Virtual Atomic And Molecular Data Center Research Articles

BASECOL2023 scientific content

Context. The global context of making numerous data produced by researchers available requires collecting and organising the data, assigning meaningful metadata, and presenting the data in a meaningful and homogeneous way. The BASECOL database, which collects inelastic rate coefficients for application to the interstellar medium and to circumstellar and cometary atmospheres, meets those requirements. Aims. We aim to present the scientific content of the BASECOL2023 edition. Methods. While the previous versions relied on finding rate coefficients in the literature, the current version is populated with published results sent by the producers of data. The paper presents the database, the type of data that can be found, the type of metadata that are used, and the Virtual Atomic and Molecular Data Centre (VAMDC) standards that are used for the metadata. Finally, we present the different datasets species by species. Results. As the BASECOL database, interconnected with the VAMDC e-infrastructure, uses the VAMDC standards, the collisional data can be extracted with tools using VAMDC standards and can be associated with spectroscopic data extracted from other VAMDC connected databases such as the Cologne database for molecular spectroscopy (CDMS), the jet propulsion laboratory molecular spectroscopy database (JPL), and the high-resolution transmission molecular absorption database (HITRAN).

Mass Spectra Resulting from Collision Processes

A new database and viewer for mass spectra resulting from collision processes is presented that follows the standards of the Virtual Atomic and Molecular Data Centre (VAMDC). A focus was placed on machine read and write access, as well as ease of use. In a browser-based viewer, mass spectra and all parameters related to a given measurement can be shown. The program additionally enables a direct comparison between two mass spectra, either by plotting them on top of each other or their difference to identify subtle variations in the data.

A Decade with VAMDC: Results and Ambitions

This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&M data from more than one database. Finally, we present our vision for the future of VAMDC.

Improvement of the NIFS Atom and Molecular Database

The NIFS (National Institute for Fusion Science) Atom and Molecular Database, which has been available online since 1997, is a numerical atomic and molecular database of collision processes that is important for fusion research. This database provides the following: (1) the cross-sections and rate coefficients for ionization, excitation, and recombination caused by electron impact; (2) the charge transfer caused by heavy particle collision and collision processes of molecules; and (3) the sputtering yields of solids and backscattering coefficients from solids. It also offers a bibliographic database. We recently reconstructed the database system. The main purpose of the reconstruction was to migrate the database into an open-source architecture to make the system more flexible and extensible. The previous system used proprietary software and was difficult to customize. The new system consists of open-source software, including PostgreSQL database and Ruby on Rails. New features were also added to the system. The most important improvement is the interface with the Virtual Atomic and Molecular Data Center (VAMDC) portal. Using this interface, researchers can search for data in the NIFS database as well as in various other online databases simultaneously.

BEAMDB and MOLD—Databases at the Serbian Virtual Observatory for Collisional and Radiative Processes

In this contribution we present a progress report on two atomic and molecular databases, BEAMDB and MolD, which are web services at the Serbian virtual observatory (SerVO) and nodes within the Virtual Atomic and Molecular Data Center (VAMDC). The Belgrade Electron/Atom (Molecule) DataBase (BEAMDB) provides collisional data for electron interactions with atoms and molecules. The Photodissociation (MolD) database contains photo-dissociation cross sections for individual rovibrational states of diatomic molecular ions and rate coefficients for the chemi-ionisation/recombination processes. We also present a progress report on the major upgrade of these databases and plans for the future. As an example of how the data from the BEAMDB may be used, a review of electron scattering from methane is described.

Stark Broadening of Cr III Spectral Lines: DO White Dwarfs

Using the modified semiempirical method of Dimitrijević and Konjević, Stark widths have been calculated for six Cr III transitions, for an electron density of 10 17 cm ‒ 3 and for temperatures from 5000–80,000 K. Results have been used for the investigation of the influence of Stark broadening on spectral lines in cool DO white dwarf atmospheres. Calculated Stark widths will be implemented in the STARK-B database, which is also a part of the Virtual Atomic and Molecular Data Center (VAMDC).

Stark Broadening of Se IV, Sn IV, Sb IV and Te IV Spectral Lines

Stark broadening parameters, line width and shift, are needed for investigations, analysis and modelling of astrophysical, laboratory, laser produced and technological plasmas. Especially in astrophysics, due to constantly increasing resolution of satellite borne spectrographs, and large terrestrial telescopes, data on trace elements, which were previously insignificant, now have increasing importance. Using the modified semiempirical method of Dimitrijević and Konjević, here, Stark widths have been calculated for 2 Se IV, 6 Sn IV, 2 Sb IV and 1 Te IV transitions. Results have been compared with existing theoretical data for Sn IV. Obtained results will be implemented in the STARK-B database, which is also a part of Virtual atomic and molecular data center (VAMDC).

Line positions and intensities for the ν3 band of 5 isotopologues of germane for planetary applications

The germane molecule, GeH4, is present in the atmospheres of giant planets Jupiter and Saturn. The ongoing NASA mission Juno has renewed interest in its spectroscopy, whose accurate modeling is essential for the retrieval of other tropospheric species. We present here the first complete analysis and modeling of line positions and intensities in the strongly absorbing ν1/ν3 stretching dyad region near 2100 cm−1, for all five germane isotopologues in natural abundance. New infrared spectra were recorded, absolute intensities were extracted through a careful procedure and modeled thanks to the formalism and programs developed in the Dijon group. A database of calculated germane lines, GeCaSDa, has been build and is available online through the Virtual Atomic and Molecular Data Centre (VAMDC) portal and at http://vamdc.icb.cnrs.fr/PHP/gecasda.php.

Semiclassical Stark Broadening Parameters of Ar VII Spectral Lines

Using the semi-classical perturbation approach in the impact approximation, full width at half maximum and shift have been determined for eight spectral lines of Ar VII, for broadening by electron-, proton-, and He III-impacts. The results are provided for temperatures from 20,000 K to 500,000 K, and for an electron density of 10 18 cm − 3 . The obtained results will be included in the STARK-B database, which is also in the virtual atomic and molecular data center (VAMDC).

EXtended CASA Line Analysis Software Suite (XCLASS)

The eXtended CASA Line Analysis Software Suite (XCLASS) is a toolbox for the Common Astronomy Software Applications package (CASA) containing new functions for modeling interferometric and single dish data. Among the tools is the myXCLASS program which calculates synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, whereas the finite source size and dust attenuation are considered as well. Molecular data required by the myXCLASS program are taken from an embedded SQLite3 database containing entries from the Cologne Database for Molecular Spectroscopy CDMS) and JPL using the Virtual Atomic and Molecular Data Center (VAMDC) portal. Additionally, the toolbox provides an interface for the model optimizer package Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX), which helps to find the best description of observational data using myXCLASS (or another external model program), i.e., finding the parameter set that most closely reproduces the data.

Mol-D a Database and a Web Service within the Serbian Virtual Observatory and the Virtual Atomic and Molecular Data Centre

AbstractIn this contribution we report the current stage of the MOLecular Dissociation (MOL-D) database which is a web service within the Serbian virtual observatory (SerVO) and node within Virtual Atomic and Molecular Data Center (VAMDC). MOL-D is an atomic and molecular (A&M) database devoted to the modelling of stellar atmospheres, laboratory plasmas, industrial plasmas etc. The initial stage of development was done at the end of 2014, when the service for data connected with hydrogen and helium molecular ions was done. In the next stage of the development of MOL-D, we include new cross-sections and rate coefficients for processes which involve species such as XH+, where X is atom of some metal. Data are important for the exploring of the interstellar medium as well as for the early Universe chemistry and for the modeling of stellar and solar atmospheres. In this poster, we present our ongoing work and plans for the future.

New model for datasets citation and extraction reproducibility in VAMDC

In this paper we present a new paradigm for the identification of datasets extracted from the Virtual Atomic and Molecular Data Centre (VAMDC) e-science infrastructure. Such identification includes information on the origin and version of the datasets, references associated to individual data in the datasets, as well as timestamps linked to the extraction procedure. This paradigm is described through the modifications of the language used to exchange data within the VAMDC and through the services that will implement those modifications. This new paradigm should enforce traceability of datasets, favor reproducibility of datasets extraction, and facilitate the systematic citation of the authors having originally measured and/or calculated the extracted atomic and molecular data.

The virtual atomic and molecular data centre (VAMDC) consortium**http://www.vamdc.eu.

The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases.

MOL-D: A Collisional Database and Web Service within the Virtual Atomic and Molecular Data Center

MOL-D database is a collection of cross-sections and rate coefficients for specific collisional processes and a web service within the Serbian Virtual Observatory (SerVO) and the Virtual Atomic and Molecular Data Center (VAMDC). This database contains photo-dissociation cross-sections for the individual ro-vibrational states of the diatomic molecular ions and rate coefficients for the atom-Rydberg atom chemi-ionization and inverse electron-ion-atom chemi-recombination processes. At the moment it contains data for photodissociation cross-sections of hydrogen H2+ and helium He2+ molecular ions and the corresponding averaged thermal photodissociation cross-sections. The ro-vibrational energy states and the corresponding dipole matrix elements are provided as well. Hydrogen and helium molecular ion data are important for calculation of solar and stellar atmosphere models and for radiative transport, as well as for kinetics of other astrophysical and laboratory plasma (i.e. early Universe).

The STARK-B database VAMDC node: a repository for spectral line broadening and shifts due to collisions with charged particles

Accurate spectroscopic diagnostics and modeling require the knowledge of numerous collisional line profiles. Access to such data via an online database has become indispensable. The STARK-B database is aimed at meeting these needs for widths and shifts of isolated lines of neutral and ionized elements due to electron and ion impacts. This database of the Paris Observatory is a result of scientific cooperation between S Sahal-Bréchot (LERMA) and M S Dimitrijević (AOB). Access to it is free, and it was opened online at the end of 2008. STARK-B is a node of the Virtual Atomic and Molecular Data Centre (VAMDC) and thus complies with VAMDC and Virtual Observatory standards. VAMDC is a European Union-funded collaboration among groups involved in the generation and use of interoperable atomic and molecular data. STARK-B now contains all our semiclassical-perturbation (SCP) calculated data for more than 123 neutral or ionized elements as published in international refereed journals. It is devoted to modeling and spectroscopic diagnostics of stellar atmospheres and envelopes, laboratory plasmas, laser equipment, and technological plasmas. Hence, the range of temperatures and densities covered by the tables is broad and depends on the ionization degree of the radiating atom. The modified semiempirical (MSE) results of calculations have begun to be implemented. In this paper, we highlight the key points of the method and the assumptions used in the calculations, which have lately been revisited. Then we present the database and its recent developments, as well as our ongoing work and our plans for the future.

Integration of CO2 spectral line parameters from the CDSD databanks into the virtual atomic and molecular data center (VAMDC)

The spectroscopic banks CDSD-296, CDSD-1000, and CDSD-4000 are presented in the context of integration into the Virtual Atomic and Molecular Data Centre (VAMDC) in order to extend the range of their users. A brief review of the VAMDC system is given concerning the purpose of this project, its infrastructure, and the data representation format. The relational structure of CDSD databases, adapted to VAMDC needs, is presented. Some of the technical problems connected with the huge volumes of stored information are considered.

SUP@VAMDC*

Atomic and molecular (A+M) data are critical for a range of applications such as astrophysics, atmospheric physics, fusion, environmental sciences, combustion chemistry, health and clinical science including radiotherapy. They underpin industries ranging from technological plasmas to lighting. The Virtual Atomic and Molecular Data Centre (VAMDC) is a major new European initiative that has built a unified, secure, documented, flexible and interoperable e-science environment-based interface to 24 existing A+M databases. SUP@VAMDC will coordinate collaborative studies and provide the supporting procedures that will develop a global e-infrastructure for the assembly, curation and access to A+M data. It will adopt and adapt VAMDC protocols to include further A+M databases and networks pathways by which common policies may be developed for an open science version of VAMDC that will extend its availability to new audiences such as schools, students, citizens and industry.

The STARK-B database as a resource for “STARK” widths and shifts data: State of advancement and program of development

“Stark” broadening theories and calculations have been extensively developed for about 50 years and can now be applied to many needs, especially for accurate spectroscopic diagnostics and modeling. This requires the knowledge of numerous collisional line profiles. Nowadays, the access to such data via an online database becomes essential. STARK-B is a collaborative project between the Astronomical Observatory of Belgrade and the Laboratoire d’Étude du Rayonnement et de la matière en Astrophysique (LERMA). It is a database of calculated widths and shifts of isolated lines of atoms and ions due to electron and ion collisions (impacts). It is devoted to modeling and spectroscopic diagnostics of stellar atmospheres and envelopes, laboratory plasmas, laser equipments and technological plasmas. Hence, the domain of temperatures and densities covered by the tables is wide and depends on the ionization degree of the considered ion. STARK-B has been fully opened since September 2008 and is in free access.The first stage of development was ended in autumn 2012, since all the existing data calculated with the impact semiclassical-perturbation method and code by Sahal-Bréchot, Dimitrijević and coworkers have now been implemented. We are now beginning the second stage of the development of STARK-B. The state of advancement of the database and our program of development are presented here, together with its context within VAMDC. VAMDC (Virtual Atomic and Molecular Data Center) is an international consortium which has built a secure, documented, flexible interoperable platform e-science permitting an automated exchange of atomic and molecular data.

A new relational database structure and online interface for the HITRAN database

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Virtual laboratory astrophysics : The STARK-B database

Stark broadening theories and calculations have been exten- sively developed for about 50 years. The theory can now be considered as mature for many applications, especially for accurate spectroscopic diagnostics and modelling. This requires the knowledge of numerous collisional line profiles, especially for very low abundant atoms and ions which are used as probes for modern spectroscopic diagnostics in as- trophysics. Nowadays, the access to such data via an on line database becomes essential. STARK-B (http://stark-b.obspm.fr )i s a col- laborative project between the Astronomical Observatory of Belgrade and the Laboratoire d'´ Etude du Rayonnement et de la matiere en Astrophysique (LERMA). It is a database of calculated widths and shifts of isolated lines of atoms and ions due to electron and ion col- lisions (impacts). It is devoted to modelling and spectroscopic diag- nostics of stellar atmospheres and envelopes, laboratory plasmas, laser equipments and technological plasmas. Hence, the domain of temper- atures and densities covered by the tables is wide and depends on the ionization degree of the considered ion. The STARK-B database is a part of VAMDC (Virtual Atomic and Molecular Data Centre, http:// www.vamdc.eu), which is an European Union funded collaboration be- tween groups involved in the generation and use of atomic and molec- ular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data.