A cloud platform for atomic pair distribution function analysis: PDFitc

Yang, Long; Culbertson, Elizabeth A.; Thomas, Nancy K.; Vuong, Hung T.; Kjær, Emil T. S.; Jensen, Kirsten M. Ø.; Tucker, Matthew G.; Billinge, Simon J. L.

doi:10.1107/S2053273320013066

Title: A cloud platform for atomic pair distribution function analysis: PDFitc

Journal Article · Tue Jan 05 00:00:00 EST 2021 · Acta Crystallographica. Section A, Foundations and Advances (Online)

DOI:https://doi.org/10.1107/S2053273320013066· OSTI ID:1712789

; Culbertson, Elizabeth A.; Thomas, Nancy K.; Vuong, Hung T.; Kjær, Emil T. S.;

; Tucker, Matthew G.;

A cloud web platform for analysis and interpretation of atomic pair distribution function (PDF) data ( PDFitc ) is described. The platform is able to host applications for PDF analysis to help researchers study the local and nanoscale structure of nanostructured materials. The applications are designed to be powerful and easy to use and can, and will, be extended over time through community adoption and development. The currently available PDF analysis applications, structureMining, spacegroupMining and similarityMapping , are described. In the first and second the user uploads a single PDF and the application returns a list of best-fit candidate structures, and the most likely space group of the underlying structure, respectively. In the third, the user can upload a set of measured or calculated PDFs and the application returns a matrix of Pearson correlations, allowing assessment of the similarity between different data sets. structureMining is presented here as an example to show the easy-to-use workflow on PDFitc . In the future, as well as using the PDFitc applications for data analysis, it is hoped that the community will contribute their own codes and software to the platform.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); European Research Council (ERC)

Grant/Contract Number:: AC05-00OR22725; DMREF-1534910; 804066

OSTI ID:: 1712789

Alternate ID(s):: OSTI ID: 1787487

Journal Information:: Acta Crystallographica. Section A, Foundations and Advances (Online), Journal Name: Acta Crystallographica. Section A, Foundations and Advances (Online) Vol. 77 Journal Issue: 1; ISSN 2053-2733

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: Denmark

Language:: English

References (34)

PDFgetN3 : atomic pair distribution functions from neutron powder diffraction data using ad hoc corrections Juhás, Pavol; Louwen, Jaap N.; van Eijck, Lambert Journal of Applied Crystallography, Vol. 51, Issue 5 https://doi.org/10.1107/S1600576718010002	journal	August 2018
HKL2MAP : a graphical user interface for macromolecular phasing with SHELX programs Pape, Thomas; Schneider, Thomas R. Journal of Applied Crystallography, Vol. 37, Issue 5 https://doi.org/10.1107/S0021889804018047	journal	September 2004
PDFgetN : a user-friendly program to extract the total scattering structure factor and the pair distribution function from neutron powder diffraction data Peterson, P. F.; Gutmann, M.; Proffen, Th. Journal of Applied Crystallography, Vol. 33, Issue 4 https://doi.org/10.1107/S0021889800007123	journal	August 2000
Teaching diffraction using computer simulations over the Internet Proffen, Th.; Neder, R. B.; Billinge, S. J. L. Journal of Applied Crystallography, Vol. 34, Issue 6 https://doi.org/10.1107/S0021889801013656	journal	November 2001
WinGX suite for small-molecule single-crystal crystallography Farrugia, Louis J. Journal of Applied Crystallography, Vol. 32, Issue 4 https://doi.org/10.1107/S0021889899006020	journal	August 1999
A short history of SHELX Sheldrick, George M. Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122 https://doi.org/10.1107/S0108767307043930	journal	December 2007
EXPGUI , a graphical user interface for GSAS Toby, Brian H. Journal of Applied Crystallography, Vol. 34, Issue 2 https://doi.org/10.1107/S0021889801002242	journal	April 2001
Stoichiometric Control over Ferroic Behavior in Ba(Ti _{1– x} Fe _x )O ₃ Nanocrystals Lombardi, Julien; Yang, Long; Pearsall, Frederick A. Chemistry of Materials, Vol. 31, Issue 4 https://doi.org/10.1021/acs.chemmater.8b04447	journal	January 2019
SIR 97: a new tool for crystal structure determination and refinement Altomare, Angela; Burla, Maria Cristina; Camalli, Mercedes Journal of Applied Crystallography, Vol. 32, Issue 1 https://doi.org/10.1107/S0021889898007717	journal	February 1999
Pair distribution function computed tomography Jacques, Simon D. M.; Di Michiel, Marco; Kimber, Simon A. J. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3536	journal	September 2013
PDFgetX3 : a rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions Juhás, P.; Davis, T.; Farrow, C. L. Journal of Applied Crystallography, Vol. 46, Issue 2 https://doi.org/10.1107/S0021889813005190	journal	March 2013
Recent advances in magnetic structure determination by neutron powder diffraction Rodríguez-Carvajal, Juan Physica B: Condensed Matter, Vol. 192, Issue 1-2 https://doi.org/10.1016/0921-4526(93)90108-I	journal	October 1993
TOPAS and TOPAS-Academic : an optimization program integrating computer algebra and crystallographic objects written in C++ Coelho, Alan A. Journal of Applied Crystallography, Vol. 51, Issue 1 https://doi.org/10.1107/S1600576718000183	journal	February 2018
Structure–property insights into nanostructured electrodes for Li-ion batteries from local structural and diffusional probes Laveda, Josefa Vidal; Johnston, Beth; Paterson, Gary W. Journal of Materials Chemistry A, Vol. 6, Issue 1 https://doi.org/10.1039/C7TA04400C	journal	January 2018
GSAS-II : the genesis of a modern open-source all purpose crystallography software package Toby, Brian H.; Von Dreele, Robert B. Journal of Applied Crystallography, Vol. 46, Issue 2 https://doi.org/10.1107/S0021889813003531	journal	March 2013
Bilbao Crystallographic Server: I. Databases and crystallographic computing programs Aroyo, Mois Ilia; Perez-Mato, Juan Manuel; Capillas, Cesar Zeitschrift für Kristallographie - Crystalline Materials, Vol. 221, Issue 1 https://doi.org/10.1524/zkri.2006.221.1.15	journal	January 2006
Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems Juhás, Pavol; Farrow, Christopher L.; Yang, Xiaohao Acta Crystallographica Section A Foundations and Advances, Vol. 71, Issue 6, p. 562-568 https://doi.org/10.1107/S2053273315014473	journal	September 2015
Next generation cloud computing: New trends and research directions Varghese, Blesson; Buyya, Rajkumar Future Generation Computer Systems, Vol. 79 https://doi.org/10.1016/j.future.2017.09.020	journal	February 2018
Bilbao Crystallographic Server. II. Representations of crystallographic point groups and space groups Aroyo, Mois I.; Kirov, Asen; Capillas, Cesar Acta Crystallographica Section A Foundations of Crystallography, Vol. 62, Issue 2 https://doi.org/10.1107/S0108767305040286	journal	March 2006
Cloud Computing: Today and Tomorrow. Kim, Won The Journal of Object Technology, Vol. 8, Issue 1 https://doi.org/10.5381/jot.2009.8.1.c4	journal	January 2009
Applications of pair distribution function methods to contemporary problems in materials chemistry Young, Callum A.; Goodwin, Andrew L. Journal of Materials Chemistry, Vol. 21, Issue 18 https://doi.org/10.1039/c0jm04415f	journal	January 2011
PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals Farrow, C. L.; Juhas, P.; Liu, J. W. Journal of Physics: Condensed Matter, Vol. 19, Issue 33 https://doi.org/10.1088/0953-8984/19/33/335219	journal	July 2007
A view of cloud computing Armbrust, Michael; Stoica, Ion; Zaharia, Matei Communications of the ACM, Vol. 53, Issue 4 https://doi.org/10.1145/1721654.1721672	journal	April 2010
Crystallography Open Database – an open-access collection of crystal structures Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T. Journal of Applied Crystallography, Vol. 42, Issue 4 https://doi.org/10.1107/S0021889809016690	journal	May 2009
Structures of Hard Phases in Thermoplastic Polyurethanes Terban, Maxwell W.; Dabbous, Raphaël; Debellis, Anthony D. Macromolecules, Vol. 49, Issue 19 https://doi.org/10.1021/acs.macromol.6b00889	journal	September 2016
Big Data and cloud computing: innovation opportunities and challenges Yang, Chaowei; Huang, Qunying; Li, Zhenlong International Journal of Digital Earth, Vol. 10, Issue 1 https://doi.org/10.1080/17538947.2016.1239771	journal	July 2016
PDFgetX2: a GUI-driven program to obtain the pair distribution function from X-ray powder diffraction data Qiu, Xiangyun; Thompson, Jeroen W.; Billinge, Simon J. L. Journal of Applied Crystallography, Vol. 37, Issue 4, p. 678-678 https://doi.org/10.1107/S0021889804011744	journal	July 2004
X-Ray Diffraction Computed Tomography for Structural Analysis of Electrode Materials in Batteries Jensen, Kirsten M. Ø.; Yang, Xiaohao; Laveda, Josefa Vidal Journal of The Electrochemical Society, Vol. 162, Issue 7 https://doi.org/10.1149/2.0771507jes	journal	January 2015
Local Environment of Terbium(III) Ions in Layered Nanocrystalline Zirconium(IV) Phosphonate–Phosphate Ion Exchange Materials Terban, Maxwell W.; Shi, Chenyang; Silbernagel, Rita Inorganic Chemistry, Vol. 56, Issue 15 https://doi.org/10.1021/acs.inorgchem.7b00666	journal	July 2017
ISODISPLACE : a web-based tool for exploring structural distortions Campbell, Branton J.; Stokes, Harold T.; Tanner, David E. Journal of Applied Crystallography, Vol. 39, Issue 4 https://doi.org/10.1107/S0021889806014075	journal	July 2006
Structure-mining: screening structure models by automated fitting to the atomic pair distribution function over large numbers of models Yang, Long; Juhás, Pavol; Terban, Maxwell W. Acta Crystallographica Section A Foundations and Advances, Vol. 76, Issue 3 https://doi.org/10.1107/S2053273320002028	journal	April 2020
Structure of nanoparticles from powder diffraction data using the pair distribution function Neder, Reinhard B.; Korsunskiy, Vladimir I. Journal of Physics: Condensed Matter, Vol. 17, Issue 5 https://doi.org/10.1088/0953-8984/17/5/013	journal	January 2005
Structures of the ferroelectric phases of barium titanate Kwei, G. H.; Lawson, A. C.; Billinge, S. J. L. The Journal of Physical Chemistry, Vol. 97, Issue 10 https://doi.org/10.1021/j100112a043	journal	March 1993
WinPLOTR: A Windows Tool for Powder Diffraction Pattern Analysis Roisnel, T.; Rodríquez-Carvajal, Juan Materials Science Forum, Vol. 378-381 https://doi.org/10.4028/www.scientific.net/MSF.378-381.118	journal	October 2001

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