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#+TITLE: ERC PTEROSOR : Data Management Plan
#+AUTHOR: A. Scemama, P.-F. Loos
#+DATE: 2020-06-05
* Project details
|------------------------+---------------------------------------------|
| 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 |
|------------------------+---------------------------------------------|
** 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.
** Research outputs
1. QuAcK (Software)
2. Quantum Package (Software)
3. Notebooks (Interactive Resource)
4. Publications (Text)
* QuAcK
** 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
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.
** FAIR data and resources
*** 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
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=).
We plan to submit all the source codes involved in this project to
the [[https://www.softwareheritage.org][Software Heritage]] archive.
*** 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.
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 closed.
*** Making data interoperable
#+BEGIN_EXAMPLE
Which standard or field-specific data and metadata vocabularies
and methods will be used?
#+END_EXAMPLE
QuAcK operates internally with text files.
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.
*** 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
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.
*** 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
coordinator provides a backup.
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.
** Quantum Package
Quantum Package is an open-source quantum chemistry package for
performing selected configuration interaction calculations. It is
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