes to be compiled, whereas only the very latest versions of C++
 %avoid recompilation of namespaces when a .cpp file is changed.
 UML nomenclature is preferred herein, for which \Tab{TS_umltrans} provides a limited 
-translation into C++ and Object Fortran. % is reproduced as Table~1 in ref~\cite{y2re332}.
+translation into C++ and Object Fortran. % is reproduced as Table~1 in~\cite{y2re332}.
 
 \begin{table}[tbph]
 \begin{center}
@@ -123,7 +123,7 @@ \subsubsection{Notation}
 \hline
 \end{tabular}
 Further insight into UML terminology may be gained from the description
-of the patterns in refs~\cite{y2re332,y2re333}.
+of the patterns in~\cite{y2re332,y2re333}.
 \end{center}
 \end{table}
 
@@ -133,7 +133,7 @@ \subsubsection{Module design}
 The focus herein is the structure within a module. Specifically, the module describes a single class or object
 (strictly speaking in UML terms, objects are instances of a class), which is
 fundamental in that it is defined without use of aggregation.
-Tthe software  - consistent with Clerman and Spector~\cite[\S\,11]{clermanspector} -
+The software  - consistent with Clerman and Spector~\cite[\S\,11]{clermanspector} -
 that is promoted by Arter et al~\cite{fprog} for an object-oriented language, recognises two sizes of fundamental class
 and it is easier to start by considering the smaller, denoted smallobj\_m.
 
@@ -219,7 +219,7 @@ \subsubsection{Module design}
 other modules. In fact a common addition to the default modules is a method function \T{getunit} that returns \T{ninbo},
 illustrating the approved way of accessing such data.
 
-%The source as mentioned in ref~\cite{y2re333} may be obtained by download of
+%The source as mentioned in~\cite{y2re333} may be obtained by download of
 %program~\I{smardda-qprog}~\cite{qprogwebsite}.
 The reason for the emphasis on input and output from and to disc (I/O)
 is to facilitate the construction of a test harness