Special Issue "Development and Perspectives of Atomic and Molecular Databases"

A special issue of Atoms (ISSN 2218-2004).

Deadline for manuscript submissions: closed (31 July 2020).

Special Issue Editor

Dr. Claudio Mendoza
E-Mail Website
Guest Editor
Department of Physics, Western Michigan University, Kalamazoo, MI 49008, USA
Interests: computation of atomic data for astrophysical applications; X-ray astrophysics; astrophysical opacities; high-density effects in plasmas; surface astrochemistry; mathematical and computational biology; scientific databases; scientific data assessment; web data services; data science; student

Special Issue Information

Dear Colleagues,

Compilations of atomic and molecular (A&M) data are of vital importance in several scientific fields (e.g., astrophysics, astrochemistry, atmospheric physics, and fusion) and in industrial applications dealing with lasers and lighting. Seminal initiatives were the tables of atomic energy levels by Charlotte E. Moore (1949) and of atomic transition probabilities by Wiese, Smith, and Glennon (1966) at the National Bureau of Standards (NBS), now the National Institute of Standards and Technology (NIST). With the advent of the Internet and the World Wide Web, numerous online A&M databases have become available to address an ever-growing demand for accurate and complete datasets. In the present Special Issue of Atoms, we intend to present a comprehensive review of the state, development, and future perspectives of such A&M databases by evaluating their data models; metadata; data collection, curation, and assessment schemes; web services and data transfer protocols; interoperability; and workspaces. We are also interested in the data-user’s point of view by comparing the A&M databases incorporated in plasma modeling codes. We therefore welcome contributions to this timely anthology in the form of reviews, research reports, short communications, and comments.

Dr. Claudio Mendoza
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • A&M databases
  • data collection
  • data curation
  • data assessment
  • data transfer
  • plasma modeling codes
  • interoperability
  • web services

Published Papers (16 papers)

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Research

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Open AccessArticle
The XSTAR Atomic Database
Atoms 2021, 9(1), 12; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms9010012 - 05 Feb 2021
Viewed by 568
Abstract
We describe the atomic database of the xstar spectral modeling code, summarizing the systematic upgrades carried out in the past twenty years to enable the modeling of K-lines from chemical elements with atomic number Z30 and recent extensions to handle high-density plasmas. Such plasma environments are found, for instance, in the inner region of accretion disks round compact objects (neutron stars and black holes), which emit rich information about the system’s physical properties. Our intention is to offer a reliable modeling tool to take advantage of the outstanding spectral capabilities of the new generation of X-ray space telescopes (e.g., xrism and athena) to be launched in the coming years. Data curatorial aspects are discussed and an updated list of reference sources is compiled to improve the database provenance metadata. Two xstar spin-offs—the ISMabs absorption model and the uaDB database—are also described. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
A Decade with VAMDC: Results and Ambitions
Atoms 2020, 8(4), 76; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8040076 - 21 Oct 2020
Cited by 8 | Viewed by 1256
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
NIFS Atomic and Molecular Numerical Database for Collision Processes
Atoms 2020, 8(4), 71; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8040071 - 09 Oct 2020
Cited by 1 | Viewed by 684
Abstract
The National Institute for Fusion Science (NIFS) has compiled and developed atomic and molecular numerical databases for various collision processes and makes it accessible from the internet to the public. The database contains numerical data of cross sections and rate coefficients for electron [...] Read more.
The National Institute for Fusion Science (NIFS) has compiled and developed atomic and molecular numerical databases for various collision processes and makes it accessible from the internet to the public. The database contains numerical data of cross sections and rate coefficients for electron collision or ion collisions with atoms and molecules, attached with bibliographic information on their data sources. The database system provides query forms to search data, and numerical data are retrievable. The graphical output is helpful to understand energy dependence of cross sections and temperature dependence of rate coefficients obtained by various studies. All data are compiled mainly from published literature, and data sources can be tracked by the bibliographic information. We also have data of sputtering yields and back-scattering coefficients for solid surfaces collided by ions in the database. All data in the database are applicable to understand atomic and molecular processes in various plasmas, such as fusion plasma, astrophysical plasma and applied plasma, as well as for understanding plasma–surface interaction in plasmas. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
BASECOL2020 New Technical Design
Atoms 2020, 8(4), 69; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8040069 - 07 Oct 2020
Cited by 1 | Viewed by 567
Abstract
The BASECOL database has been created and scientifically enriched since 2004. It contains collisional excitation rate coefficients of molecules for application to the interstellar medium and to cometary atmospheres. Recently, major technical updates have been performed in order to be compliant with international [...] Read more.
The BASECOL database has been created and scientifically enriched since 2004. It contains collisional excitation rate coefficients of molecules for application to the interstellar medium and to cometary atmospheres. Recently, major technical updates have been performed in order to be compliant with international standards for management of data and in order to provide a more friendly environment to query and to present the data. The current paper aims at presenting the key features of the technical updates and to underline the compatibility of BASECOL database with the Virtual Atomic and Molecular Data Center. This latter aims to interconnect atomic and molecular databases, thus providing a single location where users can access atomic and molecular data. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
Database NORAD-Atomic-Data for Atomic Processes in Plasma
Atoms 2020, 8(4), 68; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8040068 - 07 Oct 2020
Viewed by 604
Abstract
The online atomic database of NORAD-Atomic-Data, where NORAD stands for Nahar OSU Radiative, is part of the data sources of the two international collaborations of the Opacity Project (OP) and the Iron Project (IP). It contains large sets of parameters for the dominant [...] Read more.
The online atomic database of NORAD-Atomic-Data, where NORAD stands for Nahar OSU Radiative, is part of the data sources of the two international collaborations of the Opacity Project (OP) and the Iron Project (IP). It contains large sets of parameters for the dominant atomic processes in astrophysical plasmas, such as, (i) photo-excitation, (ii) photoionization, (iii) electron–ion recombination, (iv) electron–impact excitations. The atomic parameters correspond to tables of energy levels, level-specific total photoionization cross-sections, partial photoionization cross-sections of all bound states for leaving the residual ion in the ground state, partial cross-sections of the ground state for leaving the ion in various excited states, total level-specific electron–ion recombination rate coefficients that include both the radiative and dielectronic recombination, total recombination rate coefficients summed from contributions of an infinite number of recombined states, total photo-recombination cross-sections and rates with respect to photoelectron energy, transition probabilities, lifetimes, collision strengths. The database was created after the first two atomic databases, TOPbase under the OP and TIPbase under the IP. Hence the contents of NORAD-Atomic-Data are either new or from repeated calculations using a much larger wave function expansion making the data more complete. The results have been obtained from the R-matrix method using the close-coupling approximation developed under the OP and IP, and from atomic structure calculations using the program SUPERSTRUCTURE. They have been compared with available published results which have been obtained theoretically and experimentally, and are expected to be of high accuracy in general. All computations were carried out using the computational facilities at the Ohio Supercomputer Center (OSC) starting in 1990. At present it contains atomic data for 154 atomic species, 98 of which are lighter atomic species with nuclear charge Z ≤ 28 and 56 are heavier ones with Z > 28. New data are added with publications. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
Atomic Data Assessment with PyNeb
Atoms 2020, 8(4), 66; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8040066 - 04 Oct 2020
Cited by 3 | Viewed by 597
Abstract
PyNeb is a Python package widely used to model emission lines in gaseous nebulae. We take advantage of its object-oriented architecture, class methods, and historical atomic database to structure a practical environment for atomic data assessment. Our aim is to reduce the uncertainties [...] Read more.
PyNeb is a Python package widely used to model emission lines in gaseous nebulae. We take advantage of its object-oriented architecture, class methods, and historical atomic database to structure a practical environment for atomic data assessment. Our aim is to reduce the uncertainties in the parameter space (line ratio diagnostics, electron density and temperature, and ionic abundances) arising from the underlying atomic data by critically selecting the PyNeb default datasets. We evaluate the questioned radiative-rate accuracy of the collisionally excited forbidden lines of the N- and P-like ions (O ii, Ne iv, S ii, Cl iii, and Ar iv), which are used as density diagnostics. With the aid of observed line ratios in the dense NGC 7027 planetary nebula and careful data analysis, we arrive at emissivity ratio uncertainties from the radiative rates within 10%, a considerable improvement over a previously predicted 50%. We also examine the accuracy of an extensive dataset of electron-impact effective collision strengths for the carbon isoelectronic sequence recently published. By estimating the impact of the new data on the pivotal [N ii] and [O iii] temperature diagnostics and by benchmarking the collision strength with a measured resonance position, we question their usefulness in nebular modeling. We confirm that the effective-collision-strength scatter of selected datasets for these two ions does not lead to uncertainties in the temperature diagnostics larger than 10%. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
Development of NIST Atomic Databases and Online Tools
Atoms 2020, 8(3), 56; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8030056 - 05 Sep 2020
Cited by 7 | Viewed by 841
Abstract
Over the last 25 years, the atomic standard reference databases and online tools developed at the National Institute of Standards and Technology (NIST) have provided users around the world with the highest-quality data on various atomic parameters (e.g., level energies, transition wavelengths, and [...] Read more.
Over the last 25 years, the atomic standard reference databases and online tools developed at the National Institute of Standards and Technology (NIST) have provided users around the world with the highest-quality data on various atomic parameters (e.g., level energies, transition wavelengths, and oscillator strengths) and online capabilities for fast and reliable collisional-radiative modeling of diverse plasmas. Here we present an overview of the recent developments regarding NIST numerical and bibliographic atomic databases and outline the prospects and vision of their evolution. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties
Atoms 2020, 8(3), 49; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8030049 - 24 Aug 2020
Viewed by 741
Abstract
The AtomDB project provides models of X-ray and extreme ultraviolet emitting astrophysical spectra for optically thin, hot plasma. We present the new software package, PyAtomDB, which now underpins the entire project, providing access to the underlying database, collisional radiative model calculations, and spectrum [...] Read more.
The AtomDB project provides models of X-ray and extreme ultraviolet emitting astrophysical spectra for optically thin, hot plasma. We present the new software package, PyAtomDB, which now underpins the entire project, providing access to the underlying database, collisional radiative model calculations, and spectrum generation for a range of models. PyAtomDB is easily extensible, allowing users to build new tools and models for use in analysis packages such as XSPEC. We present two of these, the kappa and ACX models for non-Maxwellian and Charge-Exchange plasmas respectively. In addition, PyAtomDB allows for full open access to the apec code, which underlies all of the AtomDB spectra and has enabled the development of a module for estimating the sensitivity of emission lines and diagnostic line ratios to uncertainties in the underlying atomic data. We present these publicly available tools and results for several X-ray diagnostics of Fe L-shell ions and He-like ions as examples. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
Atomic Data for Plasma Spectroscopy: The CHIANTI Database, Improvements and Challenges
Atoms 2020, 8(3), 46; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8030046 - 20 Aug 2020
Cited by 4 | Viewed by 780
Abstract
CHIANTI is an atomic database and software package for modeling emission lines and continua from hot astrophysical plasmas. It is freely available to all researchers and has been widely used in the Heliophysics and Astrophysics communities for almost 25 years. In this review, [...] Read more.
CHIANTI is an atomic database and software package for modeling emission lines and continua from hot astrophysical plasmas. It is freely available to all researchers and has been widely used in the Heliophysics and Astrophysics communities for almost 25 years. In this review, we summarize the properties of the current version of the database and give an overview of the relevant atomic processes. We also discuss progress towards a complete implementation of collisional-radiative modeling, simultaneously solving for atomic level and ion populations for individual elements. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessArticle
The Spectroscopic Atomic and Molecular Databases at the Paris Observatory
Atoms 2020, 8(3), 36; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8030036 - 21 Jul 2020
Cited by 2 | Viewed by 843
Abstract
This paper is intended to give a comprehensive overview of the current status and developments of the Paris Observatory STARK-B, MOLAT and SESAM databases which can be interrogated thanks to interoperability tools. The STARK-B database provides shifting and broadening parameters of different atomic [...] Read more.
This paper is intended to give a comprehensive overview of the current status and developments of the Paris Observatory STARK-B, MOLAT and SESAM databases which can be interrogated thanks to interoperability tools. The STARK-B database provides shifting and broadening parameters of different atomic and ionic transitions due to impacts with charged particles (the so-called Stark broadening) for different temperatures and densities. The spectroscopic MOLAT and SESAM databases provide the wavelengths, the oscillator strengths or Einstein spontaneous emission coefficients of H 2 , CO and isotopologues molecules. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessEditor’s ChoiceArticle
Current Status and Developments of the Atomic Database on Rare-Earths at Mons University (DREAM)
Atoms 2020, 8(2), 18; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8020018 - 02 May 2020
Cited by 2 | Viewed by 805
Abstract
The main purpose of the Database on Rare Earths At Mons University (DREAM) is to provide the scientific community with updated spectroscopic parameters related to lanthanide atoms (Z = 57–71) in their lowest ionization stages. The radiative parameters (oscillator strengths and transitions [...] Read more.
The main purpose of the Database on Rare Earths At Mons University (DREAM) is to provide the scientific community with updated spectroscopic parameters related to lanthanide atoms (Z = 57–71) in their lowest ionization stages. The radiative parameters (oscillator strengths and transitions probabilities) listed in the database have been obtained over the past 20 years by the Atomic Physics and Astrophysics group of Mons University, Belgium, thanks to a systematic and extensive use of the pseudo-relativistic Hartree-Fock (HFR) method modified for taking core-polarization and core-penetration effects into account. Most of these theoretical results have been validated by the good agreement obtained when comparing computed radiative lifetimes and accurate experimental values measured by the time-resolved laser-induced fluorescence technique. In the present paper, we report on the current status and developments of the database that gathers radiative parameters for more than 72,000 spectral lines in neutral, singly-, doubly-, and triply-ionized lanthanides. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessEditor’s ChoiceArticle
Referencing Sources of Molecular Spectroscopic Data in the Era of Data Science: Application to the HITRAN and AMBDAS Databases
Atoms 2020, 8(2), 16; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8020016 - 30 Apr 2020
Cited by 3 | Viewed by 1255
Abstract
The application described has been designed to create bibliographic entries in large databases with diverse sources automatically, which reduces both the frequency of mistakes and the workload for the administrators. This new system uniquely identifies each reference from its digital object identifier (DOI) [...] Read more.
The application described has been designed to create bibliographic entries in large databases with diverse sources automatically, which reduces both the frequency of mistakes and the workload for the administrators. This new system uniquely identifies each reference from its digital object identifier (DOI) and retrieves the corresponding bibliographic information from any of several online services, including the SAO/NASA Astrophysics Data Systems (ADS) and CrossRef APIs. Once parsed into a relational database, the software is able to produce bibliographies in any of several formats, including HTML and BibTeX, for use on websites or printed articles. The application is provided free-of-charge for general use by any scientific database. The power of this application is demonstrated when used to populate reference data for the HITRAN and AMBDAS databases as test cases. HITRAN contains data that is provided by researchers and collaborators throughout the spectroscopic community. These contributors are accredited for their contributions through the bibliography produced alongside the data returned by an online search in HITRAN. Prior to the work presented here, HITRAN and AMBDAS created these bibliographies manually, which is a tedious, time-consuming and error-prone process. The complete code for the new referencing system can be found on the HITRANonline GitHub website. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessFeature PaperEditor’s ChoiceArticle
Empirical Line Lists in the ExoMol Database
Atoms 2020, 8(1), 7; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8010007 - 17 Feb 2020
Cited by 10 | Viewed by 1066
Abstract
The ExoMol database aims to provide comprehensive molecular line lists for exoplanetary and other hot atmospheres. The data are expanded by inclusion of empirically derived line lists taken from the literature for a series of diatomic molecules, namely CH, NH, OH, AlCl, AlF, [...] Read more.
The ExoMol database aims to provide comprehensive molecular line lists for exoplanetary and other hot atmospheres. The data are expanded by inclusion of empirically derived line lists taken from the literature for a series of diatomic molecules, namely CH, NH, OH, AlCl, AlF, OH + , CaF, MgF, KF, NaF, LiCl, LiF, MgH, TiH, CrH, FeH, C 2 , CP, CN, CaH, and triplet N 2 . Generally, these line lists are constructed from measured spectra using a combination of effective rotational Hamiltonian models for the line positions and ab initio (transition) dipole moments to provide intensities. This work results in the inclusion of 22 new molecules (36 new isotopologues) in the ExoMol database. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Review

Jump to: Research

Open AccessReview
Data Needs for Modeling Low-Temperature Non-Equilibrium Plasmas: The LXCat Project, History, Perspectives and a Tutorial
Atoms 2021, 9(1), 16; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms9010016 - 24 Feb 2021
Viewed by 815
Abstract
Technologies based on non-equilibrium, low-temperature plasmas are ubiquitous in today’s society. Plasma modeling plays an essential role in their understanding, development and optimization. An accurate description of electron and ion collisions with neutrals and their transport is required to correctly describe plasma properties [...] Read more.
Technologies based on non-equilibrium, low-temperature plasmas are ubiquitous in today’s society. Plasma modeling plays an essential role in their understanding, development and optimization. An accurate description of electron and ion collisions with neutrals and their transport is required to correctly describe plasma properties as a function of external parameters. LXCat is an open-access, web-based platform for storing, exchanging and manipulating data needed for modeling the electron and ion components of non-equilibrium, low-temperature plasmas. The data types supported by LXCat are electron- and ion-scattering cross-sections with neutrals (total and differential), interaction potentials, oscillator strengths, and electron- and ion-swarm/transport parameters. Online tools allow users to identify and compare the data through plotting routines, and use the data to generate swarm parameters and reaction rates with the integrated electron Boltzmann solver. In this review, the historical evolution of the project and some perspectives on its future are discussed together with a tutorial review for using data from LXCat. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessReview
Atomic Databases: Four of a Kind
Atoms 2020, 8(2), 30; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8020030 - 19 Jun 2020
Cited by 1 | Viewed by 855
Abstract
In the context of atomic data computations for astrophysical applications, we review four different types of databases we have implemented for data dissemination: a database for nebular modeling; TIPTOPbase; OPserver; and AtomPy. The database for nebular plasmas is briefly discussed as a study [...] Read more.
In the context of atomic data computations for astrophysical applications, we review four different types of databases we have implemented for data dissemination: a database for nebular modeling; TIPTOPbase; OPserver; and AtomPy. The database for nebular plasmas is briefly discussed as a study case of a successful project. TOPbase and the OPserver were developed during the Opacity Project, an international consortium concerned with the revision of astrophysical opacities, while TIPbase was part of the Iron Project to calculate radiative transition probabilities and electron impact excitation collision strengths for iron-group ions. AtomPy is a prototype for an open, distributed data-assessment environment to engage both producers and users. We discuss design strategies and implementation issues that may help in the undertaking of present and future scientific database projects. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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Open AccessFeature PaperEditor’s ChoiceReview
The Leiden Atomic and Molecular Database (LAMDA): Current Status, Recent Updates, and Future Plans
Atoms 2020, 8(2), 15; https://0-doi-org.brum.beds.ac.uk/10.3390/atoms8020015 - 28 Apr 2020
Cited by 6 | Viewed by 996
Abstract
The Leiden Atomic and Molecular Database (LAMDA) collects spectroscopic information and collisional rate coefficients for molecules, atoms, and ions of astrophysical and astrochemical interest. We describe the developments of the database since its inception in 2005, and outline our plans for the near [...] Read more.
The Leiden Atomic and Molecular Database (LAMDA) collects spectroscopic information and collisional rate coefficients for molecules, atoms, and ions of astrophysical and astrochemical interest. We describe the developments of the database since its inception in 2005, and outline our plans for the near future. Such a database is constrained both by the nature of its uses and by the availability of accurate data: we suggest ways to improve the synergies among users and suppliers of data. We summarize some recent developments in computation of collisional cross sections and rate coefficients. We consider atomic and molecular data that are needed to support astrophysics and astrochemistry with upcoming instruments that operate in the mid- and far-infrared parts of the spectrum. Full article
(This article belongs to the Special Issue Development and Perspectives of Atomic and Molecular Databases)
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