From b3515117a14d8e8981ba978404decbe3eb47c1b7 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Fri, 5 Jun 2020 20:13:34 +0200 Subject: [PATCH] Quack OK, QP in progress --- dmp.org | 209 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 209 insertions(+) create mode 100644 dmp.org diff --git a/dmp.org b/dmp.org new file mode 100644 index 0000000..b9e8db9 --- /dev/null +++ b/dmp.org @@ -0,0 +1,209 @@ +#+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 + + +