VAMDC Virtual Atomic and Molecular Data Centre (.org) Coordinator: M.L. Dubernet 1,2 on behalf of...

VAMDCVirtual Atomic and Molecular Data Centre

http://www.vamdc.eu (.org)

Coordinator: M.L. Dubernet1,2 on behalf of the VAMDC Consortium

1LUTH, UMR CNRS 8102,Observatoire de Paris2LPMAA, UMR CNRS 7092, Université Pierre et Marie Curie

Astrochemistry Workshop, Amsterdam, April 2011

http://www.vamdc.eu/

Agenda

• General Overview of VAMDC Program– Partners, Objectives, Program of Work

• Science Cases• Mid-Term Achievements


VAMDC in a nutshell

• International collaboration between groups involved in the generation, evaluation, and use of atomic and molecular data (A&M data).

• Aims: creating a well-documented interoperable interface to existing A&M data resources.

• Funded by EU-FP7 E-Science Infrastructures programme, started July 2009, until end 2012.

• Consortium: 15 partner institutes from six EU and three non-EU countries + external partners –


VAMDC in a nutshell

• 26 Different Departments and about 108 people: about 68 Full Time Equivalent for 42 months

• Connecting Europe to Russia, Central Europe, South America, North America Aim at worldwide connection

• Connecting Different Fields of Producers of Atomic and Molecular Physics and Chemistry

• Connecting A.& M. Producers to A. & M. Users• Connecting to Research/E-Infrastructures: Euro-VO

(IVOA), Europlanet, HELIO


Schematic diagram of the VAMDC infrastructure


Registry = Yellow Pages Cambridge & Paris Observatory

Core databases

• Developed and maintained at partner institutes, about 20 databases

• Atomic data for astrophysics − 7 databases• Molecular data − 8 databases• Solid Spectroscopy data − 2 databases• Reaction rate data for astrophysics – 2 databases+ 2 Technological Nodes

Institute of Astronomy: Cambridge University VO-Paris Data Center: Paris Observatory


CHIANTI

Astrogrid (service)

KIDA

BASECOL

CDMS

VALDVOPARIS(services)

CH4STARK-B

SPECTR-W3

Tomsk

NIST

CFA

CO2, O3, H2O

MoscowUppsala

VenezuelaTIPTOPBase,xstarDB

PAH

LASP

UMIST


Emol

GhoSST

HITRAN

Vienna Atomic Line DatabaseVALD3 is aimed at research and applications in the range of temperatures between 103 and 105 K and wide range in pressure and chemical composition. •60 million atomic transitions, Nearly 60 chemical elements, 3 ionization stages, up to 6 for some, soon up to 9.•Di-atomic molecules: 30 millions for TiO including 5 isotopes of Titanium. More coming soon. Atomic transition information: •Wavelength (Ritz and measured, when available), Species ID, Oscillator strength, Energies of the levels, Total angular momentum quantum numbers J, Landé factors, Line broadening: natural, Stark and van der Waals, Coupling for each level, Unified term designations, Electronic configuration, when available Stellar Physics – GAIA -

Upsalla (N. Piskunov), Vienna (W. Weiss), Moscow (T. Ryabchikova)


CHIANTICambridge University, DAMTP (G. del Zanna & H.

Mason)

• CHIANTI is an atomic database for spectroscopic diagnostics of astrophysical plasmas; it is the preferred reference database in solar physics


It lists experimental and calculated wavelengths, radiative data and rates for electron and proton collisions

EmolOpen University (N. Mason)

• EMol Database contains a comprehensive list of critically evaluated and regularly updated measured and calculated cross sections for electron interactions with molecular systems.


It is of interest for the plasma industry, and for the disciplines of discharge physics, fusion, aeronomy and radiation chemistry.

CDMS/JPLUniversity of Cologne (S. Schlemmer) & B.

Drouin (JPL)http://www.ph1.uni-koeln. de/ vorhersagen/

http://spec.jpl.nasa.gov/

• CDMS - Cologne Database for Molecular Spectroscopy provides recommendations for spectroscopic transition frequencies and intensities for atoms and molecules in the frequency range 0-10 THz.

• The CDMS has a MoU with its US counterpart, the JPL Jet Propulsion Laboratory Submillimeter Catalogue.– New Outputs will provide explicit quantum numbers

• Astronomical interest and for studying the Earth atmosphere


http://spec.jpl.nasa.gov/

Published (de)-excitation rate coefficientsRotational (fine, hyperfine), Ro-vib., Vib.

Currently: 47 Target molecules; Perturbers : electrons, He, H, H

2

130 collisional systems

Fully documented and referenced (759 ref.)

Fitting coefficients, visualisation tools

Energy levels, Einstein coefficients, QN

Fully checked and evaluated

Basecol Database (basecol.obspm.fr)Paris Observatory

Collaboration: Bordeaux, Besançon, Grenoble, Madrid, DurhamP.I. = ML Dubernet

Linked to CDMS and JPL Astrophysical Applications

GhoSSTObservatory of Grenoble (B. Schmitt)

http://ghosst.obs.ujf-grenoble.fr

• GhoSST (Grenoble astrophysics and planetology Solid Spectroscopy and Thermodynamics,) database service, offers spectroscopic laboratory data on molecular and atomic solids from the near UV to the far-infrared.

• Solid Spectroscopy Data Model• ISM and Planetology Applications


LASP

• LASP (Laboratorio di Astrofisica Sperimentale) Database (http://web.ct.astro.it/weblab/ dbindex.html#dbindex), contains – (i) infrared (IR) spectra of molecules in the solid phase for both

pure species and their mixtures before and after processing with energetic ions and UV photons

– (ii) IR optical constants of molecules in the solid phase and after processing with energetic

– (iii) band strengths of the IR absorption bands – (iv) density values of frozen samples

• ISM and Planetology Applications• Observatory of Catania (G. Leto, M. E. Palumbo)


UdfA (UMIST)Queen’s University of Belfast (T. Millar)

http://www.udfa.net/

• University of Manchester Institute of Science and Technology (UMIST) database for astrochemistry

• It provides reaction rate data and related software for chemical kinetic modelling of astronomical regions.

• ISM and Planetology Applications


KIDAObservatory of Bordeaux (V. Wakelam)

http://kida.obs.u-bordeaux1.fr

• KIDA - KInetic Database for Astrochemistry contains data on chemical reactions used in the modelling of the chemistry in the interstellar medium and in planetary atmospheres

• ISM and Planetology Applications


PAHObservatory of Cagliari (G. Mulas) and

« ex-CESR » (C. Joblin)http://astrochemisty.ca.astro.it/database/

• PAHs (Polycyclic Aromatic Hydrocarbon) and carbon clusters spectral database provides a number of properties for a sample of presently about 60 species in four charge states: anion, neutral, cation and dication.

• The properties include general energetic such as electron affinity and ionisation energies, static polarizability, permanent dipole moment, van der Waals coefficients, symmetry, multiplicity, and optimised geometry of the ground electronic state; harmonic vibrational analyses, i. e. normal modes, their frequencies and IR activities; and vertical electronic photoabsorption cross-sections and complex frequency-dependent electronic polarisabilities in the linear regime.

• ISM and Planetology Application


Spectr-W3

• Spectr-W3 atomic database (http://spectr-w3.snz.ru), lists experimental, calculated, and compiled data on ionization potentials, energy levels, wavelengths, radiation transition probabilities and oscillator strengths, and also parameters for analytic approximations for electron-collision cross-sections and rates for atoms and ions.

• Astrophysical Applications & Fusion• Russian Federal Nuclear Centre All-Russian Institute

of Technical Physics (RFNC VNIITF - Snezhinsk, Chelyabinsk Region, Russia) – P. Loboda


http://spectr-w3.snz.ru/

The V.E. Zuev Institute of Atmospheric Optics (IAO) in Tomsk

• CDSD - The Carbon Dioxide Spectroscopic Databank (http://cdsd.iao.ru and ftp://ftp.iao.ru/pub/CDSD-2008), containing calculated spectral line parameters for seven isotopologues of carbon dioxide

• "Spectroscopy of Atmospheric Gases" (http://spectra.iao.ru), containing the well-known databases such as HITRAN, GEISA and HITEMP.

• V. Perevalov• Earth, Planets (Solar and Exo), Brown Dwarfs• W@DIS - Water Internet @ccessible Distributed

Information System (http://wadis.saga.iao.ru) lists experimental water-vapour spectroscopy data from the literature and calculated line lists. W@DIS contains energy levels, transition positions and line intensities, and line profile characteristics.

• A. Fazliev in collaboration with J. Tennyson (UCL)


S&MPO

• Spectroscopy & Molecular Properties of Ozone) relational database (http://ozone. iao.ru and http://ozone.univ-reims.fr/) contains spectral line parameters for the ozone molecule, experimental UV cross-sections, information on ozone’s molecular properties, updated reference lists classified by type as well as programs and extended facilities for user applications.

• Earth, Exo-Planet ?• IAO-Tomsk (V. Perevalov) and University of Reims (V.

Tyuterev)


CH4 DatabaseInstitut Carnot de Bourgogne (V. Boudon)

• Database of line parameters for the three isotopologues of methane (12CH4, 13CH4 and CH3D) with positions, intensities, lineshape parameters from FIR to Visible

• Methane is a major greenhouse pollutant on Earth and an important constituent of many astrophysical bodies (giant planets, Titan, dwarf planets, brown dwarfs, methane stars, exoplanets).

• Modelling methane absorption over a wide spectral range is essential to retrieve methane vertical profiles, minor species abundances and surface propertie.


Stark-B

• This is a database of the theoretical widths and shifts of isolated lines of atoms and ions due to collisions with charged perturbers, obtained within the impact approximation.

• This database is devoted to modelling and spectroscopic diagnostics of stellar atmospheres and envelopes. In addition, it is also relevant to laboratory plasmas, laser equipment and technological plasmas. The database is currently developed in Paris, and a mirror is planned in Belgrade

• Astronomical Observatory of Belgrade (S. Dimitrijević) and Paris Observatory (S. Sahal-Bréchot)


TIPTOPBASE, OPSERVER, XSTARC. Mendoza (IVIC), N. Nunez (CPTM) in collaboration

with Cambridge (G. Rixon) & Paris Observatory (C. Zeippen)

TIPTOPbase located at the Centre de Données astronomiques de Strasbourg, France contains: •TOPbase (http://cdsweb.u-strasbg.fr/topbase/topbase.html), listing atomic data computed in the Opacity Project, namely LS-coupling energy levels, gf-values and photoionization cross sections for light elements (Z ≤ 26) of astrophysical interest. •TIPbase (http://cdsweb.u-strasbg.fr/tipbase/home.html). Intermediate-coupling energy levels, A-values and electron impact excitation cross sections and rates for astrophysical applications (Z ≤ 28), computed by the IRON Project. Opserver, located at the Ohio Supercomputer Center, USA, (http://opacities.osc.edu/), a remote, interactive server for the computation of mean opacities for stellar modelling using the monochromatic opacities computed by the Opacity Project. XSTAR database, used by the XSTAR code (http://heasarc.gsfc.nasa.gov/ docs/software/ xstar/xstar.html) for modelling photoionised plasmas.

Stellar Physics


HITRAN/HITEMP J. Tennyson (UCL) & L. Rothman (CfA, Boston)

http://www.cfa. harvard.edu/hitran/

• -HIgh-resolution TRANsmission molecular absorption database.

• It lists individual line parameters for molecules in the gas phase (microwave through to the UV), photoabsorption cross-sections for many molecules, and refractive indices of several atmospheric aerosols.

• HITEMP, a high temperature extension to HITRAN. So far HITEMP contains data for water, CO2, CO, NO and OH.

• Earth, Planets, Exo-Planets


External Partner: NISTY. Ralchenko

• Atomic Spectra Database (http://physics.nist.gov/asd3) listing critically evaluated data on about 77,000 energy levels and 144,000 spectral lines from atoms and ions of 99 elements.

• The Handbook of Atomic Spectroscopic Data (http://physics.nist.gov/Handbook) listing energy levels and prominent spectral lines for neutral and singly ionised atoms.

• The Spectral Data for the Chandra X-Ray Observatory database (http://physics.nist.gov/chandra) presenting critically compiled wavelengths (20 A to 170 A), energy levels, line classifications, and transition probabilities for several astrophysically important elements.

• SAHA, The NLTE plasma population kinetic modeling database containing theoretical data (http://nlte.nist.gov/SAHA).

• Three bibliographic databases providing references on atomic energy levels and spectra, transition probabilities and spectral line shapes and line broadening.


User Communities• Atmospheric Science

– input for complex terrestrial atmosphere/climate models, determination of concentrations and radiative transport of about 100 species, e.g. water

• Astrophysics, Astrochemistry and Planetary Science– great need for reliable A&M data because of extraordinary

range of physical conditions

• Plasma Technologies– plasma-assisted materials processing or surface

modification, e.g. manufacture of semi-conductor chips. A&M data needed for modeling chemically active plasmas.


User Communities cont’d• Lighting

– A&M databases needed for development of future light sources – new working gas species, e.g. Xe, and metal alloys such as InSb (Indium antimonide)

• Fusion Energy Research– design and operation of vital fusion device systems require

large amounts of A&M collisional and spectroscopic data

• Radiation Science– radiotherapy models exploring damage of DNA by radiation

need A&M data, e.g. electron collisions with DNA components and other biomolecules


Challenges

• Standards / data models– definitions of standard data descriptions ongoing– basis for VAMDC is XSAMS − XML Schema for Atoms,

Molecules, and Solids http://www-amdis.iaea.org/xml/– VAMDC propose new extensions and develop standards for

solid spectroscopy

• Documentation, quality assurance and references• Implementation/performance

– XML vs. CSV or VO-table; synchronous vs. a-synchronous– using Python data manipulation functions and packages, fast

data delivery is possible regardless of format


Work packages – Management and Networking Activities

1. Project Management– financial control, reporting to EU, web site, wiki– appointing Strategic Advisory Board (external experts) and

interacting with it

2. Scientific/Technical Coordination– project planning and progress monitoring– work package leader meetings– interaction with external projects, e.g. IVOA, EuroPlanet, HELIO

3. Dissemination and Training– interface of VAMDC to wider community of producers and users of

data– organization of one annual “VAMDC meeting” and 2−3 scientific

workshops per year, development of tutorials


Work packages –Service Activities

4. Infrastructure Deployment– Implementation of standards into data access protocols

for core databases, implementation of registries– Development of web portal and desktop access software– Expansion of VAMDC with new resources

5. Support to the Infrastructure– Maintainance and monitoring of the infrastructure– Technical support to users– Data preservation – backup and mirroring– Quality assurance and testing


Work packages – Joint Research Activities

6. Interoperability– extension of data model and XML schema (XSAMS), e.g.

different description of molecular states, description of line shapes, Solid Spectroscopy

– creation of dictionaries, definition of access protocols and query languages, definition of registry structure

7. Publishing Tools– developing tools and formulating procedures to include

new atomic and molecular data into VAMDC


XSAMS/VAMDC Development Group IAEA, Austria

Bas Braams D. Humbert

Observatory Paris1/LPMAA2, France 1,2M.L. Dubernet 1E. Roueff 2M. Doronin

Oak Ridge Nat. Lab, USA D.R. Schultz

VNIITF, Russia S. Gagarin P.A. Loboda

NIST, USA Yu. Ralchenko

• UCL, UK• J. Tennyson, C.Hill

• Uppsala Univ., Sweden• N. Piskunov

XSAMS tree

XSAMS

Methods

Functions

Datasources

Objects Processes

Atoms Molecules

Solids Particles

Nonrad.Radiative

Collisions

XSAMS: data sources

May include:AuthorsProduction date Source category

JournalDatabasePrivate

communicationBookReport…

Universal Resource Identifier

Digital Object Identifier Editors Publisher City Comments (any other

relevant information)

Traceability of data origins: a must!

XSAMS: radiative data

Initial and final states Transition energy, wavelength (air or

vacuum), wavenumber, frequencyObservedTheoreticalRitz

Transition probability and derivatives (f, gf, log(gf), line strength S)

Multipole orderE followed by one or more digits (E1, E2,…)M followed by one or more digits (M1, M2,

…)

XSAMS: collisions

Collisions

Initial states

Intermediate states

Final states

Threshold

Tabulated data Fit data

Process class

Validity limits

Accuracy

Fit function

Fit parameters

Physical uncertainty

Data XY

Development of a Solid Spectroscopy Data Model (SSDM) and GhoSST DB

GhoSST “Grenoble Astrophysics and Planetology Solid Spectroscopy and Thermodynamics" database service

Bernard Schmitt, Damien Albertand the SSDM Expert group*

Institut de Planétologie et Astrophysique de Grenoble (former LPG), CNRS / UJF

Solid Spectroscopy DM General Structure

SAMPLE INSTRUMENT

EXPERIMENT

PUBLICATIONS

BAND LIST

SPECIES MATTERS

Sample description

The most complex part for solids !!!

LAYERS superposition

MATERIALS (grains: simple or complexe)

mixing

CONSTITUENTS (phases)

arrangement

SPECIES (molecular, mineral)

combinations

- pure solid, molecular mixture, - polymer, clathrate, hydrate, …- adsorption, absorption, …

- heterogeneous polycrystal, - coated grains, …- crystal with adsorbed molecule

SAMPLE

Layer 2

Layer 1

nn

ATOMS(isotopes)

n

n

MATTER Sample Description

MATTER Object Description

1

1

n

n

- complex mix of constituents or species- macro-species, …

simpleco

mplex

n

Mineral

rock

- Meteorites, natural organics, …- rocks, …

VAMDC-BASECOL Java interface

April 19, 2023 Paris 41

M. Doronin, Paris

VAMDC-VALD Python interface

April 19, 2023 Paris 42

T. Marquardt, Uppsala University


8. New mining and Integration Tools– tools for manipulation of data, e.g. cross-matching data

from different databases– advanced data mining services: data access work flows

targeted at specific user groups, e.g. solar physics, astrochemistry



Tool for cross-matchingHeteregeneous data:

Herespectroscopic data

and collisional data

L. Nenadovic, Paris

Astrochemistry Workshop, Amsterdam, April 2011G. Rixon: March 2011

Science Cases

• For the Astrochemistry community


2nd Annual Meeting, March 2011 50

VAMDC infrastructure and models of interstellar clouds

PDR codes models the physics and chemistry of interstellar clouds• Radiative transfer• Thermal processes• Chemistry

Outputs :• Profiles (structure as a function of depth)

• Abundances • Level excitation (H2,HD, C, C+, CO, O2, H2O, …) • Temperature • Density • Heating and cooling rates • Local emissivities ...

• Column densities • Line intensities • Spectrum

F. Le Petit

They require atomic and molecular data : • Atomic and molecular levels• Radiative transitions (Einstein coefficients, life time, …)• Collision rates with major partners (H, H2, electrons, He)• Chemical reaction ratesNeed complete data sets

Interpretation of new instruments require to treat in detail more and more species

VAMDC infrastructure can be used to • discover easily data• build complete sets of data• get data in standard format=> Simplify the development of such codes

Meudon PDR code• Thousands chemical reactions• Computation of line intensities (from UV to sub mm) for tens of species • 30 000 UV H2 lines• 318 H2 ro-vib. levels in the ground elect. level

Meudon PDR code• Thousands chemical reactions• Computation of line intensities (from UV to sub mm) for tens of species • 30 000 UV H2 lines• 318 H2 ro-vib. levels in the ground elect. level

F. Le Petit

2nd Annual Meeting, March 2011 53

CATS Project – ASTRONET – P. Schilke (Univ. Of Cologne)

VAMDC - Achievements

• All databases able to answer queries and send back information in standardized format

• Portal From which you can query any VAMDC databases

• Standalone Tools to query VAMDC databases and manipulate retrieved files– Example of cross-matching of spectroscopic and collisional

data in order to produce combined sets directly usuable in astrophysical tools


VAMDC level-1 release

As presented to SAB meeting, September 2010

Line lists: query

• We can extract line lists from VAMDC data-services• Start with a query to the services: constrain by wavelength• A demonstration web-portal provides a UI

(This picture captured from http://casx019-zone1.ast.cam.ac.uk/xsamswithdisplay/)

(Subsequent pictures in this example are from the same site.)

http://localhost:8081/xsamswithdisplay/



Line lists: links to results

• Now we have links to results from all suitable databases• The portal has composed the links using the registry and the

standard protocol for the data services• Following each link triggers a query on that database

(Image show results of submitting query form)

Line lists: raw XSAMS

• The raw XSAMS output has all the details• Save this to disc if you want to process it locally: it’s XML• Not pretty; and more information than we need here

Line list: rendered

• The portal extracts the line list from the XML as a web page• This is just one possible transformation of XSAMS - other extracts are easily coded up

For GAIA: Simulated Spectra used to train GAIA pipeline-

Done using VAMDC Portal+ MARCS model using both VALD for atomic data and CDMS for CN data (Aks

Questions to N. Piskunov)

ICAMDATA, Vilnius, Sept 2010 60

Need More Data fromOther Databases, i.eCollisions (NLTE effects)

Quantities that can be handled for now

• Any atom or molecules with PAH, Solids• Theoretical/Experimental• Radiative processes• Non-Radiative• Inelastic and Reactive Collision• Line parameters (broadening/shifting) with

Environment


EXTENSIBLE

Conclusions

• Atomic and molecular data play a key role in many scientific areas.

• Specialised database development in each area is inefficient and may lead to significant duplication of effort and accuracy problems.

• VAMDC aims to provide unifying structures and protocols for interlinking of databases worldwide.

• Provision of the actual data remains in the hands of the experts in each particular field.


Open to Any Producers & Users from June 2012

• Open to Producers to include their data within VAMDC environment– In existing databases– Building their own database (Django publishing tools for

example) and registrying it to VAMDC registries

• Open to users to include VAMDC developed software into their own applications– Licencing will allow any use

• All Softwares & Documentation From June 2012 at http://www.vamdc.eu (org)


http://www.vamdc.eu/

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