diff --git a/GX-TimeFrequency/README.md b/GX-TimeFrequency/README.md index 8e0a78fe..f7f056c8 100644 --- a/GX-TimeFrequency/README.md +++ b/GX-TimeFrequency/README.md @@ -1,5 +1,13 @@ # GreenX Library - TimeFrequency +This library provides optimal quadrature grid points and weights for imaginary time-frequency transforms, commonly +occurring in MP2, RPA and Green's function methods. Optimisation is performed with the Minimax procedure, minimising the +maximum error of the quadrature. This typically results in an error that is more evenly distributed across the interval +of interest. Grids are provided with n-points ranging from 6 to 34, and for different values of the transition energy +ratios Rm (on average 15 R-values for each grid point). + +For additional details, please refer to the corresponding JOSS paper, included [here](../JOSS). + ## Building With CMake, change to the GreenX root, then type: @@ -14,7 +22,7 @@ make install ## Running the Tests Application tests are run with the pytest framework. Having installed `pygreenx` -(see the top-level README) change to `/` and type `ctest`. +(see the top-level [README](../README.md)) change to `/` and type `ctest`. Additionally, one can change to the test folder and explicitly run the pytest command from there: diff --git a/JOSS/README.md b/JOSS/README.md index c6b02054..051c8a97 100644 --- a/JOSS/README.md +++ b/JOSS/README.md @@ -1 +1,10 @@ -# JOSS \ No newline at end of file +# Compiling the JOSS Paper + +To build the paper with [pandoc](https://pandoc.org/installing.html) (3.0.1): + +```shell +pandoc --citeproc --bibliography=refs.bib -s paper.md -o gx_minimax.pdf --template latex.template +``` + +with a latex templated sourced from a Github [source]( https://github.com/Wandmalfarbe/pandoc-latex-template/blob/master/eisvogel.tex) +rather than the [JOSS template](https://github.com/sigsep/open-unmix-paper-joss/blob/master/latex.template). diff --git a/JOSS/latex.template b/JOSS/latex.template new file mode 100644 index 00000000..d92e8caa --- /dev/null +++ b/JOSS/latex.template @@ -0,0 +1,1088 @@ +%% +% Copyright (c) 2017 - 2023, Pascal Wagler; +% Copyright (c) 2014 - 2023, John MacFarlane +% +% All rights reserved. +% +% Redistribution and use in source and binary forms, with or without +% modification, are permitted provided that the following conditions +% are met: +% +% - Redistributions of source code must retain the above copyright +% notice, this list of conditions and the following disclaimer. +% +% - Redistributions in binary form must reproduce the above copyright +% notice, this list of conditions and the following disclaimer in the +% documentation and/or other materials provided with the distribution. +% +% - Neither the name of John MacFarlane nor the names of other +% contributors may be used to endorse or promote products derived +% from this software without specific prior written permission. +% +% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +% "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +% LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS +% FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE +% COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, +% INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +% BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +% LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +% CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +% LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN +% ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +% POSSIBILITY OF SUCH DAMAGE. +%% + +%% +% This is the Eisvogel pandoc LaTeX template. +% +% For usage information and examples visit the official GitHub page: +% https://github.com/Wandmalfarbe/pandoc-latex-template +%% + +% Options for packages loaded elsewhere +\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref} +\PassOptionsToPackage{hyphens}{url} +\PassOptionsToPackage{dvipsnames,svgnames,x11names,table}{xcolor} +$if(CJKmainfont)$ +\PassOptionsToPackage{space}{xeCJK} +$endif$ +% +\documentclass[ +$if(fontsize)$ + $fontsize$, +$endif$ +$if(papersize)$ + $papersize$paper, +$else$ + paper=a4, +$endif$ +$if(beamer)$ + ignorenonframetext, +$if(handout)$ + handout, +$endif$ +$if(aspectratio)$ + aspectratio=$aspectratio$, +$endif$ +$endif$ +$for(classoption)$ + $classoption$$sep$, +$endfor$ + ,captions=tableheading +]{$if(beamer)$$documentclass$$else$$if(book)$scrbook$else$scrartcl$endif$$endif$} +$if(beamer)$ +$if(background-image)$ +\usebackgroundtemplate{% + \includegraphics[width=\paperwidth]{$background-image$}% +} +% In beamer background-image does not work well when other images are used, so this is the workaround +\pgfdeclareimage[width=\paperwidth,height=\paperheight]{background}{$background-image$} +\usebackgroundtemplate{\pgfuseimage{background}} +$endif$ +\usepackage{pgfpages} +\setbeamertemplate{caption}[numbered] +\setbeamertemplate{caption label separator}{: } +\setbeamercolor{caption name}{fg=normal text.fg} +\beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$ +$for(beameroption)$ +\setbeameroption{$beameroption$} +$endfor$ +% Prevent slide breaks in the middle of a paragraph +\widowpenalties 1 10000 +\raggedbottom +$if(section-titles)$ +\setbeamertemplate{part page}{ + \centering + \begin{beamercolorbox}[sep=16pt,center]{part title} + \usebeamerfont{part title}\insertpart\par + \end{beamercolorbox} +} +\setbeamertemplate{section page}{ + \centering + \begin{beamercolorbox}[sep=12pt,center]{part title} + \usebeamerfont{section title}\insertsection\par + \end{beamercolorbox} +} +\setbeamertemplate{subsection page}{ + \centering + \begin{beamercolorbox}[sep=8pt,center]{part title} + \usebeamerfont{subsection title}\insertsubsection\par + \end{beamercolorbox} +} +\AtBeginPart{ + \frame{\partpage} +} +\AtBeginSection{ + \ifbibliography + \else + \frame{\sectionpage} + \fi +} +\AtBeginSubsection{ + \frame{\subsectionpage} +} +$endif$ +$endif$ +$if(beamerarticle)$ +\usepackage{beamerarticle} % needs to be loaded first +$endif$ +\usepackage{amsmath,amssymb} +$if(linestretch)$ +\usepackage{setspace} +$else$ +% Use setspace anyway because we change the default line spacing. +% The spacing is changed early to affect the titlepage and the TOC. +\usepackage{setspace} +\setstretch{1.2} +$endif$ +\usepackage{iftex} +\ifPDFTeX + \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc} + \usepackage[utf8]{inputenc} + \usepackage{textcomp} % provide euro and other symbols +\else % if luatex or xetex +$if(mathspec)$ + \ifXeTeX + \usepackage{mathspec} % this also loads fontspec + \else + \usepackage{unicode-math} % this also loads fontspec + \fi +$else$ + \usepackage{unicode-math} % this also loads fontspec +$endif$ + \defaultfontfeatures{Scale=MatchLowercase}$-- must come before Beamer theme + \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1} +\fi +$if(fontfamily)$ +$else$ +$-- Set default font before Beamer theme so the theme can override it +\usepackage{lmodern} +$endif$ +$-- Set Beamer theme before user font settings so they can override theme +$if(beamer)$ +$if(theme)$ +\usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$} +$endif$ +$if(colortheme)$ +\usecolortheme{$colortheme$} +$endif$ +$if(fonttheme)$ +\usefonttheme{$fonttheme$} +$endif$ +$if(mainfont)$ +\usefonttheme{serif} % use mainfont rather than sansfont for slide text +$endif$ +$if(innertheme)$ +\useinnertheme{$innertheme$} +$endif$ +$if(outertheme)$ +\useoutertheme{$outertheme$} +$endif$ +$endif$ +$-- User font settings (must come after default font and Beamer theme) +$if(fontfamily)$ +\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$} +$endif$ +\ifPDFTeX\else + % xetex/luatex font selection +$if(mainfont)$ + \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$} +$endif$ +$if(sansfont)$ + \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$} +$endif$ +$if(monofont)$ + \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$} +$endif$ +$for(fontfamilies)$ + \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$} +$endfor$ +$if(mathfont)$ +$if(mathspec)$ + \ifXeTeX + \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$} + \else + \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$} + \fi +$else$ + \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$} +$endif$ +$endif$ +$if(CJKmainfont)$ + \ifXeTeX + \usepackage{xeCJK} + \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$} + $if(CJKsansfont)$ + \setCJKsansfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKsansfont$} + $endif$ + $if(CJKmonofont)$ + \setCJKmonofont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmonofont$} + $endif$ + \fi +$endif$ +$if(luatexjapresetoptions)$ + \ifLuaTeX + \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset} + \fi +$endif$ +$if(CJKmainfont)$ + \ifLuaTeX + \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec} + \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$} + \fi +$endif$ +\fi +$if(zero-width-non-joiner)$ +%% Support for zero-width non-joiner characters. +\makeatletter +\def\zerowidthnonjoiner{% + % Prevent ligatures and adjust kerning, but still support hyphenating. + \texorpdfstring{% + \TextOrMath{\nobreak\discretionary{-}{}{\kern.03em}% + \ifvmode\else\nobreak\hskip\z@skip\fi}{}% + }{}% +} +\makeatother +\ifPDFTeX + \DeclareUnicodeCharacter{200C}{\zerowidthnonjoiner} +\else + \catcode`^^^^200c=\active + \protected\def ^^^^200c{\zerowidthnonjoiner} +\fi +%% End of ZWNJ support +$endif$ +% Use upquote if available, for straight quotes in verbatim environments +\IfFileExists{upquote.sty}{\usepackage{upquote}}{} +\IfFileExists{microtype.sty}{% use microtype if available + \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype} + \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts +}{} +$if(indent)$ +$else$ +\makeatletter +\@ifundefined{KOMAClassName}{% if non-KOMA class + \IfFileExists{parskip.sty}{% + \usepackage{parskip} + }{% else + \setlength{\parindent}{0pt} + \setlength{\parskip}{6pt plus 2pt minus 1pt}} +}{% if KOMA class + \KOMAoptions{parskip=half}} +\makeatother +$endif$ +$if(verbatim-in-note)$ +\usepackage{fancyvrb} +$endif$ +\usepackage{xcolor} +\definecolor{default-linkcolor}{HTML}{A50000} +\definecolor{default-filecolor}{HTML}{A50000} +\definecolor{default-citecolor}{HTML}{4077C0} +\definecolor{default-urlcolor}{HTML}{4077C0} +$if(footnotes-pretty)$ +% load footmisc in order to customize footnotes (footmisc has to be loaded before hyperref, cf. https://tex.stackexchange.com/a/169124/144087) +\usepackage[hang,flushmargin,bottom,multiple]{footmisc} +\setlength{\footnotemargin}{0.8em} % set space between footnote nr and text +\setlength{\footnotesep}{\baselineskip} % set space between multiple footnotes +\setlength{\skip\footins}{0.3cm} % set space between page content and footnote +\setlength{\footskip}{0.9cm} % set space between footnote and page bottom +$endif$ +$if(geometry)$ +$if(beamer)$ +\geometry{$for(geometry)$$geometry$$sep$,$endfor$} +$else$ +\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry} +$endif$ +$else$ +$if(beamer)$ +$else$ +\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering,$for(geometry)$$geometry$$sep$,$endfor$]{geometry} +$endif$ +$endif$ +$if(titlepage-logo)$ +\usepackage[export]{adjustbox} +\usepackage{graphicx} +$endif$ +$if(beamer)$ +\newif\ifbibliography +$endif$ +$if(listings)$ +\usepackage{listings} +\newcommand{\passthrough}[1]{#1} +\lstset{defaultdialect=[5.3]Lua} +\lstset{defaultdialect=[x86masm]Assembler} +$endif$ +$if(listings-no-page-break)$ +\usepackage{etoolbox} +\BeforeBeginEnvironment{lstlisting}{\par\noindent\begin{minipage}{\linewidth}} +\AfterEndEnvironment{lstlisting}{\end{minipage}\par\addvspace{\topskip}} +$endif$ +$if(lhs)$ +\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{} +$endif$ +$if(highlighting-macros)$ +$highlighting-macros$ + +% Workaround/bugfix from jannick0. +% See https://github.com/jgm/pandoc/issues/4302#issuecomment-360669013) +% or https://github.com/Wandmalfarbe/pandoc-latex-template/issues/2 +% +% Redefine the verbatim environment 'Highlighting' to break long lines (with +% the help of fvextra). Redefinition is necessary because it is unlikely that +% pandoc includes fvextra in the default template. +\usepackage{fvextra} +\DefineVerbatimEnvironment{Highlighting}{Verbatim}{breaklines,fontsize=$if(code-block-font-size)$$code-block-font-size$$else$\small$endif$,commandchars=\\\{\}} + +$endif$ +$if(tables)$ +\usepackage{longtable,booktabs,array} +$if(multirow)$ +\usepackage{multirow} +$endif$ +\usepackage{calc} % for calculating minipage widths +$if(beamer)$ +\usepackage{caption} +% Make caption package work with longtable +\makeatletter +\def\fnum@table{\tablename~\thetable} +\makeatother +$else$ +% Correct order of tables after \paragraph or \subparagraph +\usepackage{etoolbox} +\makeatletter +\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{} +\makeatother +% Allow footnotes in longtable head/foot +\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}} +\makesavenoteenv{longtable} +$endif$ +$endif$ +% add backlinks to footnote references, cf. https://tex.stackexchange.com/questions/302266/make-footnote-clickable-both-ways +$if(footnotes-disable-backlinks)$ +$else$ +\usepackage{footnotebackref} +$endif$ +$if(graphics)$ +\usepackage{graphicx} +\makeatletter +\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi} +\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi} +\makeatother +% Scale images if necessary, so that they will not overflow the page +% margins by default, and it is still possible to overwrite the defaults +% using explicit options in \includegraphics[width, height, ...]{} +\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio} +% Set default figure placement to htbp +\makeatletter +% Make use of float-package and set default placement for figures to H. +% The option H means 'PUT IT HERE' (as opposed to the standard h option which means 'You may put it here if you like'). +\usepackage{float} +\floatplacement{figure}{$if(float-placement-figure)$$float-placement-figure$$else$H$endif$} +\makeatother +$endif$ +$if(svg)$ +\usepackage{svg} +$endif$ +$if(strikeout)$ +$-- also used for underline +\ifLuaTeX + \usepackage{luacolor} + \usepackage[soul]{lua-ul} +\else +\usepackage{soul} +\fi +$endif$ +\setlength{\emergencystretch}{3em} % prevent overfull lines +\providecommand{\tightlist}{% + \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} +$if(numbersections)$ +\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$} +$else$ +\setcounter{secnumdepth}{-\maxdimen} % remove section numbering +$endif$ +$if(subfigure)$ +\usepackage{subcaption} +$endif$ +$if(beamer)$ +$else$ +$if(block-headings)$ +% Make \paragraph and \subparagraph free-standing +\ifx\paragraph\undefined\else + \let\oldparagraph\paragraph + \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}} +\fi +\ifx\subparagraph\undefined\else + \let\oldsubparagraph\subparagraph + \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}} +\fi +$endif$ +$endif$ +$if(pagestyle)$ +\pagestyle{$pagestyle$} +$endif$ +$if(csl-refs)$ +\newlength{\cslhangindent} +\setlength{\cslhangindent}{1.5em} +\newlength{\csllabelwidth} +\setlength{\csllabelwidth}{3em} +\newlength{\cslentryspacingunit} % times entry-spacing +\setlength{\cslentryspacingunit}{\parskip} +\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing + {% don't indent paragraphs + \setlength{\parindent}{0pt} + % turn on hanging indent if param 1 is 1 + \ifodd #1 + \let\oldpar\par + \def\par{\hangindent=\cslhangindent\oldpar} + \fi + % set entry spacing + \setlength{\parskip}{#2\cslentryspacingunit} + }% + {} +\usepackage{calc} +\newcommand{\CSLBlock}[1]{#1\hfill\break} +\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}} +\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break} +\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1} +$endif$ +$if(lang)$ +\ifLuaTeX +\usepackage[bidi=basic]{babel} +\else +\usepackage[bidi=default]{babel} +\fi +$if(babel-lang)$ +\babelprovide[main,import]{$babel-lang$} +$if(mainfont)$ +\ifPDFTeX +\else +\babelfont{rm}[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$} +\fi +$endif$ +$endif$ +$for(babel-otherlangs)$ +\babelprovide[import]{$babel-otherlangs$} +$endfor$ +$for(babelfonts/pairs)$ +\babelfont[$babelfonts.key$]{rm}{$babelfonts.value$} +$endfor$ +% get rid of language-specific shorthands (see #6817): +\let\LanguageShortHands\languageshorthands +\def\languageshorthands#1{} +$endif$ +$for(header-includes)$ +$header-includes$ +$endfor$ +\ifLuaTeX + \usepackage{selnolig} % disable illegal ligatures +\fi +$if(dir)$ +\ifPDFTeX + \TeXXeTstate=1 + \newcommand{\RL}[1]{\beginR #1\endR} + \newcommand{\LR}[1]{\beginL #1\endL} + \newenvironment{RTL}{\beginR}{\endR} + \newenvironment{LTR}{\beginL}{\endL} +\fi +$endif$ +$if(natbib)$ +\usepackage[$natbiboptions$]{natbib} +\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$} +$endif$ +$if(biblatex)$ +\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex} +$for(bibliography)$ +\addbibresource{$bibliography$} +$endfor$ +$endif$ +$if(nocite-ids)$ +\nocite{$for(nocite-ids)$$it$$sep$, $endfor$} +$endif$ +$if(csquotes)$ +\usepackage{csquotes} +$endif$ +\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}} +\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available +\urlstyle{$if(urlstyle)$$urlstyle$$else$same$endif$} +$if(links-as-notes)$ +% Make links footnotes instead of hotlinks: +\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}} +$endif$ +$if(verbatim-in-note)$ +\VerbatimFootnotes % allow verbatim text in footnotes +$endif$ +\hypersetup{ +$if(title-meta)$ + pdftitle={$title-meta$}, +$endif$ +$if(author-meta)$ + pdfauthor={$author-meta$}, +$endif$ +$if(lang)$ + pdflang={$lang$}, +$endif$ +$if(subject)$ + pdfsubject={$subject$}, +$endif$ +$if(keywords)$ + pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$}, +$endif$ +$if(colorlinks)$ + colorlinks=true, + linkcolor={$if(linkcolor)$$linkcolor$$else$default-linkcolor$endif$}, + filecolor={$if(filecolor)$$filecolor$$else$default-filecolor$endif$}, + citecolor={$if(citecolor)$$citecolor$$else$default-citecolor$endif$}, + urlcolor={$if(urlcolor)$$urlcolor$$else$default-urlcolor$endif$}, +$else$ + hidelinks, +$endif$ + breaklinks=true, + pdfcreator={LaTeX via pandoc with the Eisvogel template}} +$if(title)$ +\title{$title$$if(thanks)$\thanks{$thanks$}$endif$} +$endif$ +$if(subtitle)$ +$if(beamer)$ +$else$ +\usepackage{etoolbox} +\makeatletter +\providecommand{\subtitle}[1]{% add subtitle to \maketitle + \apptocmd{\@title}{\par {\large #1 \par}}{}{} +} +\makeatother +$endif$ +\subtitle{$subtitle$} +$endif$ +\author{$for(author)$$author$$sep$ \and $endfor$} +\date{$date$} +$if(beamer)$ +$if(institute)$ +\institute{$for(institute)$$institute$$sep$ \and $endfor$} +$endif$ +$if(titlegraphic)$ +\titlegraphic{\includegraphics{$titlegraphic$}} +$endif$ +$if(logo)$ +\logo{\includegraphics{$logo$}} +$endif$ +$endif$ + + + +%% +%% added +%% + +$if(page-background)$ +\usepackage[pages=all]{background} +$endif$ + +% +% for the background color of the title page +% +$if(titlepage)$ +\usepackage{pagecolor} +\usepackage{afterpage} +$if(titlepage-background)$ +\usepackage{tikz} +$endif$ +$if(geometry)$ +$else$ +\usepackage[margin=2.5cm,includehead=true,includefoot=true,centering]{geometry} +$endif$ +$endif$ + +% +% break urls +% +\PassOptionsToPackage{hyphens}{url} + +% +% When using babel or polyglossia with biblatex, loading csquotes is recommended +% to ensure that quoted texts are typeset according to the rules of your main language. +% +\usepackage{csquotes} + +% +% captions +% +\definecolor{caption-color}{HTML}{777777} +$if(beamer)$ +$else$ +\usepackage[font={stretch=1.2}, textfont={color=caption-color}, position=top, skip=4mm, labelfont=bf, singlelinecheck=false, justification=$if(caption-justification)$$caption-justification$$else$raggedright$endif$]{caption} +\setcapindent{0em} +$endif$ + +% +% blockquote +% +\definecolor{blockquote-border}{RGB}{221,221,221} +\definecolor{blockquote-text}{RGB}{119,119,119} +\usepackage{mdframed} +\newmdenv[rightline=false,bottomline=false,topline=false,linewidth=3pt,linecolor=blockquote-border,skipabove=\parskip]{customblockquote} +\renewenvironment{quote}{\begin{customblockquote}\list{}{\rightmargin=0em\leftmargin=0em}% +\item\relax\color{blockquote-text}\ignorespaces}{\unskip\unskip\endlist\end{customblockquote}} + +% +% Source Sans Pro as the default font family +% Source Code Pro for monospace text +% +% 'default' option sets the default +% font family to Source Sans Pro, not \sfdefault. +% +\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex + $if(fontfamily)$ + $else$ + \usepackage[default]{sourcesanspro} + \usepackage{sourcecodepro} + $endif$ +\else % if not pdftex + $if(mainfont)$ + $else$ + \usepackage[default]{sourcesanspro} + \usepackage{sourcecodepro} + + % XeLaTeX specific adjustments for straight quotes: https://tex.stackexchange.com/a/354887 + % This issue is already fixed (see https://github.com/silkeh/latex-sourcecodepro/pull/5) but the + % fix is still unreleased. + % TODO: Remove this workaround when the new version of sourcecodepro is released on CTAN. + \ifxetex + \makeatletter + \defaultfontfeatures[\ttfamily] + { Numbers = \sourcecodepro@figurestyle, + Scale = \SourceCodePro@scale, + Extension = .otf } + \setmonofont + [ UprightFont = *-\sourcecodepro@regstyle, + ItalicFont = *-\sourcecodepro@regstyle It, + BoldFont = *-\sourcecodepro@boldstyle, + BoldItalicFont = *-\sourcecodepro@boldstyle It ] + {SourceCodePro} + \makeatother + \fi + $endif$ +\fi + +% +% heading color +% +\definecolor{heading-color}{RGB}{40,40,40} +$if(beamer)$ +$else$ +\addtokomafont{section}{\color{heading-color}} +$endif$ +% When using the classes report, scrreprt, book, +% scrbook or memoir, uncomment the following line. +%\addtokomafont{chapter}{\color{heading-color}} + +% +% variables for title, author and date +% +$if(beamer)$ +$else$ +\usepackage{titling} +\title{$title$} +\author{$for(author)$$author$$sep$, $endfor$} +\date{$date$} +$endif$ + +% +% tables +% +$if(tables)$ + +\definecolor{table-row-color}{HTML}{F5F5F5} +\definecolor{table-rule-color}{HTML}{999999} + +%\arrayrulecolor{black!40} +\arrayrulecolor{table-rule-color} % color of \toprule, \midrule, \bottomrule +\setlength\heavyrulewidth{0.3ex} % thickness of \toprule, \bottomrule +\renewcommand{\arraystretch}{1.3} % spacing (padding) + +$if(table-use-row-colors)$ +% TODO: This doesn't work anymore. I don't know why. +% Reset rownum counter so that each table +% starts with the same row colors. +% https://tex.stackexchange.com/questions/170637/restarting-rowcolors +% +% Unfortunately the colored cells extend beyond the edge of the +% table because pandoc uses @-expressions (@{}) like so: +% +% \begin{longtable}[]{@{}ll@{}} +% \end{longtable} +% +% https://en.wikibooks.org/wiki/LaTeX/Tables#.40-expressions +\let\oldlongtable\longtable +\let\endoldlongtable\endlongtable +\renewenvironment{longtable}{ +\rowcolors{3}{}{table-row-color!100} % row color +\oldlongtable} { +\endoldlongtable +\global\rownum=0\relax} +$endif$ +$endif$ + +% +% remove paragraph indention +% +\setlength{\parindent}{0pt} +\setlength{\parskip}{6pt plus 2pt minus 1pt} +\setlength{\emergencystretch}{3em} % prevent overfull lines + +% +% +% Listings +% +% + +$if(listings)$ + +% +% general listing colors +% +\definecolor{listing-background}{HTML}{F7F7F7} +\definecolor{listing-rule}{HTML}{B3B2B3} 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\color{listing-identifier} +} +$endif$ + +% +% header and footer +% +$if(beamer)$ +$else$ +$if(disable-header-and-footer)$ +$else$ +\usepackage[headsepline,footsepline]{scrlayer-scrpage} + +\newpairofpagestyles{eisvogel-header-footer}{ + \clearpairofpagestyles + \ihead*{$if(header-left)$$header-left$$else$$title$$endif$} + \chead*{$if(header-center)$$header-center$$else$$endif$} + \ohead*{$if(header-right)$$header-right$$else$$date$$endif$} + \ifoot*{$if(footer-left)$$footer-left$$else$$for(author)$$author$$sep$, $endfor$$endif$} + \cfoot*{$if(footer-center)$$footer-center$$else$$endif$} + \ofoot*{$if(footer-right)$$footer-right$$else$\thepage$endif$} + \addtokomafont{pageheadfoot}{\upshape} +} +\pagestyle{eisvogel-header-footer} + +$if(book)$ +\deftripstyle{ChapterStyle}{}{}{}{}{\pagemark}{} +\renewcommand*{\chapterpagestyle}{ChapterStyle} +$endif$ + +$if(page-background)$ +\backgroundsetup{ +scale=1, +color=black, 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+\color[HTML]{$if(titlepage-text-color)$$titlepage-text-color$$else$5F5F5F$endif$} +\makebox[0pt][l]{\colorRule[$if(titlepage-rule-color)$$titlepage-rule-color$$else$435488$endif$]{1.3\textwidth}{$if(titlepage-rule-height)$$titlepage-rule-height$$else$4$endif$pt}} +\par +\noindent + +$if(titlepage-background)$ +% The titlepage with a background image has other text spacing and text size +{ + \setstretch{2} + \vfill + \vskip -8em + \noindent {\huge \textbf{\textsf{$title$}}} + $if(subtitle)$ + \vskip 1em + {\Large \textsf{$subtitle$}} + $endif$ + \vskip 2em + \noindent {\Large \textsf{$for(author)$$author$$sep$, $endfor$} \vskip 0.6em \textsf{$date$}} + \vfill +} +$else$ +{ + \setstretch{1.4} + \vfill + \noindent {\huge \textbf{\textsf{$title$}}} + $if(subtitle)$ + \vskip 1em + {\Large \textsf{$subtitle$}} + $endif$ + \vskip 2em + \noindent {\Large \textsf{$for(author)$$author$$sep$, $endfor$}} + \vfill +} +$endif$ + +$if(titlepage-logo)$ +\noindent +\includegraphics[width=$if(logo-width)$$logo-width$$else$35mm$endif$, left]{$titlepage-logo$} +$endif$ + +$if(titlepage-background)$ +$else$ +\textsf{$date$} +$endif$ +\end{flushleft} +\end{titlepage} +\restoregeometry +\pagenumbering{arabic} +$endif$ +$endif$ + +%% +%% end titlepage +%% + +$if(has-frontmatter)$ +\frontmatter +$endif$ +$if(title)$ +$if(beamer)$ +\frame{\titlepage} +% don't generate the default title +% $else$ +% \maketitle +$endif$ +$if(abstract)$ +\begin{abstract} +$abstract$ +\end{abstract} +$endif$ +$endif$ + +$if(first-chapter)$ +\setcounter{chapter}{$first-chapter$} +\addtocounter{chapter}{-1} +$endif$ + +$for(include-before)$ +$include-before$ + +$endfor$ +$if(toc)$ +$if(toc-title)$ +\renewcommand*\contentsname{$toc-title$} +$endif$ +$if(beamer)$ +\begin{frame}[allowframebreaks] +$if(toc-title)$ + \frametitle{$toc-title$} +$endif$ + \tableofcontents[hideallsubsections] +\end{frame} +$if(toc-own-page)$ +\newpage +$endif$ +$else$ +{ +$if(colorlinks)$ +\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$} +$endif$ +\setcounter{tocdepth}{$toc-depth$} +\tableofcontents +$if(toc-own-page)$ +\newpage +$endif$ +} +$endif$ +$endif$ +$if(lof)$ +\listoffigures +$endif$ +$if(lot)$ +\listoftables +$endif$ +$if(linestretch)$ +\setstretch{$linestretch$} +$endif$ +$if(has-frontmatter)$ +\mainmatter +$endif$ +$body$ + +$if(has-frontmatter)$ +\backmatter +$endif$ +$if(natbib)$ +$if(bibliography)$ +$if(biblio-title)$ +$if(has-chapters)$ +\renewcommand\bibname{$biblio-title$} +$else$ +\renewcommand\refname{$biblio-title$} +$endif$ +$endif$ +$if(beamer)$ +\begin{frame}[allowframebreaks]{$biblio-title$} + \bibliographytrue +$endif$ + \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$} +$if(beamer)$ +\end{frame} +$endif$ + +$endif$ +$endif$ +$if(biblatex)$ +$if(beamer)$ +\begin{frame}[allowframebreaks]{$biblio-title$} + \bibliographytrue + \printbibliography[heading=none] +\end{frame} +$else$ +\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$ +$endif$ + +$endif$ +$for(include-after)$ +$include-after$ + +$endfor$ +\end{document} \ No newline at end of file diff --git a/JOSS/paper.md b/JOSS/paper.md index 24b0a402..76809ad1 100644 --- a/JOSS/paper.md +++ b/JOSS/paper.md @@ -149,58 +149,57 @@ Our library requires as input the grid size $n$, the minimal eigenvalue differen \end{align} with $\mathbb{I}$ being the identity matrix. Inputs and outputs are in atomic units. -| Output| Description|Methods using the output|Computation| -|---|--------|---------|-------| -|$\{\tau_j^\text{mat}\}_{j=1}^n$    | time points | LT-dMP2, ls RPA, ls \textit{GW} | tabulated + rescaling | -|$\{\sigma_j^\text{mat}\}_{j=1}^n$ | time integration weights | LT-dMP2 | tabulated + rescaling -|$\{\omega_k^\text{mat}\}_{k=1}^n$ | frequency points | ls & canonical RPA, ls \textit{GW} | tabulated + rescaling | -|$\{\gamma_k^\text{mat}\}_{k=1}^n$ | freq. integration weights | ls & canonical RPA | tabulated + rescaling | -|$\{\delta_{kj}\}_{k,j=1}^n$ | Fourier weights | ls RPA, ls \textit{GW} | on-the-fly L2 opt -| $\{\eta_{jk}\}_{k,j=1}^n$ | Fourier weights | ls \textit{GW} | on-the-fly L2 opt| -|$\{\lambda_{kj}\}_{k,j=1}^n$ | Fourier weights | ls \textit{GW} | on-the-fly L2 opt -| $\Delta_\text{CT}$ | duality error cosine transforms | ls \textit{GW} | on-the-fly | +| Output | Description | Methods using the output | Computation | +|----------------------------------------------|---------------------------------|------------------------------------|-----------------------| +| $\{\tau_j^\text{mat}\}_{j=1}^n$    | time points | LT-dMP2, ls RPA, ls \textit{GW} | tabulated + rescaling | +| $\{\sigma_j^\text{mat}\}_{j=1}^n$ | time integration weights | LT-dMP2 | tabulated + rescaling | +| $\{\omega_k^\text{mat}\}_{k=1}^n$ | frequency points | ls & canonical RPA, ls \textit{GW} | tabulated + rescaling | +| $\{\gamma_k^\text{mat}\}_{k=1}^n$ | freq. integration weights | ls & canonical RPA | tabulated + rescaling | +| $\{\delta_{kj}\}_{k,j=1}^n$ | Fourier weights | ls RPA, ls \textit{GW} | on-the-fly L2 opt | +| $\{\eta_{jk}\}_{k,j=1}^n$ | Fourier weights | ls \textit{GW} | on-the-fly L2 opt | +| $\{\lambda_{kj}\}_{k,j=1}^n$ | Fourier weights | ls \textit{GW} | on-the-fly L2 opt | +| $\Delta_\text{CT}$ | duality error cosine transforms | ls \textit{GW} | on-the-fly | : Output returned by the Green-X library. We abbreviate low-scaling as ls, and least-squares optimization as L2 opt.\label{tab:output} # Structure of the library The Green-X library [@GitHub;@azizi_minimax] will eventually provide a variety of tools for advanced electronic structure calculations. In this work, we focus on the 'GX-common' and 'GX-TimeFrequency' components. 'GX-common' provides functionality for all library components, such as error handling and unit conversion utilities. 'GX-TimeFrequency' provides an API directory for the time-frequency transformations, a source directory, and a test directory with scripts for verifying the implementation. The relevant directory tree section is: -```bash -. -├── CMakeLists.txt -├── developers.md -├── Doxyfile -├── GX-common -│   ├── CMakeLists.txt -│   └── src -│   ├── constants.f90 -│   ├── error_handling.f90 -│   ├── kinds.f90 -│   ├── lapack_interfaces.f90 -│   └── unit_conversion.f90 -├── GX-TimeFrequency -│   ├── api -│   │   ├── api_utilities.f90 -│   │   └── gx_minimax.f90 -│   ├── CITATION.cff -│   ├── CMakeLists.txt -│   ├── LICENSE.txt -│   ├── README.md -│   ├── src -│   │   ├── gx_common.h -│   │   ├── minimax_grids.F90 -│   │   ├── minimax_omega.F90 -│   │   ├── minimax_tau.F90 -│   │   └── minimax_utils.F90 -│   ├── test -│   │   ├── conftest.py -│   │   ├── test_gx_minimax_grid.f90 -│   │   ├── test_gx_minimax_grid.py -│   │   └── test_gx_tabulate_minimax.py -│   └── utilities -│   └── gx_tabulate_minimax.F90 -├── LICENSE.txt -└── README.md +```plaintext + |- CMakeLists.txt + |- developers.md + |- Doxyfile + |- GX-common + | |- CMakeLists.txt + | |- src + | | |- constants.f90 + | | |- error_handling.f90 + | | |- kinds.f90 + | | |- lapack_interfaces.f90 + | | |- unit_conversion.f90 + |- GX-TimeFrequency + | |- api + | | |- api_utilities.f90 + | | |- gx_minimax.f90 + | |- CITATION.cff + | |- CMakeLists.txt + | |- LICENSE.txt + | |- README.md + | |- src + | | |- gx_common.h + | | |- minimax_grids.F90 + | | |- minimax_omega.F90 + | | |- minimax_tau.F90 + | | |- minimax_utils.F90 + | |- test + | | |- conftest.py + | | |- test_gx_minimax_grid.f90 + | | |- test_gx_minimax_grid.py + | | |- test_gx_tabulate_minimax.py + | |- utilities + | | |- gx_tabulate_minimax.F90 + |- LICENSE.txt + |- README.md ``` Green-X is written in Fortran 2008. Functionality needed for testing and error handling is written in C and Python. We utilize modern Fortran features such as object-oriented programming and intrinsic procedures that are available in Fortran 2008. We have developed a clear interface between the module code (our library) and the client code (MBPT code), promoting better modularity and reusability. Additionally, we use allocatable arrays and automatic deallocation to simplify the code and avoid memory-related issues, such as leaks and dangling pointers. The implementation is robust and reliable, as we use error handling techniques to highlight and recover from exceptions. diff --git a/JOSS/refs.bib b/JOSS/refs.bib index 712d9a6c..aaf38977 100644 --- a/JOSS/refs.bib +++ b/JOSS/refs.bib @@ -1,83 +1,61 @@ -@article{wang2021assessing, - title={Assessing the G 0 W 0$\Gamma$0 (1) Approach: Beyond G 0 W 0 with Hedin’s Full Second-Order Self-Energy Contribution}, - author={Wang, Yanyong and Rinke, Patrick and Ren, Xinguo}, - journal={Journal of Chemical Theory and Computation}, - volume={17}, - number={8}, - pages={5140--5154}, - year={2021}, - doi = {10.1021/acs.jctc.1c00488}, - publisher={ACS Publications} -} -@article{ren2015beyond, - title={Beyond the G W approximation: A second-order screened exchange correction}, - author={Ren, Xinguo and Marom, Noa and Caruso, Fabio and Scheffler, Matthias and Rinke, Patrick}, - journal={Physical Review B}, - volume={92}, - number={8}, - pages={081104}, - year={2015}, - doi= {10.1103/PhysRevB.92.081104}, - publisher={APS} -} @article{Pearson:2017, - url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, - Archiveprefix = {arXiv}, - Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, - Eprint = {1703.04627}, - Journal = {ArXiv e-prints}, - Keywords = {Astrophysics - Astrophysics of Galaxies}, - Month = mar, - doi = {10.1038/s41550-017-0220-3}, - Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, - Year = 2017 + url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P}, + Archiveprefix = {arXiv}, + Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.}, + Eprint = {1703.04627}, + Journal = {ArXiv e-prints}, + Keywords = {Astrophysics - Astrophysics of Galaxies}, + Month = mar, + doi = {10.1038/s41550-017-0220-3}, + Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}}, + Year = 2017 } @article{azizi_minimax, - Author = {{Azizi}, M. and {Wilhelm}, J. and {Panadés-Barrueta}, R.~L. and {Golze}, D. and {Giantomassi}, M. and {Delesma}, F.~A. and {Rinke}, P. and {Gonze}, X.}, - Journal = {Unpublished}, - year = {2023}, - doi = {--}, - Title = {{Validation of the Green-X library time-frequency component for GW and RPA calculations}}, + Author = {{Azizi}, M. and {Wilhelm}, J. and {Panadés-Barrueta}, R.~L. and {Golze}, D. and {Giantomassi}, M. and {Delesma}, F.~A. and {Rinke}, P. and {Gonze}, X.}, + Journal = {Unpublished}, + year = {2023}, + doi = {--}, + Title = {{Validation of the Green-X library time-frequency component for GW and RPA calculations}}, } @book{Binney:2008, - url = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, - Author = {{Binney}, J. and {Tremaine}, S.}, - Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, - Publisher = {Princeton University Press}, - Title = {{Galactic Dynamics: Second Edition}}, - doi = {10.2307/j.ctvc778ff}, - Year = 2008 + url = {http://adsabs.harvard.edu/abs/2008gady.book.....B}, + Author = {{Binney}, J. and {Tremaine}, S.}, + Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.}, + Publisher = {Princeton University Press}, + Title = {{Galactic Dynamics: Second Edition}}, + doi = {10.2307/j.ctvc778ff}, + Year = 2008 } @article{gaia, - author = {{Gaia Collaboration}}, - title = "{The Gaia mission}", - journal = {Astronomy and Astrophysics}, - archivePrefix = "arXiv", - eprint = {1609.04153}, - primaryClass = "astro-ph.IM", - keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, - year = 2016, - month = nov, - volume = 595, - doi = {10.1051/0004-6361/201629272}, - url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, + author = {{Gaia Collaboration}}, + title = "{The Gaia mission}", + journal = {Astronomy and Astrophysics}, + archivePrefix = "arXiv", + eprint = {1609.04153}, + primaryClass = "astro-ph.IM", + keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes}, + year = 2016, + month = nov, + volume = 595, + doi = {10.1051/0004-6361/201629272}, + url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G}, } @article{astropy, - author = {{Astropy Collaboration}}, - title = "{Astropy: A community Python package for astronomy}", - journal = {Astronomy and Astrophysics}, - archivePrefix = "arXiv", - eprint = {1307.6212}, - primaryClass = "astro-ph.IM", - keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, - year = 2013, - month = oct, - volume = 558, - doi = {10.1051/0004-6361/201322068}, - url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A} + author = {{Astropy Collaboration}}, + title = "{Astropy: A community Python package for astronomy}", + journal = {Astronomy and Astrophysics}, + archivePrefix = "arXiv", + eprint = {1307.6212}, + primaryClass = "astro-ph.IM", + keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools}, + year = 2013, + month = oct, + volume = 558, + doi = {10.1051/0004-6361/201322068}, + url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A} } @misc{fidgit, @@ -90,8 +68,6 @@ @misc{fidgit url = {https://github.com/arfon/fidgit} } - - @book{braess2012nonlinear, title={Nonlinear approximation theory}, author={Braess, Dietrich}, @@ -140,42 +116,42 @@ @article{hackbusch2019computation publisher={Springer} } @article{Takatsuka2008, - author = {Takatsuka, Akio and Ten-no, Seiichiro and Hackbusch, Wolfgang}, - title = "{Minimax approximation for the decomposition of energy denominators in Laplace-transformed Møller–Plesset perturbation theories}", - journal = {The Journal of Chemical Physics}, - volume = {129}, - number = {4}, - year = {2008}, - month = {07}, - doi = {10.1007/s00791-018-00308-4} + author = {Takatsuka, Akio and Ten-no, Seiichiro and Hackbusch, Wolfgang}, + title = "{Minimax approximation for the decomposition of energy denominators in Laplace-transformed Møller–Plesset perturbation theories}", + journal = {The Journal of Chemical Physics}, + volume = {129}, + number = {4}, + year = {2008}, + month = {07}, + doi = {10.1007/s00791-018-00308-4} } @article{Adler1962, - author = "Adler, Stephen L.", - issn = "0031-899X", - journal = "Physical Review", - month = "April", - number = "2", - pages = "413-420", - publisher = "American Physical Society (APS)", - source = "Crossref", - title = "Quantum Theory of the Dielectric Constant in Real Solids", - doi = {10.1103/PhysRev.126.413}, - volume = "126", - year = "1962" + author = "Adler, Stephen L.", + issn = "0031-899X", + journal = "Physical Review", + month = "April", + number = "2", + pages = "413-420", + publisher = "American Physical Society (APS)", + source = "Crossref", + title = "Quantum Theory of the Dielectric Constant in Real Solids", + doi = {10.1103/PhysRev.126.413}, + volume = "126", + year = "1962" } @article{Wiser1963, - author = "Wiser, Nathan", - issn = "0031-899X", - journal = "Physical Review", - month = "January", - number = "1", - pages = "62-69", - publisher = "American Physical Society (APS)", - source = "Crossref", - title = "Dielectric Constant with Local Field Effects Included", - doi = {10.1103/PhysRev.129.62}, - volume = "129", - year = "1963" + author = "Wiser, Nathan", + issn = "0031-899X", + journal = "Physical Review", + month = "January", + number = "1", + pages = "62-69", + publisher = "American Physical Society (APS)", + source = "Crossref", + title = "Dielectric Constant with Local Field Effects Included", + doi = {10.1103/PhysRev.129.62}, + volume = "129", + year = "1963" } @article{haser1992laplace, title={Laplace transform techniques in Mo/ller-Plesset perturbation theory}, @@ -190,7 +166,7 @@ @article{haser1992laplace } @article{kaltak2014low, title={Low scaling algorithms for the random phase approximation: Imaginary time and Laplace transformations}, - author={Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}{\'\i} and Kresse, Georg}, + author={Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}\'{i} and Kresse, Georg}, journal={Journal of Chemical Theory and Computation}, volume={10}, number={6}, @@ -201,18 +177,18 @@ @article{kaltak2014low } @article{kaltak2014cubic, title={Cubic scaling algorithm for the random phase approximation: Self-interstitials and vacancies in {S}i}, - author={Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}{\'\i} and Kresse, Georg}, + author={Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}\'{i} and Kresse, Georg}, journal={Physical Review B}, volume={90}, number={5}, pages={054115}, year={2014}, - doi = {10.1103/PhysRevB.90.054115 }, + doi = {10.1103/PhysRevB.90.054115}, publisher={APS} } @article{liu2016cubic, title={Cubic scaling {GW}: Towards fast quasiparticle calculations}, - author={Liu, Peitao and Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}{\'\i} and Kresse, Georg}, + author={Liu, Peitao and Kaltak, Merzuk and Klime{\v{s}}, Ji{\v{r}}\'{i} and Kresse, Georg}, journal={Physical Review B}, volume={94}, number={16}, @@ -254,9 +230,9 @@ @article{remez1934determination year={1934} } @misc{GitHub, - author={GreenX}, - year={2023}, - howpublished="\url{https://github.com/nomad-coe/greenX}" + author={GreenX}, + year={2023}, + howpublished="\url{https://github.com/nomad-coe/greenX}" } @article{hedin1965new, title={New method for calculating the one-particle {G}reen's function with application to the electron-gas problem}, @@ -304,7 +280,7 @@ @article{li2005quasiparticle } @article{wilhelm2016gw, title={{GW} in the {G}aussian and plane waves scheme with application to linear acenes}, - author={Wilhelm, Jan and Del Ben, Mauro and Hutter, Jürg}, + author={Wilhelm, Jan and Del Ben, Mauro and Hutter, J\"{u}rg}, journal={Journal of Chemical Theory and Computation}, volume={12}, number={8}, @@ -401,7 +377,7 @@ @article{vidberg1977solving } @misc{cp2k, - howpublished="\url{https://www.cp2k.org}" + howpublished="\url{https://www.cp2k.org}" } @book{baker1975essentials, @@ -496,151 +472,151 @@ @article{del2019large publisher={Elsevier} } @article{delben2015enabling, -title = {Enabling simulation at the fifth rung of DFT: Large scale RPA calculations with excellent time to solution}, -journal = {Computer Physics Communications}, -volume = {187}, -pages = {120-129}, -year = {2015}, -issn = {0010-4655}, -doi = {10.1016/j.cpc.2014.10.021}, -author = {Mauro {Del Ben} and Ole Schütt and Tim Wentz and Peter Messmer and Jürg Hutter and Joost VandeVondele}, + title = {Enabling simulation at the fifth rung of DFT: Large scale RPA calculations with excellent time to solution}, + journal = {Computer Physics Communications}, + volume = {187}, + pages = {120-129}, + year = {2015}, + issn = {0010-4655}, + doi = {10.1016/j.cpc.2014.10.021}, + author = {Mauro {Del Ben} and Ole Schütt and Tim Wentz and Peter Messmer and Jürg Hutter and Joost VandeVondele}, } @article{vansetten2015GW100, -author = {{van Setten}, M. J. and Caruso, Fabio and Sharifzadeh, Sahar and Ren, Xinguo and Scheffler, Matthias and Liu, Fang and Lischner, Johannes and Lin, Lin and Deslippe, Jack R. and Louie, Steven G. and Yang, Chao and Weigend, Florian and Neaton, Jeffrey B. and Evers, Ferdinand and Rinke, Patrick}, -title = {{GW100: Benchmarking $G_0W_0$ for Molecular Systems}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {11}, -number = {12}, -pages = {5665-5687}, -year = {2015}, + author = {{van Setten}, M. J. and Caruso, Fabio and Sharifzadeh, Sahar and Ren, Xinguo and Scheffler, Matthias and Liu, Fang and Lischner, Johannes and Lin, Lin and Deslippe, Jack R. and Louie, Steven G. and Yang, Chao and Weigend, Florian and Neaton, Jeffrey B. and Evers, Ferdinand and Rinke, Patrick}, + title = {{GW100: Benchmarking $G_0W_0$ for Molecular Systems}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {11}, + number = {12}, + pages = {5665-5687}, + year = {2015}, } @article{duchemin2020robust, -author = {Duchemin, Ivan and Blase, Xavier}, -title = {{Robust Analytic-Continuation Approach to Many-Body GW Calculations}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {16}, -number = {3}, -pages = {1742-1756}, -doi = {10.1021/acs.jctc.9b01235}, -year = {2020}, + author = {Duchemin, Ivan and Blase, Xavier}, + title = {{Robust Analytic-Continuation Approach to Many-Body GW Calculations}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {16}, + number = {3}, + pages = {1742-1756}, + doi = {10.1021/acs.jctc.9b01235}, + year = {2020}, } @article{rangel2020reproducability, -author = {Tonatiuh Rangel and Mauro {Del Ben} and Daniele Varsano and Gabriel Antonius and Fabien Bruneval and Felipe H. {da Jornada} and Michiel J. {van Setten} and Okan K. Orhan and David D. O’Regan and Andrew Canning and Andrea Ferretti and Andrea Marini and Gian-Marco Rignanese and Jack Deslippe and Steven G. Louie and Jeffrey B. Neaton}, -title = {{Reproducibility in $G_0W_0$ calculations for solids}}, -journal = {Computer Physics Communications}, -volume = {255}, -pages = {107242}, -year = {2020}, + author = {Tonatiuh Rangel and Mauro {Del Ben} and Daniele Varsano and Gabriel Antonius and Fabien Bruneval and Felipe H. {da Jornada} and Michiel J. {van Setten} and Okan K. Orhan and David D. O’Regan and Andrew Canning and Andrea Ferretti and Andrea Marini and Gian-Marco Rignanese and Jack Deslippe and Steven G. Louie and Jeffrey B. Neaton}, + title = {{Reproducibility in $G_0W_0$ calculations for solids}}, + journal = {Computer Physics Communications}, + volume = {255}, + pages = {107242}, + year = {2020}, } @article{duchemin2021cubic, -author = {Duchemin, Ivan and Blase, Xavier}, -title = {{Cubic-Scaling All-Electron GW Calculations with a Separable Density-Fitting Space–Time Approach}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {17}, -number = {4}, -pages = {2383-2393}, -doi = {10.1021/acs.jctc.1c00101}, -year = {2021}, + author = {Duchemin, Ivan and Blase, Xavier}, + title = {{Cubic-Scaling All-Electron GW Calculations with a Separable Density-Fitting Space–Time Approach}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {17}, + number = {4}, + pages = {2383-2393}, + doi = {10.1021/acs.jctc.1c00101}, + year = {2021}, } @article{foerster2021GW100, -author = {Förster, Arno and Visscher, Lucas}, -title = {{GW100: A Slater-Type Orbital Perspective}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {17}, -number = {8}, -pages = {5080-5097}, -doi = {10.1021/acs.jctc.1c00308}, -year = {2021}, + author = {Förster, Arno and Visscher, Lucas}, + title = {{GW100: A Slater-Type Orbital Perspective}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {17}, + number = {8}, + pages = {5080-5097}, + doi = {10.1021/acs.jctc.1c00308}, + year = {2021}, } @article{foerster2021loworder, -AUTHOR={Förster, Arno and Visscher, Lucas}, -TITLE={{Low-Order Scaling Quasiparticle Self-Consistent GW for Molecules}}, -JOURNAL={Frontiers in Chemistry}, -VOLUME={9}, -pages={736591}, -doi = {10.3389/fchem.2021.736591}, -YEAR={2021}, + AUTHOR={Förster, Arno and Visscher, Lucas}, + TITLE={{Low-Order Scaling Quasiparticle Self-Consistent GW for Molecules}}, + JOURNAL={Frontiers in Chemistry}, + VOLUME={9}, + pages={736591}, + doi = {10.3389/fchem.2021.736591}, + YEAR={2021}, } @article{foerster2023twocomponent, - title={{Two-component GW calculations: Cubic scaling implementation and comparison of partially self-consistent variants}}, - author={Arno Förster and Erik van Lenthe and Edoardo Spadetto and Lucas Visscher}, - year={2023}, - pages={2303.09979}, - doi = {10.48550/arXiv.2303.09979}, - journal={arXiv}, + title={{Two-component GW calculations: Cubic scaling implementation and comparison of partially self-consistent variants}}, + author={Arno Förster and Erik van Lenthe and Edoardo Spadetto and Lucas Visscher}, + year={2023}, + pages={2303.09979}, + doi = {10.48550/arXiv.2303.09979}, + journal={arXiv}, } @article{glasbrenner2020efficient, -author = {Glasbrenner, Michael and Graf, Daniel and Ochsenfeld, Christian}, -title = {{Efficient Reduced-Scaling Second-Order Møller–Plesset Perturbation Theory with Cholesky-Decomposed Densities and an Attenuated Coulomb Metric}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {16}, -number = {11}, -pages = {6856-6868}, -doi = {10.1021/acs.jctc.0c00600}, -year = {2020}, + author = {Glasbrenner, Michael and Graf, Daniel and Ochsenfeld, Christian}, + title = {{Efficient Reduced-Scaling Second-Order Møller–Plesset Perturbation Theory with Cholesky-Decomposed Densities and an Attenuated Coulomb Metric}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {16}, + number = {11}, + pages = {6856-6868}, + doi = {10.1021/acs.jctc.0c00600}, + year = {2020}, } @article{graf2018accurate, -author = {Graf, Daniel and Beuerle, Matthias and Schurkus, Henry F. and Luenser, Arne and Savasci, Gökcen and Ochsenfeld, Christian}, -title = {{Accurate and Efficient Parallel Implementation of an Effective Linear-Scaling Direct Random Phase Approximation Method}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {14}, -number = {5}, -pages = {2505-2515}, -doi = {10.1021/acs.jctc.8b00177}, -year = {2018}, + author = {Graf, Daniel and Beuerle, Matthias and Schurkus, Henry F. and Luenser, Arne and Savasci, Gökcen and Ochsenfeld, Christian}, + title = {{Accurate and Efficient Parallel Implementation of an Effective Linear-Scaling Direct Random Phase Approximation Method}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {14}, + number = {5}, + pages = {2505-2515}, + doi = {10.1021/acs.jctc.8b00177}, + year = {2018}, } @article{luenser2017, -author = {Luenser, Arne and Schurkus, Henry F. and Ochsenfeld, Christian}, -title = {{Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {13}, -number = {4}, -pages = {1647-1655}, -doi = {10.1021/acs.jctc.6b01235}, -year = {2017}, + author = {Luenser, Arne and Schurkus, Henry F. and Ochsenfeld, Christian}, + title = {{Vanishing-Overhead Linear-Scaling Random Phase Approximation by Cholesky Decomposition and an Attenuated Coulomb-Metric}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {13}, + number = {4}, + pages = {1647-1655}, + doi = {10.1021/acs.jctc.6b01235}, + year = {2017}, } @article{drontschenko2022efficient, -author = {Drontschenko, Viktoria and Graf, Daniel and Laqua, Henryk and Ochsenfeld, Christian}, -title = {{Efficient Method for the Computation of Frozen-Core Nuclear Gradients within the Random Phase Approximation}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {18}, -number = {12}, -pages = {7359-7372}, -doi = {10.1021/acs.jctc.2c00774}, -year = {2022}, + author = {Drontschenko, Viktoria and Graf, Daniel and Laqua, Henryk and Ochsenfeld, Christian}, + title = {{Efficient Method for the Computation of Frozen-Core Nuclear Gradients within the Random Phase Approximation}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {18}, + number = {12}, + pages = {7359-7372}, + doi = {10.1021/acs.jctc.2c00774}, + year = {2022}, } @article{duchemin2019separable, -author = {Duchemin,Ivan and Blase,Xavier }, -title = {{Separable resolution-of-the-identity with all-electron Gaussian bases: Application to cubic-scaling RPA}}, -journal = {The Journal of Chemical Physics}, -volume = {150}, -number = {17}, -pages = {174120}, -doi = {10.1063/1.5090605}, -year = {2019}, + author = {Duchemin,Ivan and Blase,Xavier }, + title = {{Separable resolution-of-the-identity with all-electron Gaussian bases: Application to cubic-scaling RPA}}, + journal = {The Journal of Chemical Physics}, + volume = {150}, + number = {17}, + pages = {174120}, + doi = {10.1063/1.5090605}, + year = {2019}, } @article{almloef1991elimination, -title = {{Elimination of energy denominators in Møller-Plesset perturbation theory by a Laplace transform approach}}, -journal = {Chemical Physics Letters}, -volume = {181}, -number = {4}, -pages = {319-320}, -year = {1991}, -doi = {10.1016/0009-2614(91)80078-C}, -author = {Jan Almlöf}, + title = {{Elimination of energy denominators in Møller-Plesset perturbation theory by a Laplace transform approach}}, + journal = {Chemical Physics Letters}, + volume = {181}, + number = {4}, + pages = {319-320}, + year = {1991}, + doi = {10.1016/0009-2614(91)80078-C}, + author = {Jan Almlöf}, } @article{jung2004scaled, -author = {Jung,Yousung and Lochan,Rohini C. and Dutoi,Anthony D. and Head-Gordon,Martin }, -title = {{Scaled opposite-spin second order Møller–Plesset correlation energy: An economical electronic structure method}}, -journal = {The Journal of Chemical Physics}, -volume = {121}, -number = {20}, -pages = {9793-9802}, -doi = {10.1063/1.1809602}, -year = {2004}, + author = {Jung,Yousung and Lochan,Rohini C. and Dutoi,Anthony D. and Head-Gordon,Martin }, + title = {{Scaled opposite-spin second order Møller–Plesset correlation energy: An economical electronic structure method}}, + journal = {The Journal of Chemical Physics}, + volume = {121}, + number = {20}, + pages = {9793-9802}, + doi = {10.1063/1.1809602}, + year = {2004}, } @article{nabok2016accurate, title={{Accurate all-electron G$_0$W$_0$ quasiparticle energies employing the full-potential augmented plane-wave method}}, @@ -654,43 +630,43 @@ @article{nabok2016accurate publisher={APS} } @article{ren2012random, -author={Ren, Xinguo + author={Ren, Xinguo and Rinke, Patrick and Joas, Christian and Scheffler, Matthias}, -title={Random-phase approximation and its applications in computational chemistry and materials science}, -journal={Journal of Materials Science}, -year={2012}, -month={Nov}, -day={01}, -volume={47}, -number={21}, -doi = {10.1007/s10853-012-6570-4}, -pages={7447-7471}, + title={Random-phase approximation and its applications in computational chemistry and materials science}, + journal={Journal of Materials Science}, + year={2012}, + month={Nov}, + day={01}, + volume={47}, + number={21}, + doi = {10.1007/s10853-012-6570-4}, + pages={7447-7471}, } @article{eshuis2012electron, -author={Eshuis, Henk + author={Eshuis, Henk and Bates, Jefferson E. and Furche, Filipp}, -title={Electron correlation methods based on the random phase approximation}, -journal={Theoretical Chemistry Accounts}, -year={2012}, -month={Jan}, -day={14}, -volume={131}, -number={1}, -doi = {10.1007/s00214-011-1084-8}, -pages={1084}, + title={Electron correlation methods based on the random phase approximation}, + journal={Theoretical Chemistry Accounts}, + year={2012}, + month={Jan}, + day={14}, + volume={131}, + number={1}, + doi = {10.1007/s00214-011-1084-8}, + pages={1084}, } @article{delben2013electron, -author = {Del Ben, Mauro and Hutter, Jürg and VandeVondele, Joost}, -title = {{Electron Correlation in the Condensed Phase from a Resolution of Identity Approach Based on the Gaussian and Plane Waves Scheme}}, -journal = {Journal of Chemical Theory and Computation}, -volume = {9}, -number = {6}, -pages = {2654-2671}, -doi = {10.1021/ct4002202}, -year = {2013}, + author = {Del Ben, Mauro and Hutter, Jürg and VandeVondele, Joost}, + title = {{Electron Correlation in the Condensed Phase from a Resolution of Identity Approach Based on the Gaussian and Plane Waves Scheme}}, + journal = {Journal of Chemical Theory and Computation}, + volume = {9}, + number = {6}, + pages = {2654-2671}, + doi = {10.1021/ct4002202}, + year = {2013}, } @article{onida2002electronic, title={Electronic excitations: density-functional versus many-body Green’s-function approaches}, @@ -736,14 +712,14 @@ @article{wilhelm2016large publisher={ACS Publications} } @article{wilhelm2016rpa, -author = {Wilhelm, Jan and Seewald, Patrick and Del Ben, Mauro and Hutter, Jürg}, -title = {Large-Scale Cubic-Scaling Random Phase Approximation Correlation Energy Calculations Using a Gaussian Basis}, -journal = {Journal of Chemical Theory and Computation}, -volume = {12}, -number = {12}, -pages = {5851-5859}, -doi = {10.1021/acs.jctc.6b00840}, -year = {2016}, + author = {Wilhelm, Jan and Seewald, Patrick and Del Ben, Mauro and Hutter, Jürg}, + title = {Large-Scale Cubic-Scaling Random Phase Approximation Correlation Energy Calculations Using a Gaussian Basis}, + journal = {Journal of Chemical Theory and Computation}, + volume = {12}, + number = {12}, + pages = {5851-5859}, + doi = {10.1021/acs.jctc.6b00840}, + year = {2016}, } @article{kutepov2012electronic, title={{Electronic structure of Pu and Am metals by self-consistent relativistic GW method}}, @@ -776,9 +752,3 @@ @article{Graml2023 Title = {{Low-scaling GW algorithm applied to twisted transition-metal dichalcogenide heterobilayers}}, Year = 2023 } - - - - - - diff --git a/README.md b/README.md index 99633af7..4dd2f4b9 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,12 @@ The Green X library is developed under Work Package 2 of the NOMAD Center of Excellence. It is available under the APACHE2 [license](LICENSE.txt). +## Libraries + +* [GX Time-frequency](GX-TimeFrequency/README.md): Optimised quadrature grids and weights for + RPA and GW imaginary time-frequency transforms. + + ## Installation Green X has been designed as a collection of libraries, which can be built relatively diff --git a/docs/gx_time_frequency.md b/docs/gx_time_frequency.md new file mode 100644 index 00000000..59297e52 --- /dev/null +++ b/docs/gx_time_frequency.md @@ -0,0 +1,25 @@ +--- +layout: page +title: Time-Frequency component +tagline: GreenX Time-Frequency +description: Time-Frequency component +--- + +# Benchmarks + +## CH4 RPA + +In this test, we evaluate the RPA total energy of CH4 using a Gauss-Legendre grid, a modified Gauss-Legendre grid (so +far the standard in FHI-aims and abinit), and minimax grids. An accuracy of 10^-6 eV is reached with 10 minimax grid +points while the modified Gauss-Legendre grids requires 36 points for this accuracy. + +[CH4 benchmark](./img/ch4_bench.png) + +Error differences of the total RPA energy [eV] of methane calculated using the Gauss-Legendre, modified Gauss-Legendre +and minimax imaginary frequency grid points. These differences were calculated with respect to the lowest RPA energy +obtained with 34 minimax grid points. The ground state energy was calculated using the PBE exchange correlation +functional in combination of the Tier2 basis set. The global resolution of identity (RI-V) approach was used for the +calculation of the exact exchange and RPA correlation energy. The auxiliary basis functions for the RI-V method were +generated automatically on the fly. + +--- diff --git a/docs/img/ch4_bench.png b/docs/img/ch4_bench.png new file mode 100644 index 00000000..fd3a5c43 Binary files /dev/null and b/docs/img/ch4_bench.png differ diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..6faad533 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,18 @@ +--- +layout: page +title: GreenX Library +tagline: GreenX +description: Library for Many-body Greens Functions on HPC +--- + +# GreenX + +A new open-source exascale library of Green-function-based methodologies. Its layered design will separate higher-level +functionalities (distinguishing between code-independent and code-family-specific parts) from architecture-dependent +numerical routines, common to all code families. + +## Components + +- [Minimax Time-Frequency](gx_time_frequency.md) + +--- \ No newline at end of file diff --git a/docs/pages/gx_time_frequency.html b/docs/pages/gx_time_frequency.html new file mode 100644 index 00000000..e69de29b