diff --git a/DMP-PTEROSOR.pdf b/DMP-PTEROSOR.pdf new file mode 100644 index 0000000..d4c9230 Binary files /dev/null and b/DMP-PTEROSOR.pdf differ diff --git a/DMP-PTEROSOR.tex b/DMP-PTEROSOR.tex new file mode 100644 index 0000000..5c364a6 --- /dev/null +++ b/DMP-PTEROSOR.tex @@ -0,0 +1,206 @@ +% Created 2020-06-30 Tue 19:22 +% Intended LaTeX compiler: pdflatex +\documentclass[12pt,onecolumn,notitlepage]{revtex4-1} +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} +\usepackage{graphicx} +\usepackage{grffile} +\usepackage{longtable} +\usepackage{wrapfig} +\usepackage{rotating} +\usepackage[normalem]{ulem} +\usepackage{amsmath} +\usepackage{textcomp} +\usepackage{amssymb} +\usepackage{capt-of} +\usepackage{mathpazo,amssymb} +\usepackage[pdftex]{hyperref} +\hypersetup{colorlinks=true} +\begin{document} +\author{A. Scemama, P.-F. Loos} +\date{\today} +\title{ERC PTEROSOR\\\medskip +\large Data Management Plan} +\hypersetup{ + pdfauthor={A. Scemama, P.-F. Loos}, + pdftitle={ERC PTEROSOR}, + pdfkeywords={Software, Notebooks, Publications, Presentations}, + pdfsubject={Org-mode document for \LaTeX{} export}, + pdfcreator={Emacs 26.3 (Org mode 9.1.9)}, + pdflang={English}} + +\maketitle + +\section{Project details} +\label{sec:org2420f0d} + +\begin{center} +\begin{tabular}{ll} +\hline +Title & PTEROSOR\\ +Funder & European Research Council, ERC\\ +Number & 863481\\ +Principal Investigator & Pierre-Francois Loos\\ +ORCID iD & 0000-0003-0598-7425\\ +Affiliation & Laboratoire de Chimie et Phisque Quantiques\\ + & (LCPQ) CNRS\\ +Data Contact Person & Anthony Scemama\\ +\hline +\end{tabular} +\end{center} + +\section{Summary} +\label{sec:org6ff096b} + +Catalysis and solar cell technologies are underpinned by a fundamental +process: that of exciting systems to a higher energy level than the +ground state. Defining an effective method to achieve this that also +provides accurate energies of the excited states is often a +challenge. The EU-funded PTEROSOR project will tackle this fundamental +problem using mathematical techniques. The researchers' novel approach +for measuring the energies of excited states and defining wave +functions in molecular systems will hinge on the use of a general +class of Hamiltonians with parity-time (PT) symmetry. The gateway +between ground and excited states will be provided by exceptional +points which lie at the boundary between broken and unbroken +PT-symmetric regions. + + +\section{Research outputs} +\label{sec:org86ec923} + +\begin{enumerate} +\item QuAcK (Software) +\item Quantum Package (Software) +\item Notebooks (Interactive Resource) +\item Textual data (Text) +\end{enumerate} + + + +\section{Dataset summary} +\label{sec:org102e22d} + +QuAcK is a small quantum chemistry package written in Fortran by the +coordinator of the project. It is mostly used for prototyping. +The size of the archive containing the source code is around 4MiB, and +is composed of Fortran source files, Python and Bash scripts, and +Makefiles. + +Quantum Package is an open-source quantum chemistry package for +performing selected configuration interaction calculations with +perturbation theory for molecules and solids. +The project was initiated in 2015 at the LCPQ, and it is now +developed on three sites : Toulouse (LCPQ Toulouse, France), Paris +(LCT Paris, France) and Argonne (USA). Quantum Package is one of +the flagship codes of the TREX European Center of Excellence. +The size of the archive is around 11MiB, and is composed of IRPF90 +source files, Python, Bash scripts, Makefiles and standard atomic +basis sets and pseudo-potentials. + +All along the project, Mathematica / Jupyter / Org-mode notebooks will +be produced by researchers and students. Each notebook will take a +few megabytes. + +PDF files for reports, publications, presentations and posters will +be produced in this project. Each pdf file will take a few megabytes. +Care will be taken to maintain the size of these documents as small +as possible. + + + + +\section{FAIR data and resources} +\label{sec:orgb381d48} + +\subsection{Making data findable} +\label{sec:orgede707c} + +QuAcK is hosted on GitHub (\url{https://github.com/pfloos/quack}), with a +mirror on the Git repository of the LCPQ +(\url{https://git.irsamc.ups-tlse.fr/scemama/quack}). The latest +version was uploaded on Zenodo (\url{doi:10.5281/zenodo.3745928}). + +Quantum Package is hosted on GitHub +(\url{https://github.com/QuantumPackage/qp2}), with a mirror on the Git +repository of the LCPQ (\url{https://git.irsamc.ups-tlse.fr/LCPQ/qp2}). +The latest version of the program was presented in a \href{doi:10.1021/acs.jctc.9b00176}{peer-reviewed +article}, and the corresponding preprint was published on \href{https://arxiv.org/abs/1902.08154}{ArXiv} and \href{https://hal.archives-ouvertes.fr/hal-02045595}{HAL}. +The associated source code was uploaded on Zenodo +(\url{doi:10.5281/zenodo.3677565}), and the source code contains a +\texttt{CITATION.cff} file providing metadata in standard YAML format. +Quantum Package has its dedicated website +(\url{https://quantumpackage.github.io/qp2}) providing links to the +GitHub repository, the documentation +(\url{https://quantum-package.readthedocs.io}), and video tutorials +hosted on a YouTube channel +(\url{https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw}). Quantum +Package has also a twitter account (\texttt{@quantum\_package}). + +All the notebooks will be versioned in the Git repository of the LCPQ +(\url{https://git.irsamc.ups-tlse.fr}), publicly accessible. +These documents will be archived on Figshare or Zenodo, and the +DOIs will be provided in publications. + +The \LaTeX{} source files relative to reports, publications, +presentations and posters will be versioned in the Git repository +of the LCPQ, publicly accessible. + +We plan to submit all the source codes involved in this project to +the \href{https://www.softwareheritage.org}{Software Heritage} archive. + +A web site for the project will be created, centralizing all the +links to the archived data. Care will be taken to provide useful +metadata in the HTML headers to help the search engines reference +this web site. + +\subsection{Making data openly accessible} +\label{sec:orge50b55e} + +QuAcK is released under the GPL v3 license. +Quantum Package is released under the AGPL v3 license. + +Both GitHub repositories are set up to automatically upload on +Zenodo every new release. For each publication requiring a +modification of the source code, a release will be made and the +Zenodo DOI will be cited. + +The project doesn't require any part of the codes to be confidential. + +\subsection{Making data interoperable} +\label{sec:org88e2f8b} +Standard \texttt{xyz} format is used for atomic coordinates and \texttt{GAMESS/US} +format for atomic basis sets is used. The Basis Set Exchange (BSE) +website (\url{https://www.basissetexchange.org}) provides data in this +format. + +Quantum Package is already interfaced with multiple codes of the +community (GAMESS, Molpro, Gaussian, QMCPack, QMC=Chem, \ldots{}) + +QuAcK operates internally with text files, using the same +conventions as Quantum Package. Hence, the two codes are +compatible and easily interoperable. + +\subsection{Increase data reuse} +\label{sec:org91c0714} + +Along the project, the code will be structured in independent +inter-operating components to make easier the extraction of a +particular feature of the package. + +Continuous integration will be set up to guarantee that the package is +functional in the main branch. Developments will be made in a +secondary development branch. + +\subsection{Allocation of resources and data security} +\label{sec:org7d33d8b} + +The mirroring of the GitHub repository in the institute of the +coordinator provides a backup of both QuAcK and Quantum Package. + +The automatic upload of new releases on Zenodo provides secure storage +and long-term preservation of the source code. + +We also plan to upload the code in the Software Heritage digital +archive. +\end{document} diff --git a/dmp.org b/dmp.org index ea28ae1..40888be 100644 --- a/dmp.org +++ b/dmp.org @@ -7,10 +7,11 @@ #+DATE: \today #+LANGUAGE: English #+EXPORT_FILE_NAME: DMP-PTEROSOR.pdf -#+LATEX_CLASS: revtex4-1 -#+LATEX_CLASS_OPTIONS: aip,jcp,showkeys -#+LATEX_HEADER: \usepackage{mathpazo,hyperref,amssymb} -#+LATEX_HEADER_EXTRA: +#+LATEX_CLASS: article +#+LATEX_CLASS_OPTIONS: [12pt,reprint] +#+LATEX_HEADER: \usepackage{mathpazo,amssymb} +#+LATEX_HEADER: \usepackage[pdftex]{hyperref} +#+LATEX_HEADER_EXTRA: \hypersetup{colorlinks=true} #+DESCRIPTION: Org-mode document for LaTeX export #+KEYWORDS: Software, Notebooks, Publications, Presentations #+LATEX_COMPILER: pdflatex @@ -31,184 +32,182 @@ | Data Contact Person | Anthony Scemama | |------------------------+---------------------------------------------| -** Summary +* Summary -Catalysis and solar cell technologies are underpinned by a fundamental -process: that of exciting systems to a higher energy level than the -ground state. Defining an effective method to achieve this that also -provides accurate energies of the excited states is often a -challenge. The EU-funded PTEROSOR project will tackle this fundamental -problem using mathematical techniques. The researchers' novel approach -for measuring the energies of excited states and defining wave -functions in molecular systems will hinge on the use of a general -class of Hamiltonians with parity-time (PT) symmetry. The gateway -between ground and excited states will be provided by exceptional -points which lie at the boundary between broken and unbroken -PT-symmetric regions. + Catalysis and solar cell technologies are underpinned by a fundamental + process: that of exciting systems to a higher energy level than the + ground state. Defining an effective method to achieve this that also + provides accurate energies of the excited states is often a + challenge. The EU-funded PTEROSOR project will tackle this fundamental + problem using mathematical techniques. The researchers' novel approach + for measuring the energies of excited states and defining wave + functions in molecular systems will hinge on the use of a general + class of Hamiltonians with parity-time (PT) symmetry. The gateway + between ground and excited states will be provided by exceptional + points which lie at the boundary between broken and unbroken + PT-symmetric regions. -** Research outputs +* Research outputs - 1. QuAcK (Software) - 2. Quantum Package (Software) - 3. Notebooks (Interactive Resource) - 4. Textual data (Text) + 1. QuAcK (Software) + 2. Quantum Package (Software) + 3. Notebooks (Interactive Resource) + 4. Textual data (Text) + + + +* Dataset summary + + QuAcK is a small quantum chemistry package written in Fortran by the + coordinator of the project. It is mostly used for prototyping. + The size of the archive containing the source code is around 4MiB, and + is composed of Fortran source files, Python and Bash scripts, and + Makefiles. + + Quantum Package is an open-source quantum chemistry package for + performing selected configuration interaction calculations with + perturbation theory for molecules and solids. + The project was initiated in 2015 at the LCPQ, and it is now + developed on three sites : Toulouse (LCPQ Toulouse, France), Paris + (LCT Paris, France) and Argonne (USA). Quantum Package is one of + the flagship codes of the TREX European Center of Excellence. + The size of the archive is around 11MiB, and is composed of IRPF90 + source files, Python, Bash scripts, Makefiles and standard atomic + basis sets and pseudo-potentials. + + All along the project, Mathematica / Jupyter / Org-mode notebooks will + be produced by researchers and students. Each notebook will take a + few megabytes. + + PDF files for reports, publications, presentations and posters will + be produced in this project. Each pdf file will take a few megabytes. + Care will be taken to maintain the size of these documents as small + as possible. + +** Guidelines :noexport: + This should include: + + dataset reference and name + + origin and expected size of the data generated/collected + + data types and formats -* QuAcK + +* FAIR data and resources -** Dataset summary +** Making data findable - QuAcK is a small quantum chemistry package written in Fortran by the - coordinator of the project. It is mostly used for prototyping. - The size of the archive containing the source code is around 4MiB, and - is composed of Fortran source files, Python and Bash scripts, and - Makefiles. + QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a + mirror on the Git repository of the LCPQ + (https://git.irsamc.ups-tlse.fr/scemama/quack). The latest + version was uploaded on Zenodo (doi:10.5281/zenodo.3745928). - Quantum Package is an open-source quantum chemistry package for - performing selected configuration interaction calculations with - perturbation theory for molecules and solids. - The project was initiated in 2015 at the LCPQ, and it is now - developed on three sites : Toulouse (LCPQ Toulouse, France), Paris - (LCT Paris, France) and Argonne (USA). Quantum Package is one of - the flagship codes of the TREX European Center of Excellence. - The size of the archive is around 11MiB, and is composed of IRPF90 - source files, Python, Bash scripts, Makefiles and standard atomic - basis sets and pseudo-potentials. + Quantum Package is hosted on GitHub + (https://github.com/QuantumPackage/qp2), with a mirror on the Git + repository of the LCPQ (https://git.irsamc.ups-tlse.fr/LCPQ/qp2). + The latest version of the program was presented in a [[doi:10.1021/acs.jctc.9b00176][peer-reviewed + article]], and the corresponding preprint was published on [[https://arxiv.org/abs/1902.08154][ArXiv]] and [[https://hal.archives-ouvertes.fr/hal-02045595][HAL]]. + The associated source code was uploaded on Zenodo + (doi:10.5281/zenodo.3677565), and the source code contains a + =CITATION.cff= file providing metadata in standard YAML format. + Quantum Package has its dedicated website + (https://quantumpackage.github.io/qp2) providing links to the + GitHub repository, the documentation + (https://quantum-package.readthedocs.io), and video tutorials + hosted on a YouTube channel + (https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum + Package has also a twitter account (=@quantum_package=). - All along the project, Mathematica / Jupyter / Org-mode notebooks will - be produced by researchers and students. Each notebook will take a - few megabytes. + All the notebooks will be versioned in the Git repository of the LCPQ + (https://git.irsamc.ups-tlse.fr), publicly accessible. + These documents will be archived on Figshare or Zenodo, and the + DOIs will be provided in publications. + + The LaTeX source files relative to reports, publications, + presentations and posters will be versioned in the Git repository + of the LCPQ, publicly accessible. - PDF files for reports, publications, presentations and posters will - be produced in this project. Each pdf file will take a few megabytes. - Care will be taken to maintain the size of these documents as small - as possible. + We plan to submit all the source codes involved in this project to + the [[https://www.softwareheritage.org][Software Heritage]] archive. + + A web site for the project will be created, centralizing all the + links to the archived data. Care will be taken to provide useful + metadata in the HTML headers to help the search engines reference + this web site. *** Guidelines :noexport: - This should include: + This should consider the dataset description: metadata, persistent + and unique identifiers e.g., DOI - dataset reference and name +** Making data openly accessible - origin and expected size of the data generated/collected + QuAcK is released under the GPL v3 license. + Quantum Package is released under the AGPL v3 license. - data types and formats + Both GitHub repositories are set up to automatically upload on + Zenodo every new release. For each publication requiring a + modification of the source code, a release will be made and the + Zenodo DOI will be cited. + The project doesn't require any part of the codes to be confidential. - - -** FAIR data and resources - -*** Making data findable - - QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a - mirror on the Git repository of the LCPQ - (https://git.irsamc.ups-tlse.fr/scemama/quack). The latest - version was uploaded on Zenodo (doi:10.5281/zenodo.3745928). - - Quantum Package is hosted on GitHub - (https://github.com/QuantumPackage/qp2), with a mirror on the Git - repository of the LCPQ (https://git.irsamc.ups-tlse.fr/LCPQ/qp2). - The latest version of the program was presented in a [[doi:10.1021/acs.jctc.9b00176][peer-reviewed - article]], and the corresponding preprint was published on [[https://arxiv.org/abs/1902.08154][ArXiv]] and [[https://hal.archives-ouvertes.fr/hal-02045595][HAL]]. - The associated source code was uploaded on Zenodo - (doi:10.5281/zenodo.3677565), and the source code contains a - =CITATION.cff= file providing metadata in standard YAML format. - Quantum Package has its dedicated website - (https://quantumpackage.github.io/qp2) providing links to the - GitHub repository, the documentation - (https://quantum-package.readthedocs.io), and video tutorials - hosted on a YouTube channel - (https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum - Package has also a twitter account (=@quantum_package=). - - All the notebooks will be versioned in the Git repository of the LCPQ - (https://git.irsamc.ups-tlse.fr), publicly accessible. - These documents will be archived on Figshare or Zenodo, and the - DOIs will be provided in publications. - - The LaTeX source files relative to reports, publications, - presentations and posters will be versioned in the Git repository - of the LCPQ, publicly accessible. - - We plan to submit all the source codes involved in this project to - the [[https://www.softwareheritage.org][Software Heritage]] archive. - - A web site for the project will be created, centralizing all the - links to the archived data. Care will be taken to provide useful - metadata in the HTML headers to help the search engines reference - this web site. - -**** Guidelines :noexport: - This should consider the dataset description: metadata, persistent - and unique identifiers e.g., DOI - -*** Making data openly accessible - - QuAcK is released under the GPL v3 license. - Quantum Package is released under the AGPL v3 license. - - Both GitHub repositories are set up to automatically upload on - Zenodo every new release. For each publication requiring a - modification of the source code, a release will be made and the - Zenodo DOI will be cited. - - The project doesn't require any part of the codes to be confidential. - -**** Guidelines :noexport: +*** Guidelines :noexport: * Which data will be made openly available and if some datasets remain closed, the reasons for not giving access? * Where the data and associated metadata, documentation and code are deposited (which repository)? * How the data can be accessed? Are relevant software tools/methods provided? -*** Making data interoperable - Standard =xyz= format is used for atomic coordinates and =GAMESS/US= - format for atomic basis sets is used. The Basis Set Exchange (BSE) - website (https://www.basissetexchange.org) provides data in this - format. +** Making data interoperable + Standard =xyz= format is used for atomic coordinates and =GAMESS/US= + format for atomic basis sets is used. The Basis Set Exchange (BSE) + website (https://www.basissetexchange.org) provides data in this + format. - Quantum Package is already interfaced with multiple codes of the - community (GAMESS, Molpro, Gaussian, QMCPack, QMC=Chem, ...) + Quantum Package is already interfaced with multiple codes of the + community (GAMESS, Molpro, Gaussian, QMCPack, QMC=Chem, ...) - QuAcK operates internally with text files, using the same - conventions as Quantum Package. Hence, the two codes are - compatible and easily interoperable. + QuAcK operates internally with text files, using the same + conventions as Quantum Package. Hence, the two codes are + compatible and easily interoperable. -**** Guidelines :noexport: +*** Guidelines :noexport: Which standard or field-specific data and metadata vocabularies and methods will be used? -*** Increase data reuse +** Increase data reuse - Along the project, the code will be structured in independent - inter-operating components to make easier the extraction of a - particular feature of the package. + Along the project, the code will be structured in independent + inter-operating components to make easier the extraction of a + particular feature of the package. - Continuous integration will be set up to guarantee that the package is - functional in the main branch. Developments will be made in a - secondary development branch. + Continuous integration will be set up to guarantee that the package is + functional in the main branch. Developments will be made in a + secondary development branch. -**** Guidelines :noexport: +*** Guidelines :noexport: * What data will remain re-usable and for how long? * Is embargo foreseen? * How the data is licensed? * Any data quality assurance procedures? -*** Allocation of resources and data security +** Allocation of resources and data security - The mirroring of the GitHub repository in the institute of the - coordinator provides a backup of both QuAcK and Quantum Package. + The mirroring of the GitHub repository in the institute of the + coordinator provides a backup of both QuAcK and Quantum Package. - The automatic upload of new releases on Zenodo provides secure storage - and long-term preservation of the source code. + The automatic upload of new releases on Zenodo provides secure storage + and long-term preservation of the source code. - We also plan to upload the code in the Software Heritage digital - archive. + We also plan to upload the code in the Software Heritage digital + archive. -**** Guidelines :noexport: +*** Guidelines :noexport: * Estimated costs for making the project data open access and potential value of long-term data preservation. * Procedures for data backup and recovery. diff --git a/patch b/patch new file mode 100644 index 0000000..2698058 --- /dev/null +++ b/patch @@ -0,0 +1,37 @@ +--- DMP-PTEROSOR.tex 2020-06-30 19:27:05.715752767 +0200 ++++ DMP-PTEROSOR_revtex.tex 2020-06-30 19:27:43.263090046 +0200 +@@ -1,6 +1,6 @@ + % Created 2020-06-30 Tue 19:22 + % Intended LaTeX compiler: pdflatex +-\documentclass[12pt,reprint]{article} ++\documentclass[12pt,onecolumn,notitlepage]{revtex4-1} + \usepackage[utf8]{inputenc} + \usepackage[T1]{fontenc} + \usepackage{graphicx} +@@ -13,10 +13,10 @@ + \usepackage{textcomp} + \usepackage{amssymb} + \usepackage{capt-of} +-\usepackage{hyperref} + \usepackage{mathpazo,amssymb} + \usepackage[pdftex]{hyperref} + \hypersetup{colorlinks=true} ++\begin{document} + \author{A. Scemama, P.-F. Loos} + \date{\today} + \title{ERC PTEROSOR\\\medskip +@@ -28,7 +28,6 @@ + pdfsubject={Org-mode document for \LaTeX{} export}, + pdfcreator={Emacs 26.3 (Org mode 9.1.9)}, + pdflang={English}} +-\begin{document} + + \maketitle + +@@ -204,4 +203,4 @@ + + We also plan to upload the code in the Software Heritage digital + archive. +-\end{document} +\ No newline at end of file ++\end{document}