Crystallography Open Database (COD), Predicted Crystallography …€¦ · Nye J.-F. (1985),...
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CONCLUSIONS COD server is technically in position to store and serve all structures that are currently solved. COD deposition procedure ensures syntactic correctness and presence of the most essential CIF data. COD and PCOD are constantly expanded to meet more needs of crystallographic community MPOD currently serves the uploaded data. Automatic uploading and checking is Planned and under development. We rely on the help of crystallographic community to add more data and ensure the data correctness! Use and Add more structures properties to: http://www.crystallography.net/ http://www.materialproperties.org/ THANK YOU ! REFERENCES [1] http://www.crystallography.net/ [2] S. Grazulis et al., (2009). J. Appl. Cryst. 42, 726-729. [3] A. Le Bail (2010). Phys. Chem. Chem. Phys. 12, 8521-8530. [4] A. Le Bail (2008). Powder Diffr. Suppl. 23, S5-S12. [5] http://www.materialproperties.org/ [6] Kocks U.F., Tomé C.N., Wenk H.-R. (1998). [7] "Texture and Anisotropy", Cambridge University Press Nye J.-F. (1985), "Physical Properties of Crystals: their representation by tensors and matrices", Lavoisier publishers [8] Chateigner D. (2010). "Combined analysis", Wiley-ISTE COD/PCOD contact: [email protected] Crystallography Open Database (COD), Predicted Crystallography Open Database (PCOD) and Material Properties Open Database (MPOD) Saulius Gražulis a , Giancarlo Pepponi b , Justas Butkus a , Andrius Merkys a , Adriana Daškevič a , Armel Le Bail c , Robert Downs d , Luca Lutterotti e , Peter Moeck f , Alexandre F.T. Yokochi g , Miguel Quirós Olozábal h , Daniel Chateigner i a Vilnius University Institute of Biotechnology, Vilnius, Lithuania b Fondazione Bruno Kessler, Trento, Italia c Laboratoire des Oxydes et Fluorures, CNRS and Université du Maine, Le Mans, France d Department of Geosciences, University of Arizona, Tucson, Arizona, USA f Portland State University, Department of Physics, Portland, Oregon, USA g School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA h Departamento de Química Inorgánica, Universidad de Granada, Granada, Spain i CRISMAT-ENSICAEN, IUT-Caen, Université de Caen Basse-Normandie, Caen, France [email protected] Deposit your data to COD for publication! http://www.crystallography.net/ MPOD Material Property Open Database www.materialproperties.org Inspiered by the COD, the MPOD aims to collect and make freely available published material properties data, keeping the connection to the structural information. The data is stored in MPOD files that can be searched for and downloaded from the website. Moreover an online view of the datafile formatting tensors into matrices, of the property and publication details are also available. MPOD Coded Properties The initial set includes mechanical properties, elastic stiffness and compliance, internal friction; electrical properties, resistivity, dielectric permittivity and stiffness, thermodynamic properties, heat capacity, thermal conductivity, diffusivity and expansion; electromechanical properties, piezoelectricity, electrostriction, electromechanical coupling; optical properties; piezooptic and photoelastic properties; superconducting properties, critical fields, penetration and coherence lengths. Properties are reported in mpod files where the original published paper containing the data is cited and structural and experimental information is also given. One mpod file contains information relative to only one publication and one phase. Expanding the PCOD 2010 update : 898.707 SiO 2 entries were added from ZEFSAII zeolite predictions and the contributions from GRINSP increased to 163.520 (silicates, phosphates, sulfates of Al, Ti, V, Ga, Nb, Zr, or zeolites, fluorides, etc). The PCOD is the first database to attain and offer more than one million of CIF entries. Software : a new GRINSP version is now available [3] for parallel computing (for instance using fully the 8 processors of an INTEL core i7). Other data from other prediction computer programs (CASTEP, CERIUS2, CRYSTAL, G42, GULP, USPEX…) are expected, just send them, please. Acknowledgments The Vilnius COD development group is financed by the Research Council of Lithuania, contract No. MIP-124/2010 We thank Adriana Daškevič and Andrius Merkys for help with software development and data curation. Authors thank to all CIF donators, listed on our Web page, and to numerous anonymous volunteers who help to collect data and keep COD running. The COD Advisory Board thanks commercial supporters for donated hardware and financial support. The MPOD development was partially carried out within the Xmat project (“Combination of X-Ray diffraction and X-Ray Fluorescence techniques in material science”), supported by the Provincia Autonoma di Trento and the European Union in the framework of the Marie Curie COFUND program - Call for proposals 4 - researcher 2009 – Outgoing. PCOD Powder P2D2 All powder patterns (> 1 million) were calculated and gathered in the P2D2 (Predicted Powder Diffraction Database [4]), they can be used for search- match purposes with EVA (Bruker), Highscore (Panalytical) and more soon. Trying to solve the zeolite LZ-200 unknown crystal structure by using PCOD/ P2D2 and search- match identification techniques [x] VIRTUAL MODELS in PCOD Zeolites B 2 O 3 nanotubes [Ca 3 Al 4 F 21 ] 3- Titanosilicates COD - Introduction Data are arriving in ever increasing rates. Thus, automated software tools are needed to cope with the growing amount of data, to provide consistent, uniform and accurate information. The following goals are set by COD team: build automated structure deposition tools; build a collaboration platform for structure validation and curation; ensure data quality – uniformity, integrity, and trustworthiness; make scientific data freely accessible to anyone. COD - Automatic data deposition MPOD – datafile view MPOD – search phase Article/reference view MPOD Coded Properties As its inspirator, MPOD files use a Starfile syntax used and developed for the Crystallographic Information Files (CIF). For the structural information, available items in the CORE CIF dictionary are used. A dictionary containing new definitions for the material properties has been written according to the Dictionary Definition Language DDL1. However some tricks were adopted to adapt the relatively strict Starfile syntax to allow for multiple entries still avoiding ambiguousness. The value of a property tag is a label. This label is then used in a _loop where the tensorial index and the actual value is given. Units are univocally define in the dictionary itself. Experimantal conditions (temperature, pressure, … ) can also be inserted in the loop.
Transcript of Crystallography Open Database (COD), Predicted Crystallography …€¦ · Nye J.-F. (1985),...
CONCLUSIONS
COD server is technically in position to store and serve all structures that are currently solved. COD deposition procedure ensures syntactic correctness and presence of
the most essential CIF data. COD and PCOD are constantly expanded to meet more
needs of crystallographic community MPOD currently serves the uploaded data.
Automatic uploading and checking is Planned and under development.
We rely on the help of crystallographic community to add more data and ensure the data correctness!
Use and Add more structures properties to:
http://www.crystallography.net/ http://www.materialproperties.org/
THANK YOU !
REFERENCES
[1] http://www.crystallography.net/ [2] S. Grazulis et al., (2009). J. Appl. Cryst. 42, 726-729. [3] A. Le Bail (2010). Phys. Chem. Chem. Phys. 12, 8521-8530. [4] A. Le Bail (2008). Powder Diffr. Suppl. 23, S5-S12. [5] http://www.materialproperties.org/ [6] Kocks U.F., Tomé C.N., Wenk H.-R. (1998). [7] "Texture and Anisotropy", Cambridge University Press Nye J.-F. (1985), "Physical Properties of Crystals: their representation by tensors and matrices", Lavoisier publishers [8] Chateigner D. (2010). "Combined analysis", Wiley-ISTE COD/PCOD contact: [email protected]
Crystallography Open Database (COD), Predicted Crystallography Open Database (PCOD)
and Material Properties Open Database (MPOD) Saulius Gražulisa, Giancarlo Pepponib, Justas Butkusa, Andrius Merkysa, Adriana Daškeviča, Armel Le Bailc, Robert Downsd, Luca Lutterottie,
Peter Moeckf, Alexandre F.T. Yokochig, Miguel Quirós Olozábalh, Daniel Chateigneri
a Vilnius University Institute of Biotechnology, Vilnius, Lithuania b Fondazione Bruno Kessler, Trento, Italia c Laboratoire des Oxydes et Fluorures, CNRS and Université du Maine, Le Mans, France d Department of Geosciences, University of Arizona, Tucson, Arizona, USA f Portland State University, Department of Physics, Portland, Oregon, USA g School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA h Departamento de Química Inorgánica, Universidad de Granada, Granada, Spain i CRISMAT-ENSICAEN, IUT-Caen, Université de Caen Basse-Normandie, Caen, France [email protected]
Deposit your data to COD for publication!
http://www.crystallography.net/
MPOD Material Property Open Database
www.materialproperties.org Inspiered by the COD, the MPOD aims to collect and make freely available published material properties data, keeping the connection to the structural information. The data is stored in MPOD files that can be searched for and downloaded from the website. Moreover an online view of the datafile formatting tensors into matrices, of the property and publication details are also available.
MPOD Coded Properties
The initial set includes mechanical properties, elastic stiffness and compliance, internal friction; electrical properties, resistivity, dielectric permittivity and stiffness, thermodynamic properties, heat capacity, thermal conductivity, diffusivity and expansion; electromechanical properties, piezoelectricity, electrostriction, electromechanical coupling; optical properties; piezooptic and photoelastic properties; superconducting properties, critical fields, penetration and coherence lengths. Properties are reported in mpod files where the original published paper containing the data is cited and structural and experimental information is also given. One mpod file contains information relative to only one publication and one phase.
Expanding the PCOD 2010 update : 898.707 SiO2 entries were added from ZEFSAII zeolite predictions and the contributions from GRINSP increased to 163.520 (silicates, phosphates, sulfates of Al, Ti, V, Ga, Nb, Zr, or zeolites, fluorides, etc). The PCOD is the first database to attain and offer more than one million of CIF entries.
Software : a new GRINSP version is now available [3] for parallel computing (for instance using fully the 8 processors of an INTEL core i7).
Other data from other prediction computer programs (CASTEP, CERIUS2, CRYSTAL, G42, GULP, USPEX…) are expected, just send them, please.
Acknowledgments The Vilnius COD development group is financed by the Research Council of Lithuania, contract No. MIP-124/2010 We thank Adriana Daškevič and Andrius Merkys for help with software development and data curation. Authors thank to all CIF donators, listed on our Web page, and to numerous anonymous volunteers who help to collect data and keep COD running. The COD Advisory Board thanks commercial supporters for donated hardware and financial support. The MPOD development was partially carried out within the Xmat project (“Combination of X-Ray diffraction and X-Ray Fluorescence techniques in material science”), supported by the Provincia Autonoma di Trento and the European Union in the framework of the Marie Curie COFUND program - Call for proposals 4 - researcher 2009 – Outgoing.
PCOD Powder P2D2
All powder patterns (> 1 million) were calculated and gathered in the P2D2 (Predicted Powder Diffraction Database [4]), they can be used for search-match purposes with EVA (Bruker), Highscore (Panalytical) and more soon.
Trying to solve the zeolite
LZ-200 unknown crystal structure by using PCOD/P2D2 and search-
match identification techniques [x]
VIRTUAL MODELS in PCOD
Zeolites B2O3 nanotubes
[Ca3Al4F21]3-
Titanosilicates
COD - Introduction Data are arriving in ever increasing rates. Thus, automated software tools are needed to cope with the growing amount of data, to provide consistent, uniform and accurate information. The following goals are set by COD team: l build automated structure deposition tools; l build a collaboration platform for structure validation and curation; l ensure data quality – uniformity, integrity, and trustworthiness; l make scientific data freely accessible to anyone.
COD - Automatic data deposition
MPOD – datafile view
MPOD – search phase
Article/reference view
MPOD Coded Properties
As its inspirator, MPOD files use a Starfile syntax used and developed for the Crystallographic Information Files (CIF). For the structural information, available items in the CORE CIF dictionary are used. A dictionary containing new definitions for the material properties has been written according to the Dictionary Definition Language DDL1. However some tricks were adopted to adapt the relatively strict Starfile syntax to allow for multiple entries still avoiding ambiguousness. The value of a property tag is a label. This label is then used in a _loop where the tensorial index and the actual value is given. Units are univocally define in the dictionary itself. Experimantal conditions (temperature, pressure, … ) can also be inserted in the loop.
