diff --git a/BD/BD.tex b/BD/BD.tex index c4059a4..d80a696 100644 --- a/BD/BD.tex +++ b/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 diff --git a/DDF/basic_objects.tex b/DDF/basic_objects.tex index 371004e..def3a02 100644 --- a/DDF/basic_objects.tex +++ b/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}. diff --git a/DDF/desipatt.tex b/DDF/desipatt.tex index b2c9c07..20e1769 100644 --- a/DDF/desipatt.tex +++ b/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. diff --git a/DDF/functions.tex b/DDF/functions.tex index 998f2dc..627b879 100644 --- a/DDF/functions.tex +++ b/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 diff --git a/DJF/general.tex b/DJF/general.tex index 5a1f5fe..288ed90 100644 --- a/DJF/general.tex +++ b/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, diff --git a/MGT/MGT_intro.tex b/MGT/MGT_intro.tex index d628547..968e0c6 100644 --- a/MGT/MGT_intro.tex +++ b/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 diff --git a/MGT/charter.tex b/MGT/charter.tex index 96a9a87..0facb44 100644 --- a/MGT/charter.tex +++ b/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}. diff --git a/MGT/dudson.tex b/MGT/dudson.tex index 4e8f024..ee1900d 100644 --- a/MGT/dudson.tex +++ b/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 diff --git a/OP/DevMan.tex b/OP/DevMan.tex index 56c206a..022253e 100644 --- a/OP/DevMan.tex +++ b/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. diff --git a/OP/UMan.tex b/OP/UMan.tex index 6b9b22c..903726f 100644 --- a/OP/UMan.tex +++ b/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 diff --git a/OP/objdisc.tex b/OP/objdisc.tex index 3dc0c4a..abbf6f0 100644 --- a/OP/objdisc.tex +++ b/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}} diff --git a/OP/opmgt.tex b/OP/opmgt.tex index af0913a..ba25376 100644 --- a/OP/opmgt.tex +++ b/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} diff --git a/PN/PN.tex b/PN/PN.tex index f287294..887729a 100644 --- a/PN/PN.tex +++ b/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} diff --git a/RB/edgeprop.tex b/RB/edgeprop.tex index 2b32ed3..63e3d0d 100644 --- a/RB/edgeprop.tex +++ b/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 diff --git a/README.md b/README.md index f3ad723..f2df4ad 100644 --- a/README.md +++ b/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) diff --git a/REF/acro.tex b/REF/acro.tex index 57f7a30..dd94840 100644 --- a/REF/acro.tex +++ b/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 \\ diff --git a/REF/symb.tex b/REF/symb.tex index 22112f8..93102b6 100644 --- a/REF/symb.tex +++ b/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 & $J m^{-2} s^{-1}$ \\ diff --git a/TS/mgt.tex b/TS/mgt.tex index 0c1e06f..e177516 100644 --- a/TS/mgt.tex +++ b/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), diff --git a/TS/naming.tex b/TS/naming.tex index 91310ab..058e649 100644 --- a/TS/naming.tex +++ b/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' diff --git a/TS/nonfunc.tex b/TS/nonfunc.tex index 3d7e0d6..550e3ef 100644 --- a/TS/nonfunc.tex +++ b/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 diff --git a/TS/overall_capabilities.tex b/TS/overall_capabilities.tex index 97bfeb0..e13e92d 100644 --- a/TS/overall_capabilities.tex +++ b/TS/overall_capabilities.tex @@ -161,7 +161,7 @@ \subsubsection{Version control and user support.} software practices. Project \nep \ also have involvement from UKAEA RSEs. -User support will be provided through issue trackers, a project Slack channel, +User support will be provided through issue trackers, a project Slack or Zulip channel, and where relevant, through training sessions. Project \nep \ anticipates supporting several classes of user, from those with limited software knowledge, diff --git a/TS/physics_model.tex b/TS/physics_model.tex index 2857734..0967617 100644 --- a/TS/physics_model.tex +++ b/TS/physics_model.tex @@ -23,7 +23,7 @@ \subsubsection{General requirements} ``Photon opacity effects need to be included in the model.'' \end{quote} -The treatment of effects due to radiation are discussed in Annex~A of ref~\cite{pappeqs2} +The treatment of effects due to radiation are discussed in Annex~A of~\cite{pappeqs2} (``the equations document"). Initial implementation will account only for usage~(1) \emph{the calculation of source/loss terms}, with usage~(2) \emph{the production of synthetic spectra}, depending very much on input from experimentalists, @@ -105,7 +105,7 @@ \subsubsection{High fidelity simulations} The favourable properties of this approach are valuable, but as with any novel approach there is an inherent risk of the scheme not -working. Thus as described in ref~\cite[\S\,1.1]{pappeqs2}, in the event that +working. Thus as described in~\cite[\S\,1.1]{pappeqs2}, in the event that this approach is not feasible, the kinetic calculations will use a Particle-in-Cell (PIC) approach. While full orbit PIC is potentially extremely expensive relative to gyrokinetics, diff --git a/approboxw.tex b/approboxw.tex index 88533b4..02082a5 100644 --- a/approboxw.tex +++ b/approboxw.tex @@ -25,18 +25,19 @@ \hline Prepared By: & \culhamauthor & N/A & \culhamdate \\ & \culhamauthora & N/A & \culhamdate \\ +& \culhamauthord & N/A & \culhamdate \\ & \culhamauthorb & N/A & \culhamdate \\ & \culhamauthorc & N/A & \culhamdate \\ & & & \\ -& BD & & \\ +& CD & & \\ \hline -Reviewed By: & \culhamcontactname & \includegraphics[width=3.0cm]{./corpics/blanksign.png}& \culhamdatea \\ +Reviewed By: & \culhamauthor & \includegraphics[width=3.0cm]{./corpics/blanksign.png}& \culhamdatea \\ & & & \\ -& Advanced Computing Dept. Manager & & \\ +& Technical Lead & & \\ \hline -Approved By: & \culhamcontactname & \includegraphics[width=3.0cm]{./corpics/blanksign.png} & \culhamdateb \\ +Approved By: & \culhamauthor & \includegraphics[width=3.0cm]{./corpics/blanksign.png} & \culhamdateb \\ & & & \\ -& Advanced Computing Dept. Manager & &\\ +& Technical Lead & &\\ \hline \hline \end{tabular} diff --git a/bib/exc.bib b/bib/exc.bib index 81e0b08..0f4fe9a 100644 --- a/bib/exc.bib +++ b/bib/exc.bib @@ -1,4 +1,4 @@ -@misc{neptunesearchebsite, +@misc{neptunesearchwebsite, title={{ExCALIBUR-NEPTUNE Reports in Searchable Repo}}, HOWPUBLISHED={\url{https://excalibur-neptune.github.io/Documents}}, year={2023}, diff --git a/main.tex b/main.tex index e4a2a2c..3033632 100644 --- a/main.tex +++ b/main.tex @@ -97,7 +97,7 @@ % ensure sans-serif font used throughout \renewcommand{\familydefault}{\sfdefault} -\newcommand{\culhamissueno}{1.00}%<==edit +\newcommand{\culhamissueno}{1.02}%<==edit \newcommand{\culhamshorttitle}{CD/EXCALIBUR-FMS/0054}%<==edit \newcommand{\Sec}[1]{Section~\hyperref[sec:#1]{\ref*{sec:#1}}} \newcommand{\Fig}[1]{Figure~\hyperref[fig:#1]{\ref*{fig:#1}}} @@ -149,10 +149,11 @@ \newcommand{\culhamauthora}{Ed Threlfall}%<==edit \newcommand{\culhamauthorb}{Joseph Parker}%<==edit \newcommand{\culhamauthorc}{Will Saunders}%<==edit +\newcommand{\culhamauthord}{Matthew Barton}%<==edit -\newcommand{\culhamdate}{2023 January 16}%<=edit -\newcommand{\culhamdatea}{2023 January 16}%<=edit -\newcommand{\culhamdateb}{2023 January 16}%<=edit +\newcommand{\culhamdate}{2024 February 19}%<=edit +\newcommand{\culhamdatea}{2024 February 19}%<=edit +\newcommand{\culhamdateb}{2024 February 19}%<=edit %\renewcommand{\cite}[1]{} diff --git a/proxyapps/nektar-1d-sol.tex b/proxyapps/nektar-1d-sol.tex index c888688..5a3daf2 100644 --- a/proxyapps/nektar-1d-sol.tex +++ b/proxyapps/nektar-1d-sol.tex @@ -1,7 +1,7 @@ \newsection{Nektar-1D-SOL}{sec:Nektar1DSOl} The Nektar-1D-SOL proxyapp models plasma transport in the scrape-off layer (SOL). -The SOL is treated as a 1D flux tube, with mass being added continously near the centre of the domain and flowing out to a divertor at either end. +The SOL is treated as a 1D flux tube, with mass being added continuously near the centre of the domain and flowing out to a divertor at either end. Neutral species are ignored and the plasma is assumed to have an ideal-gas equation of state. The proxyapp was built using Nektar's solver framework and is based on existing solver types that were designed for unsteady advection problems. @@ -23,7 +23,7 @@ \end{align} The relative weight of time-dependent terms, $U_r$, is set to unity and the diffusivity coefficient, $\kappa_d$, to zero, yielding a system that closely resembles the compressible Euler equations. Source terms and boundary conditions are then chosen so as to simulate mass deposition at the domain centre due to cross-field-line transport, and sonic outflow at each end (see \cite{y3re222} for a detailed description). -The domain is discretised using the Discontinous Galerkin method and time integration is performed using a 4$^{\rm th}$ order Runge-Kutta scheme. +The domain is discretised using the Discontinuous Galerkin method and time integration is performed using a 4$^{\rm th}$ order Runge-Kutta scheme. Running the proxyapp produces a number of output files containing the values of the $n$, $nu$, and $E$ fields for each fluid element, which can be postprocessed using Nektar's `FieldConvert` tool to produce equilibrium profiles for $n$, $u$, and $T$. These profiles closely match the analytical solutions derived in \cite{detach-rp2} and the results obtained using the \textsc{soldrake} code.