asov janvier 2012
DESCRIPTION
Development of a Solid Spectroscopy Data Model (SSDM) and the GhoSST DataBase GhoSST “ G renoble Astrop h ysics and Planet o logy S olid S pectroscopy and T hermodynamics" database service Bernard Schmitt , Damien Albert, Philippe Bollard, Lydie Bonal, Maria - PowerPoint PPT PresentationTRANSCRIPT
ASOV Janvier 2012
Development of a Solid Spectroscopy Data Model (SSDM) and the GhoSST DataBase
GhoSST “Grenoble Astrophysics and Planetology Solid Spectroscopy and Thermodynamics" database service
Bernard Schmitt, Damien Albert, Philippe Bollard, Lydie Bonal, Maria Gorbacheva, (Pierre Volcke) and the SSDM Expert group*
Institut de Planétologie et Astrophysique de Grenoble (former LPG), CNRS / UJF
Task “New databases” of IDIS/Europlanet (WP25)
+ interoperability/deployment of VAMDC (WP6 / WP4)
Laboratory spectroscopic databases for solids :
- Develop a Solid spectroscopy data model (SSDM)
- Develop a generic database infrastructure (+ some tools) for spectroscopic data of solids (intended to be available to other data producers, in a second step).
- Generate a first new database (GhoSST) covering :- UV-to-FIR transmission spectroscopy of ices and simple organics
- UV-to-NIR bidirectional reflection spectroscopy of solid surfaces (planetary materials; minerals and ices, meteorites, organics, adsorption, processed, …)
- Raman and Fluorescence micro-spectrometry (minerals, meteorites, organics…)
- Infrared micro-spectroscopy- Band list of molecular solids and adsorbed molecules
prototype delivery: July 2011
VO compliant infrastructure
Why a Solid Spectroscopy Data Model ?
• For efficient interoperability (cross search …) we develop
an uniform and as complete as possible description of the solid samples, instruments & techniques used and of the spectral data (spectra and band list) produced by experimentalist of this field.
Development of a “Solid Spectroscopy Data Model” (SSDM) that we intend to propose to be, at least, an European standard, and possibly an international one.
Include in the data model schema, up to some limited complexity level, the requirements of most of the European solid spectroscopy data producers (SSDM Expert Group*)
General aims and (current) limitations
To describe:
- Most Solid samples and their internal structure, up to some degree of complexity, from layers down to atoms
- synthetic and natural materials, simple to complex
- adsorption on / absorption in solids, processed solids, …
- All spectroscopic techniques from VUV up to mm
- absorption, reflection (all types), emission, Raman, fluorescence,
micro-spectrometry, ellipsometry, ATR, …
- All associated types of spectra and their products
- from raw calibrated spectra (level 1) to, e.g., optical constants (level 4)
- Individual vibration bands of molecules and molecular ions in molecular solids and ad/absorbed on/in other solids (no mineral/rocks except as substrate)
Types of planetary / astrophysical solids
- Molecular solids : ices, volatile molecules, hydrates, clathrates, …
- Organic materials : simples, polymers, macromolecular, … - Minerals, salts, hydrated minerals, rocks, …
- Natural and extraterrestrial samples (meteorites, IDP's, Stardust, Lunar, ...)
- Solids with adsorbed and/or absorbed molecules (H2O, …)
- Processed solids with various type of energy sources (UV, ions, …)
- Optical components (windows, filters, fibers, reflectors, radiators, ...)
SSDM General Structure
SAMPLE INSTRUMENT
EXPERIMENT
PUBLICATIONS
BAND LIST
SPECIES MATTERS OBJECTS
SSDM General Structure
SAMPLE INSTRUMENT
EXPERIMENT
PUBLICATIONS
BAND LIST
SPECIES MATTERS MineralsMeteorites, …
Lab spectraObservations
Transmission, Reflection, Raman, Fluo, Microscopy
FTIR, Gonio, Raman, Fluo, Microscope, …
Ices, Minerals, OrganicsMeteorites, Adsorption…
MoleculesMineralsAtoms
Ices, simple OrganicsAdsorption…
Processings: thermal, pressure, chemical, irradiation, …
OBJECTS Meteorites, IDPs, …
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, …
Layers organization - layers_number
- layer_addition
Layer 2
Layer 1 Sample
n n
Sample-Layers-Materials description
Name + references - name - parent_sample
Physical characteristics
- thickness
- thickness_error
- mass, …
Sample processingsThermal processing
- temperature
- temperature_error
- annealing_temperature
- annealing_timePressure processing
Fluid processing
Irradiation processing
Layer organization - layer_order
- layer_type
Layer abundance
- thickness
- mass
Formation conditions
- deposition_rate
- deposition_condition
- deposition_temperature
Materials mixing
- materials_number
- materials_mixing
- Materials_list
Material type
- matter_origin
- matter_family
Material abundance
- mass
- mass_fraction, …
Formation conditions (synthetic)
Precursor materials and mixing
- precursors_list + _mixing
Precursors materials processing
- processing_method
- processing_temperature
- processing_fluid
Material texture
- grain size distribution
- grain texture
LAYERS MATERIALS SAMPLE
Physical characteristics
- density - porosity …
Material type
- matter_origin
- matter_family
Material abundance
- mass
- mass_fraction, …
Formation conditions (synthetic)
Precursor materials and mixing
- precursors_list + _mixing
Precursors materials processing
- processing_method
- processing_temperature
- processing_fluid
Material texture
- grain_size_distribution
- grain_texture
MATERIALS
Materials-Constituents-Species descriptionCONSTITUENTS SPECIES
n n
Constituent organization
- constituents_number
- constituents_mixing
- constituents_list
Constituent type + orga
- family
- arrangement
Constituent abundance
- mass_fraction
- mole_fraction
Constituent state
- phase_type
- phase
- texture
Species organization
- number
- compound_type
- species_list
Matters and Species type
- family
- compound_state
Species abundance
- mass_fraction
- mole_fraction
Molecule composition
- structural_formula
- atom_list + number
- isotopic composition
Molecule name + identifier
- iupac_name
- inchi
- inchikey
Instruments and Techniques
- The instrument is defined by “instrument and technique descriptions” and by "spectral parameters".
Depending on the instrument and technique there are also additional or optional "spatial parameters", "angular parameters", "polarization parameters", and/or "Raman source parameters".
Measurement technics - absorption, reflection (bidirectional, directional-hemispheric, specular)- emission (hemispheric, directional, …)
- Raman, fluorescence, infrared microscopy
Spectral / Angular / Spatial - range - resolution - sampling, …
polarization, …
Experiment
An Experiment is defined as one or a series of spectrum measurement(s) of a single sample with an unique instrument and one of its technique.
During an experiment :
- several types of instrument (measurements) parameters can be changed (e.g. goniometer angles, spectral range, …) without limitation.
- a sample can be subjected to simple changes of a single parameter.
Spectral products: spectra
The spectroscopic data consist of a spectrum file and some "file and spectrum information". The spectrum is linked with an "experiment" which connect to the "sample" and the "instrument parameters" used.
Case of transmission spectroscopy:
o Transmission spectrum (level 1)
o Normalized absorbance spectrum (level 2)
o Absorption coefficient spectrum (level 3)
o Optical constants spectrum (level 4)
- reflection spectra, polarized spectra, BRDF, spectral scattering functions
- emission spectra, spectral emissivity, …
- Raman, Fluorescence, micro-spectroscopy, …
Spectral products: spectra
- Absorbance spectra (level. 2) Optical constants (level. 4)
Spectral products: vibrations band list
A band list contains individual information on each known vibration bands of one particular species inside a constituent in a given phase and physical conditions.
This band information may have different and complementary origins in term of measurement type (absorption, reflection, emission, Raman, …)
- Description of the molecule in its constituent, and the physical conditions
- Description of the vibration band:
- Frequency [+ uncertainty]- Width (FWHM) [+ uncertainty]- Peak Intensity (abs. coeff., or k) [+ uncertainty]- Integrated intensity (abs. coeff., or k) [+ uncertainty]- Vibration mode (ex: 21 + 2 + 3 3)- Vibration mode type (ex: O-H stretching)- Reference list (1st measurement/attribution)
Spectral products: molecular parameters list
The molecular parameters list contain quantum numbers and interaction parameters on defined molecular solid.
Derived from the analysis and attribution of the known absorption bands and allow to calculate the band position (and intensity ?) of the fundamental, overtone and combination internal vibration modes, measured or not.
This band information may have different and complementary origins in term of measurement type (absorption, reflection, emission, Raman, …)
- Description of the molecule in its constituent, and the physical conditions
- Description of the vibration parameters:
- Fundamental modes - Vibration parameters and band position equation- Reference list (model, parameter)
Dictionary of the Solid Spectroscopy Data Model (SSDM version 0.3.4e).
SSDM implementation schema
SampleBand list
Material
Species
Publis
ExperimentInstrumentSpectra
Opt. Cte
User
Exp. Param.
GhoSST Prototype
• Samples: Layers/Material/Constituents Stable Done• Species:
– Molecular and atomic Done Done
– Minerals Done TBD soon
• Matters: – Minerals / Rocks Done TBD soon
– Meteorites Draft TBC TBD
• Instruments/techniques:– Transmission + reflection Done Done
– Emission + Raman/Fluo Done Done
• Spectra and products:– Transmission Done Done
– Reflection Done Done
– Emission + Raman/Fluo Done Done
• Band lists– Molecular solids + adsorption in progress TBD
• Publications Done in progress
SSDM + GhoSST Implementation : planning
For prototype of GhoSST
•Samples: Layers/Material/Constituents Test set + TBD•Species:
– Molecular and atomic Partly Done + TBC
– Minerals TBD
•Matters: – Minerals TBD
– Meteorites TBD
•Spectra and products:– Transmission / molecular solids Test set + TBD
– Reflection / ices (H2O, CO2) Test set + TBD
– Reflection / minerals + adsorption Test set + TBD
– Raman / Meteorites TBD
•Band lists– Molecular solids + adsorption TBD
Data feeding: planning
Extensions of SSDM• Completion of the band list DM (vibration modes of solids, …)• Development of “matters” data model: meteorites• Gas phase (XSAMS) and solid phase (SSDM) datamodels Mapping
Data validation• Scientific validation of spectra (quality, errors, analysis, metadata, …)• Band list : Analysis of spectra, bibliography compilations, …• Tools for determination of vibration modes in solids & bands prediction
Feeding GhoSST database• Species: molecules (continued), minerals• Matters: mineral samples, meteorites, • Spectra: samples, instruments, spectra (transmission, reflection,
Raman) • Band list: lab data + critical biblio compilation
Still a lot of work to be done!
Public version of GhoSST: July 2012
Ongoing developments: SSDM
GhoSST: data import and validation• Administration tools for database feeding interface (data import & survey)• Metadata validation by logical checks on parameters• Update and correction tools• Generic database: adaptation to other data producers
GhoSST: data query, comparison and delivery• User tools for data consultation (favorites, download history, email warning…)• Advanced data visualization and comparison tools• Export in different formats + conversions• Development of VO data access layer
GhoSST: development of “Band list” interface• Database feeding tools• Query and visualization tools – links with spectra• Delivery formats• Integration in the VO layer
Public version of GhoSST: July 2012
Ongoing developments: GhoSST