Quack OK, QP in progress
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#+TITLE: ERC PTEROSOR : Data Management Plan
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#+AUTHOR: A. Scemama, P.-F. Loos
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#+DATE: 2020-06-05
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* Project details
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|------------------------+---------------------------------------------|
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| Title | PTEROSOR |
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| Funder | European Research Council, ERC |
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| Number | 863481 |
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| Principal Investigator | Pierre-Francois Loos |
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| ORCID iD | 0000-0003-0598-7425 |
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| Affiliation | Laboratoire de Chimie et Phisque Quantiques |
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| | (LCPQ) CNRS |
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| Data Contact Person | Anthony Scemama |
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|------------------------+---------------------------------------------|
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** Summary
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Catalysis and solar cell technologies are underpinned by a fundamental
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process: that of exciting systems to a higher energy level than the
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ground state. Defining an effective method to achieve this that also
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provides accurate energies of the excited states is often a
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challenge. The EU-funded PTEROSOR project will tackle this fundamental
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problem using mathematical techniques. The researchers' novel approach
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for measuring the energies of excited states and defining wave
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functions in molecular systems will hinge on the use of a general
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class of Hamiltonians with parity-time (PT) symmetry. The gateway
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between ground and excited states will be provided by exceptional
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points which lie at the boundary between broken and unbroken
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PT-symmetric regions.
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** Research outputs
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1. QuAcK (Software)
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2. Quantum Package (Software)
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3. Notebooks (Interactive Resource)
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4. Publications (Text)
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* QuAcK
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** Dataset summary
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#+BEGIN_EXAMPLE
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This should include:
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dataset reference and name
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origin and expected size of the data generated/collected
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data types and formats
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#+END_EXAMPLE
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QuAcK is a small quantum chemistry package written in Fortran by the
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coordinator of the project. It is mostly used for prototyping.
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The size of the archive containing the source code is around 4MiB, and
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is composed of Fortran source files, Python and Bash scripts, and
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Makefiles.
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Quantum Package is an open-source quantum chemistry package for
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performing selected configuration interaction calculations with
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perturbation theory for molecules and solids.
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The project was initiated in 2015 at the LCPQ, and it is now
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developed on three sites : Toulouse (LCPQ Toulouse, France), Paris
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(LCT Paris, France) and Argonne (USA). Quantum Package is one of
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the flagship codes of the TREX European Center of Excellence.
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The size of the archive is around 11MiB, and is composed of IRPF90
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source files, Python, Bash scripts, Makefiles and standard atomic
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basis sets and pseudo-potentials.
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** FAIR data and resources
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*** Making data findable
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#+BEGIN_EXAMPLE
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This should consider the dataset description: metadata, persistent
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and unique identifiers e.g., DOI
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#+END_EXAMPLE
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QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a
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mirror on the Git repository of the LCPQ
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(https://git.irsamc.ups-tlse.fr/scemama/quack). The latest
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version was uploaded on Zenodo (doi:10.5281/zenodo.3745928).
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Quantum Package is hosted on GitHub
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(https://github.com/QuantumPackage/qp2), with a mirror on the Git
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repository of the LCPQ (https://git.irsamc.ups-tlse.fr/LCPQ/qp2).
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The latest version of the program was presented in a [[doi:10.1021/acs.jctc.9b00176][peer-reviewed
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article]], and the corresponding preprint was published on [[https://arxiv.org/abs/1902.08154][ArXiv]] and [[https://hal.archives-ouvertes.fr/hal-02045595][HAL]].
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The associated source code was uploaded on Zenodo
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(doi:10.5281/zenodo.3677565), and the source code contains a
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=CITATION.cff= file providing metadata in standard YAML format.
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Quantum Package has its dedicated website
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(https://quantumpackage.github.io/qp2) providing links to the
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GitHub repository, the documentation
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(https://quantum-package.readthedocs.io), and video tutorials
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hosted on a YouTube channel
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(https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum
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Package has also a twitter account (=@quantum_package=).
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We plan to submit all the source codes involved in this project to
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the [[https://www.softwareheritage.org][Software Heritage]] archive.
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*** Making data openly accessible
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#+BEGIN_EXAMPLE
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* Which data will be made openly available and if some datasets remain closed,
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the reasons for not giving access?
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* Where the data and associated metadata, documentation and code are deposited
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(which repository)?
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* How the data can be accessed? Are relevant software tools/methods provided?
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#+END_EXAMPLE
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QuAcK is released under the GPL v3 license.
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Quantum Package is released under the AGPL v3 license.
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Both GitHub repositories are set up to automatically upload on
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Zenodo every new release. For each publication requiring a
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modification of the source code, a release will be made and the
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Zenodo DOI will be cited.
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The project doesn't require any part of the codes to be closed.
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*** Making data interoperable
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#+BEGIN_EXAMPLE
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Which standard or field-specific data and metadata vocabularies
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and methods will be used?
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#+END_EXAMPLE
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QuAcK operates internally with text files.
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Standard =xyz= format is used for atomic coordinates and =GAMESS/US=
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format for atomic basis sets is used. The Basis Set Exchange (BSE)
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website (https://www.basissetexchange.org) provides data in this
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format.
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*** Increase data reuse
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#+BEGIN_EXAMPLE
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* What data will remain re-usable and for how long?
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* Is embargo foreseen?
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* How the data is licensed?
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* Any data quality assurance procedures?
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#+END_EXAMPLE
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Along the project, the code will be structured in independent
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inter-operating components to make easier the extraction of a
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particular feature of the package.
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Continuous integration will be set up to guarantee that the package is
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functional in the main branch. Developments will be made in a
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secondary development branch.
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*** Allocation of resources and data security
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#+BEGIN_EXAMPLE
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* Estimated costs for making the project data open access and potential value
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of long-term data preservation.
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* Procedures for data backup and recovery.
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* Transfer of sensitive data and secure storage in repositories for long term
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preservation and curation.
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#+END_EXAMPLE
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The mirroring of the GitHub repository in the institute of the
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coordinator provides a backup.
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The automatic upload of new releases on Zenodo provides secure storage
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and long-term preservation of the source code.
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We also plan to upload the code in the Software Heritage digital
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archive.
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** Quantum Package
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Quantum Package is an open-source quantum chemistry package for
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performing selected configuration interaction calculations. It is
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developed on three sites : Toulouse (LCPQ), Paris (LCT) and Argonne
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(USA).
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The code is under the AGPL v3 license and is hosted on GitHub
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(https://github.com/QuantumPackage/qp2), with a mirror on the Git
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repository of the institute of the coordinator of the project
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(https://git.irsamc.ups-tlse.fr/LCPQ/qp2).
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The latest version was uploaded on Zenodo
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(doi:10.5281/zenodo.3677565), and the GitHub repository is set up to
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automatically upload on Zenodo every new release. For each publication
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requiring a modification of Quantum Package, a release will be made
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and the zenodo DOI will be cited.
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** Notebooks
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All along the project, Mathematica / Jupyter / Org-mode notebooks will
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be produced. All this data will be versioned in the Git repository of
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the LCPQ (https://git.irsamc.ups-tlse.fr),
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publicly accessible. All the notebooks will be archived on Zenodo, and
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the DOIs will be provided in publications.
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** Publications
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