Molecular Data Centre Research Articles

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.

The Cologne Database for Molecular Spectroscopy, CDMS, in the Virtual Atomic and Molecular Data Centre, VAMDC

The Cologne Database for Molecular Spectroscopy, CDMS, was founded 1998 to provide in its catalog section line lists of mostly molecular species which are or may be observed in various astronomical sources (usually) by radio astronomical means. The line lists contain transition frequencies with qualified accuracies, intensities, quantum numbers, as well as further auxiliary information. They have been generated from critically evaluated experimental line lists, mostly from laboratory experiments, employing established Hamiltonian models. Separate entries exist for different isotopic species and usually also for different vibrational states. As of December 2015, the number of entries is 792. They are available online as ascii tables with additional files documenting information on the entries.The Virtual Atomic and Molecular Data Centre, VAMDC, was founded more than 5years ago as a common platform for atomic and molecular data. This platform facilitates exchange not only between spectroscopic databases related to astrophysics or astrochemistry, but also with collisional and kinetic databases. A dedicated infrastructure was developed to provide a common data format in the various databases enabling queries to a large variety of databases on atomic and molecular data at once.For CDMS, the incorporation in VAMDC was combined with several modifications on the generation of CDMS catalog entries. Here we introduce related changes to the data structure and the data content in the CDMS. The new data scheme allows us to incorporate all previous data entries but in addition allows us also to include entries based on new theoretical descriptions. Moreover, the CDMS entries have been transferred into a mySQL database format. These developments within the VAMDC framework have in part been driven by the needs of the astronomical community to be able to deal efficiently with large data sets obtained with the Herschel Space Telescope or, more recently, with the Atacama Large Millimeter Array.

Stark Widths of Spectral Lines of Neutral Neon

In order to complete Stark broadening data for Ne I spectral lines which are needed for analysis of stellar atmospheres, collisional widths and shifts (the so-called Stark broadening parameters) of 29 isolated spectral lines of neutral neon have been determined within the impact semiclassical perturbation method. Calculations have been performed for the broadening by collisions with electrons, protons and ionized helium for astrophysical applications, and for collisions with ionized neon and argon for laboratory plasma diagnostics. The shifts have been compared with existing experimental values. The obtained data will be included in the STARK-B database, which is a part of the Virtual Atomic and Molecular Data Center – VAMDC.

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).

On the Stark Broadening of Lu III Spectral Lines

The electron-impact widths for 27 Lu III spectral lines have been calculated by using the modified semiempirical method. Calculations have been also performed with the published relativistic Hartree-Fock oscillator strengths and additionally, with the approximate formula of Cowley. With the obtained results, the influence of Stark broadening on Lu III lines was investigated in the spectra of A-type stars. The obtained data will be included in the STARK-B database, which is part of the Virtual Atomic and Molecular Data Center – VAMDC.

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.

Atomic and molecular data for optical stellar spectroscopy

High-precision spectroscopy of large stellar samples plays a crucial role for several topical issues in astrophysics. Examples include studying the chemical structure and evolution of the Milky Way Galaxy, tracing the origin of chemical elements, and characterizing planetary host stars. Data are accumulating from instruments that obtain high-quality spectra of stars in the ultraviolet, optical and infrared wavelength regions on a routine basis. These instruments are located at ground-based 2–10 m class telescopes around the world, in addition to the spectrographs with unique capabilities available at the Hubble Space Telescope. The interpretation of these spectra requires high-quality transition data for numerous species, in particular neutral and singly ionized atoms, and di- or triatomic molecules. We rely heavily on the continuous efforts of laboratory astrophysics groups that produce and improve the relevant experimental and theoretical atomic and molecular data. The compilation of the best available data is facilitated by databases and electronic infrastructures such as the NIST Atomic Spectra Database, the VALD database, or the Virtual Atomic and Molecular Data Centre. We illustrate the current status of atomic data for optical stellar spectra with the example of the Gaia-ESO Public Spectroscopic Survey. Data sources for 35 chemical elements were reviewed in an effort to construct a line list for a homogeneous abundance analysis of up to 105 stars.

Development of collisional data base for elementary processes of electron scattering by atoms and molecules

We present a progress report on the development of the Belgrade electron/molecule data base which is hosted by The Institute of Physics, University of Belgrade and The Astronomical Observatory Belgrade. The data base has been developed under the standards of Virtual Atomic Molecular Data Centre (VAMDC) project which provides a common portal for several European data bases that maintain atomic and molecular data. The Belgrade data base (BEAMDB) covers collisional data of electron interactions with atoms and molecules in the form of differential (DCS) and integrated cross sections as well as energy loss spectra. The final goal of BEAMDB becoming both a node within the VAMDC consortium and within the radiation damage RADAM data base has been achieved.

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.

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.

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.

MeCaSDa and ECaSDa: Methane and ethene calculated spectroscopic databases for the virtual atomic and molecular data centre

Two spectroscopic relational databases, denoted MeCaSDa and ECaSDa, have been implemented for methane and ethene, and included in VAMDC (Virtual Atomic and Molecular Data Centre, http://portal.vamdc.eu/vamdc_portal/home.seam). These databases collect calculated spectroscopic data from the accurate analyses previously performed for the electronic ground state of methane, ethene, and some of their isotopologues: 12CH4, 13CH4, and 12C2H4. Both infrared absorption and Raman scattering lines are included. The polyad structures are reported and the transitions are precisely described by their energy, their intensity and the full description of the lower and upper states involved in the transitions. The relational schemas of ECaSDa and MeCaSDa databases are equivalent and optimised to enable the better compromise between data retrieval and compatibility with the XSAMS (XML Schema for Atoms, Molecules, and Solids) format adopted within the VAMDC European project.

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.

BASECOL2012: A collisional database repository and web service within the Virtual Atomic and Molecular Data Centre (VAMDC)

The BASECOL2012 database is a repository of collisional data and a web service within the Virtual Atomic and Molecular Data Centre (VAMDC, http://www.vamdc.eu). It contains rate coefficients for the collisional excitation of rotational, ro-vibrational, vibrational, fine, and hyperfine levels of molecules by atoms, molecules, and electrons, as well as fine-structure excitation of some atoms that are relevant to interstellar and circumstellar astrophysical applications. Submissions of new published collisional rate coefficients sets are welcome, and they will be critically evaluated before inclusion in the database. In addition, BASECOL2012 provides spectroscopic data queried dynamically from various spectroscopic databases using the VAMDC technology. These spectroscopic data are conveniently matched to the in-house collisional excitation rate coefficients using the SPECTCOL sofware package (http:// vamdc.eu/software), and the combined sets of data can be downloaded from the BASECOL2012 website. As a partner of the VAMDC, BASECOL2012 is accessible from the general VAMDC portal (http://portal.vamdc.eu) and from user tools such as SPECTCOL.

Virtual Laboratory Astrophysics: the STARK-B database for spectral line broadening by collisions with charged particles and its link to the European project VAMDC

Atomic physics in plasmas has been an essential tool for many years. Accurate spectroscopic diagnostics and modeling require the knowledge of numerous collisional line profiles. "Stark broadening" theories and calculations have been extensively developed for about 50 years. Nowadays, the access to such data via an on line database becomes essential. The aim of STARK-B is to reply to this need. It is a collaborative project between the Astronomical Observatory of Belgrade (AOB) and the "Laboratoire d'Étude du Rayonnement et de la matière en Astrophysique" (LERMA) of the Paris Observatory and CNRS. It is a database of widths and shifts of isolated lines of atoms and ions due to electron and ion impacts that we have calculated and published in international refereed journals (more than 150 papers by Dimitrijević & Sahal-Bréchot, and colleagues). It is devoted to modeling and spectroscopic diagnostics of stellar atmospheres and envelopes, laboratory plasmas, magnetic fusion 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. The STARK-B database is in free access and is is a part of VAMDC: the Virtual Atomic and Molecular Data Centre is an European Union funded collaboration between groups involved in the generation and use of atomic and molecular data. VAMDC aims to build a secure, documented, flexible and interoperable e-science environment-based interface to existing atomic and molecular data. STARK-B and its VAMDC context are presented in this paper.

VADMC: The Infrastructure

Abstract The Virtual Atomic and Molecular Data Centre (VAMDC; http://www.vamdc.eu) is a European-Union-funded collaboration between several groups involved in the generation, evaluation, and use of atomic and molecular data. VAMDC aims at building a secure, documented, flexible and interoperable e-Science environment-based interface to existing atomic and molecular databases. The global infrastructure of this project uses technologies derived from the International Virtual Observatory Alliance (IVOA). The infrastructure, as well as the first database prototypes will be described.

Virtual Atomic and Molecular Data Centre: Level 3 Service and Future Prospects

AbstractThe Virtual Atomic and Molecular Data Centre (VAMDC, http://www.vamdc.eu) is an international Consortium that has created an interoperable e-science infrastructure for the exchange of atomic and molecular data. The VAMDC defines standards for the exchange of atomic and molecular data, develop reference implementation of those standards, deploys registries of internet resources (yellow pages), designs user applications in order to meet the user needs, builds data access layers above databases to provide unified outputs from these databases, cares about asynchronous queries with workflows and connects its infrastructure to the grid. The paper describes the current service deployment of the VAMDC data infrastructure across our registered databases and the key features of the current infrastructure.