A new parallel and GPU version of aTREOR-based algorithm for indexing powder diffraction data

2015 ◽  
Vol 48 (1) ◽  
pp. 166-170 ◽  
Author(s):  
Ivan Šimeček ◽  
Jan Rohlíček ◽  
Tomáš Zahradnický ◽  
Daniel Langr
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Graphics Processing Units ◽  
Solution Process ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Indexing Method ◽  
Brute Force Approach ◽  
Graphics Processing

One of the key parts of the crystal structure solution process from powder diffraction data is indexing – the determination of the lattice parameters from experimental data. This paper presents a modification of theTREORindexing method that makes the algorithm suitable and efficient for execution on graphics processing units. TheTREORalgorithm was implemented in its pure form, which can be simply described as a `brute-force' approach. The effectiveness and time consumption of such an algorithm was tested on several data sets including monoclinic and triclinic examples. The results show the potential of using GPUs for indexing powder diffraction data.

scholarly journals A new parallel version of a dichotomy based algorithm for indexing powder diffraction data

2020 ◽  
Vol 235 (6-7) ◽  
pp. 203-212
Author(s):  
Ivan Šimeček ◽  
Aleksandr Zaloga ◽  
Jan Trdlička
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Solution Process ◽  
Search Space ◽  
Powder Diffraction Data ◽  
Indexing Methods ◽  
Parallel Version ◽  
Structure Solution ◽  
Indexing Method

AbstractOne of the key parts of the crystal structure solution process from powder diffraction data is the determination of the lattice parameters from experimental data shortly called indexing. The successive dichotomy method is one of the most common ones for this process because it allows an exhaustive search. In this paper, we discuss several improvements for this indexing method that significantly reduces the search space and decrease the solution time. We also propose a combination of this method with other indexing methods: grid search and TREOR. The effectiveness and time-consumption of such algorithm were tested on several datasets, including orthorhombic, monoclinic, and triclinic examples. Finally, we discuss the impacts of the proposed improvements.

Molecular, crystallographic and algorithmic factors in structure determination from powder diffraction data by simulated annealing

2002 ◽  
Vol 35 (4) ◽  
pp. 443-454 ◽  
Author(s):  
Kenneth Shankland ◽  
Lorraine McBride ◽  
William I. F. David ◽  
Norman Shankland ◽  
Gerald Steele
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Solution Process ◽  
Search Space ◽  
Systematic Investigation ◽  
Monoclinic Space Group ◽  
Powder Diffraction Data ◽  
Structure Solution

The crystal structure of famotidine form B has been solved directly from powder diffraction data by the application of simulated annealing. The molecule crystallizes in the monoclinic space groupP21/cwith refined unit-cell dimensionsa = 17.6547 (4),b= 5.2932 (1),c= 18.2590 (3) Å and β = 123.558 (1)° atT= 130 K. The core of this work is a systematic investigation of the influence of algorithmic, crystallographic and molecular factors on the structure solution process. With an appropriate choice of annealing schedule, molecular description and diffraction data range, the overall number of successes in solving the crystal structure is close to 100%. Other factors, including crystallographic search space restrictions and parameter sampling method, have little effect on the structure solution process. The basic principles elucidated here have been factored into the design of theDASHstructure solution program.

GALLOP: Accelerated molecular crystal structure determination from powder diffraction data

CrystEngComm ◽  
2021 ◽  
Author(s):  
Mark J Spillman ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Graphics Processing Units ◽  
Molecular Crystal ◽  
Global Optimisation ◽  
Crystal Structure Determination ◽  
Powder Diffraction Data ◽  
Graphics Processing

A combined local and global optimisation approach to crystal structure determination from powder diffraction data (SDPD) is presented. Using graphics processing units (GPUs) to accelerate the underpinning calculations, the speed...

Jpowder: a Java-based program for the display and examination of powder diffraction data

2010 ◽  
Vol 43 (6) ◽  
pp. 1532-1534
Author(s):  
Anders J. Markvardsen ◽  
Kreecha Puphaiboon ◽  
Mohammad Arjeneh ◽  
Kenneth Shankland ◽  
Hannah L. Guest ◽  
...  
Keyword(s):  
Data Analysis ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Software Package ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Network Access ◽  
Web Page ◽  
Analysis Process ◽  
Structure Solution

The ability to display and inspect powder diffraction data quickly and efficiently is a central part of the data analysis process. Whilst many computer programs are capable of displaying powder data, their focus is typically on advanced operations such as structure solution or Rietveld refinement. This article describes a lightweight software package,Jpowder, whose focus is fast and convenient visualization and comparison of powder data sets in a variety of formats from computers with network access.Jpowderis written in Java and uses its associated Web Start technology to allow `single-click deployment' from a web page, http://www.jpowder.org.Jpowderis open source, free and available for use by anyone.

FIDDLE. Simultaneous Indexing and Structure Solution from Powder Diffraction Data using a Genetic Algorithm and Correlation Functions

2019 ◽  
Author(s):  
Carmen Guguta ◽  
Jan M.M. Smits ◽  
Rene de Gelder
Keyword(s):  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Correlation Functions ◽  
Cross Correlation ◽  
Simultaneous Optimization ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Matching Technique

A method for the determination of crystal structures from powder diffraction data is presented that circumvents the difficulties associated with separate indexing. For the simultaneous optimization of the parameters that describe a crystal structure a genetic algorithm is used together with a pattern matching technique based on auto and cross correlation functions.<br>

Gaining insights into the evolutionary behaviour in genetic algorithm calculations, with applications in structure solution from powder diffraction data

2002 ◽  
Vol 353 (3-4) ◽  
pp. 185-194 ◽  
Author(s):  
Scott Habershon ◽  
Kenneth D.M. Harris ◽  
Roy L. Johnston ◽  
Giles W. Turner ◽  
Jennifer M. Johnston
Keyword(s):  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
Structure Solution

Challenging structure determination from powder diffraction data: two pharmaceutical salts and one cocrystal with Z′ = 2

2019 ◽  
Vol 234 (4) ◽  
pp. 257-268 ◽  
Author(s):  
Carina Schlesinger ◽  
Michael Bolte ◽  
Martin U. Schmidt
Keyword(s):  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Real Space ◽  
Powder Diffraction Data ◽  
The Real ◽  
Pharmaceutical Salts ◽  
Structure Solution ◽  
Space Method

Abstract Structure solution of molecular crystals from powder diffraction data by real-space methods becomes challenging when the total number of degrees of freedom (DoF) for molecular position, orientation and intramolecular torsions exceeds a value of 20. Here we describe the structure determination from powder diffraction data of three pharmaceutical salts or cocrystals, each with four molecules per asymmetric unit on general position: Lamivudine camphorsulfonate (1, P 21, Z=4, Z′=2; 31 DoF), Theophylline benzamide (2, P 41, Z=8, Z′=2; 23 DoF) and Aminoglutethimide camphorsulfonate hemihydrate [3, P 21, Z=4, Z′=2; 31 DoF (if the H2O molecule is ignored)]. In the salts 1 and 3 the cations and anions have two intramolecular DoF each. The molecules in the cocrystal 2 are rigid. The structures of 1 and 2 could be solved without major problems by DASH using simulated annealing. For compound 3, indexing, space group determination and Pawley fit proceeded without problems, but the structure could not be solved by the real-space method, despite extensive trials. By chance, a single crystal of 3 was obtained and the structure was determined by single-crystal X-ray diffraction. A post-analysis revealed that the failure of the real-space method could neither be explained by common sources of error such as incorrect indexing, wrong space group, phase impurities, preferred orientation, spottiness or wrong assumptions on the molecular geometry or other user errors, nor by the real-space method itself. Finally, is turned out that the structure solution failed because of problems in the extraction of the integrated reflection intensities in the Pawley fit. With suitable extracted reflection intensities the structure of 3 could be determined in a routine way.

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