The PSML format and library for norm-conserving pseudopotential data curation and interoperability

Alberto García; Matthieu J. Verstraete; Yann Pouillon; Javier Junquera

doi:10.1016/j.cpc.2018.02.011

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

Alberto García^*
, Matthieu J. Verstraete
, Yann Pouillon
, Javier Junquera

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability. Program summary: Program title: libPSML Program Files doi: http://dx.doi.org/10.17632/3pgbsjy4vf.1 Licensing provisions: BSD 3-clause Programming language: Fortran External routines/libraries: xmlf90 for XML handling in Fortran (http://launchpad.net/xmlf90) Nature of problem: Enhancing the interoperability of electronic-structure codes by sharing pseudopotential data Solution method: Create an XML-based pseudopotential format (PSML), complete with a formal schema, and a processing library (libPSML) that transparently connects client codes to the information in the format. References: http://esl.cecam.org/PSML

Original language	English
Pages (from-to)	51-71
Number of pages	21
Journal	Computer Physics Communications
Volume	227
DOIs	https://doi.org/10.1016/j.cpc.2018.02.011
Publication status	Published - Jun 2018
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2018 The Author(s)

Funding

We thank Xavier Gonze in particular for backing this project and providing useful comments. Many constructive discussions are acknowledged with Don Hamann, Matteo Giantomassi, Michiel Van Setten, Paolo Giannozzi, Gian-Marco Rignanese, and François Gygi. This work was supported by CECAM through the Electronic Structure Library (ESL) initiative and the ETSF through the libpspio project. MJV acknowledges support from ULg and CfWB through ARC projects AIMED and TheMoTherm ( GA 15/19-09 and 10/15-03 ) and a FNRS PDR project ( GA T.1077.15-1/7 ). A.G. was funded by EU H2020 grant 676598 (“MaX: Materials at the eXascale” CoE), Spain’s MINECO (grants FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P , and the “Severo Ochoa” Program grant SEV-2015-0496 ), and GenCat ( 2014 SGR 301 ). JJ and YP acknowledge support from Spain’s MINECO (grants RTC-2016-5681-7 and FIS2015-64886-C5-2-P ). Appendix A

Funders	Funder number
GA 15/19-09, 10/15-03
CECAM
ETSF
EU H2020
FNRS PDR	GA T.1077.15-1/7
MINECO	SEV-2015-0496, FIS2015-64886-C5-4-P, 2014 SGR 301, FIS2012-37549-C05-05
Spain’s MINECO	FIS2015-64886-C5-2-P, RTC-2016-5681-7
Horizon 2020 Framework Programme	676598

Keywords

Density functional
Electronic structure
Pseudopotential

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10.1016/j.cpc.2018.02.011

Cite this

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title = "The PSML format and library for norm-conserving pseudopotential data curation and interoperability",

abstract = "Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability. Program summary: Program title: libPSML Program Files doi: http://dx.doi.org/10.17632/3pgbsjy4vf.1 Licensing provisions: BSD 3-clause Programming language: Fortran External routines/libraries: xmlf90 for XML handling in Fortran (http://launchpad.net/xmlf90) Nature of problem: Enhancing the interoperability of electronic-structure codes by sharing pseudopotential data Solution method: Create an XML-based pseudopotential format (PSML), complete with a formal schema, and a processing library (libPSML) that transparently connects client codes to the information in the format. References: http://esl.cecam.org/PSML",

keywords = "Density functional, Electronic structure, Pseudopotential",

author = "Alberto Garc{\'i}a and Verstraete, \{Matthieu J.\} and Yann Pouillon and Javier Junquera",

note = "Publisher Copyright: {\textcopyright} 2018 The Author(s)",

year = "2018",

month = jun,

doi = "10.1016/j.cpc.2018.02.011",

language = "English",

volume = "227",

pages = "51--71",

journal = "Computer Physics Communications",

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T1 - The PSML format and library for norm-conserving pseudopotential data curation and interoperability

AU - García, Alberto

AU - Verstraete, Matthieu J.

AU - Pouillon, Yann

AU - Junquera, Javier

PY - 2018/6

Y1 - 2018/6

N2 - Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability. Program summary: Program title: libPSML Program Files doi: http://dx.doi.org/10.17632/3pgbsjy4vf.1 Licensing provisions: BSD 3-clause Programming language: Fortran External routines/libraries: xmlf90 for XML handling in Fortran (http://launchpad.net/xmlf90) Nature of problem: Enhancing the interoperability of electronic-structure codes by sharing pseudopotential data Solution method: Create an XML-based pseudopotential format (PSML), complete with a formal schema, and a processing library (libPSML) that transparently connects client codes to the information in the format. References: http://esl.cecam.org/PSML

AB - Norm-conserving pseudopotentials are used by a significant number of electronic-structure packages, but the practical differences among codes in the handling of the associated data hinder their interoperability and make it difficult to compare their results. At the same time, existing formats lack provenance data, which makes it difficult to track and document computational workflows. To address these problems, we first propose a file format (PSML) that maps the basic concepts of the norm-conserving pseudopotential domain in a flexible form and supports the inclusion of provenance information and other important metadata. Second, we provide a software library (libPSML) that can be used by electronic structure codes to transparently extract the information in the file and adapt it to their own data structures, or to create converters for other formats. Support for the new file format has been already implemented in several pseudopotential generator programs (including ATOM and ONCVPSP), and the library has been linked with SIESTA and ABINIT, allowing them to work with the same pseudopotential operator (with the same local part and fully non-local projectors) thus easing the comparison of their results for the structural and electronic properties, as shown for several example systems. This methodology can be easily transferred to any other package that uses norm-conserving pseudopotentials, and offers a proof-of-concept for a general approach to interoperability. Program summary: Program title: libPSML Program Files doi: http://dx.doi.org/10.17632/3pgbsjy4vf.1 Licensing provisions: BSD 3-clause Programming language: Fortran External routines/libraries: xmlf90 for XML handling in Fortran (http://launchpad.net/xmlf90) Nature of problem: Enhancing the interoperability of electronic-structure codes by sharing pseudopotential data Solution method: Create an XML-based pseudopotential format (PSML), complete with a formal schema, and a processing library (libPSML) that transparently connects client codes to the information in the format. References: http://esl.cecam.org/PSML

KW - Density functional

KW - Electronic structure

KW - Pseudopotential

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M3 - Article

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ER -

The PSML format and library for norm-conserving pseudopotential data curation and interoperability

Abstract

Bibliographical note

Funding

Keywords

Access to Document

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