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@ -1,7 +1,22 @@
#+TITLE: ERC PTEROSOR : Data Management Plan # -*- mode: org; org-confirm-babel-evaluate: nil; org-babel-noweb-wrap-start: "«"; org-babel-noweb-wrap-end: "»"; -*-
#+AUTHOR: A. Scemama, P.-F. Loos
#+DATE: 2020-06-05
#+TITLE: ERC PTEROSOR
#+SUBTITLE: Data Management Plan
#+AUTHOR: A. Scemama, P.-F. Loos
#+EMAIL: scemama@irsamc.ups-tlse.fr
#+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:
#+DESCRIPTION: Org-mode document for LaTeX export
#+KEYWORDS: Software, Notebooks, Publications, Presentations
#+LATEX_COMPILER: pdflatex
#+OPTIONS: tags:t tasks:t tex:t timestamp:t toc:nil todo:t |:t
#+SELECT_TAGS: export
#+EXCLUDE_TAGS: noexport nolatex
* Project details * Project details
@ -37,23 +52,13 @@ PT-symmetric regions.
1. QuAcK (Software) 1. QuAcK (Software)
2. Quantum Package (Software) 2. Quantum Package (Software)
3. Notebooks (Interactive Resource) 3. Notebooks (Interactive Resource)
4. Publications (Text) 4. Textual data (Text)
* QuAcK * QuAcK
** Dataset summary ** Dataset summary
#+BEGIN_EXAMPLE
This should include:
dataset reference and name
origin and expected size of the data generated/collected
data types and formats
#+END_EXAMPLE
QuAcK is a small quantum chemistry package written in Fortran by the QuAcK is a small quantum chemistry package written in Fortran by the
coordinator of the project. It is mostly used for prototyping. coordinator of the project. It is mostly used for prototyping.
@ -72,15 +77,30 @@ This should include:
source files, Python, Bash scripts, Makefiles and standard atomic source files, Python, Bash scripts, Makefiles and standard atomic
basis sets and pseudo-potentials. 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
** FAIR data and resources ** FAIR data and resources
*** Making data findable *** Making data findable
#+BEGIN_EXAMPLE
This should consider the dataset description: metadata, persistent
and unique identifiers e.g., DOI
#+END_EXAMPLE
QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a
mirror on the Git repository of the LCPQ mirror on the Git repository of the LCPQ
@ -103,17 +123,28 @@ and unique identifiers e.g., DOI
(https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum (https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum
Package has also a twitter account (=@quantum_package=). 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, 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 We plan to submit all the source codes involved in this project to
the [[https://www.softwareheritage.org][Software Heritage]] archive. 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 *** Making data openly accessible
#+BEGIN_EXAMPLE
* 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?
#+END_EXAMPLE
QuAcK is released under the GPL v3 license. QuAcK is released under the GPL v3 license.
Quantum Package is released under the AGPL v3 license. Quantum Package is released under the AGPL v3 license.
@ -125,12 +156,15 @@ and unique identifiers e.g., DOI
The project doesn't require any part of the codes to be closed. The project doesn't require any part of the codes to be closed.
*** Making data interoperable **** Guidelines :noexport:
#+BEGIN_EXAMPLE * Which data will be made openly available and if some datasets remain closed,
Which standard or field-specific data and metadata vocabularies the reasons for not giving access?
and methods will be used? * Where the data and associated metadata, documentation and code are deposited
#+END_EXAMPLE (which repository)?
* How the data can be accessed? Are relevant software tools/methods provided?
*** Making data interoperable
QuAcK operates internally with text files. QuAcK operates internally with text files.
Standard =xyz= format is used for atomic coordinates and =GAMESS/US= Standard =xyz= format is used for atomic coordinates and =GAMESS/US=
@ -138,14 +172,12 @@ and unique identifiers e.g., DOI
website (https://www.basissetexchange.org) provides data in this website (https://www.basissetexchange.org) provides data in this
format. format.
**** Guidelines :noexport:
Which standard or field-specific data and metadata vocabularies
and methods will be used?
*** Increase data reuse *** Increase data reuse
#+BEGIN_EXAMPLE
* What data will remain re-usable and for how long?
* Is embargo foreseen?
* How the data is licensed?
* Any data quality assurance procedures?
#+END_EXAMPLE
Along the project, the code will be structured in independent Along the project, the code will be structured in independent
inter-operating components to make easier the extraction of a inter-operating components to make easier the extraction of a
@ -155,15 +187,13 @@ and unique identifiers e.g., DOI
functional in the main branch. Developments will be made in a functional in the main branch. Developments will be made in a
secondary development branch. secondary development branch.
**** 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
#+BEGIN_EXAMPLE
* Estimated costs for making the project data open access and potential value
of long-term data preservation.
* Procedures for data backup and recovery.
* Transfer of sensitive data and secure storage in repositories for long term
preservation and curation.
#+END_EXAMPLE
The mirroring of the GitHub repository in the institute of the The mirroring of the GitHub repository in the institute of the
coordinator provides a backup. coordinator provides a backup.
@ -174,36 +204,14 @@ and unique identifiers e.g., DOI
We also plan to upload the code in the Software Heritage digital We also plan to upload the code in the Software Heritage digital
archive. archive.
**** Guidelines :noexport:
* Estimated costs for making the project data open access and potential value
** Quantum Package of long-term data preservation.
* Procedures for data backup and recovery.
Quantum Package is an open-source quantum chemistry package for * Transfer of sensitive data and secure storage in repositories for long term
performing selected configuration interaction calculations. It is preservation and curation.
developed on three sites : Toulouse (LCPQ), Paris (LCT) and Argonne
(USA).
The code is under the AGPL v3 license and is hosted on GitHub
(https://github.com/QuantumPackage/qp2), with a mirror on the Git
repository of the institute of the coordinator of the project
(https://git.irsamc.ups-tlse.fr/LCPQ/qp2).
The latest version was uploaded on Zenodo
(doi:10.5281/zenodo.3677565), and the GitHub repository is set up to
automatically upload on Zenodo every new release. For each publication
requiring a modification of Quantum Package, a release will be made
and the zenodo DOI will be cited.
** Notebooks
All along the project, Mathematica / Jupyter / Org-mode notebooks will
be produced. All this data will be versioned in the Git repository of
the LCPQ (https://git.irsamc.ups-tlse.fr),
publicly accessible. All the notebooks will be archived on Zenodo, and
the DOIs will be provided in publications.
** Publications