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.

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.

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>

Determination of the [Pt(NH3)5Cl]Br3 crystal structure from X-ray powder diffraction data using multi-population genetic algorithm

2017 ◽  
Vol 32 (S1) ◽  
pp. S110-S117 ◽  
Author(s):  
A. N. Zaloga ◽  
I. S. Yakimov ◽  
P. S. Dubinin
Keyword(s):  
Crystal Structure ◽  
Genetic Algorithm ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Population Genetic ◽  
Powder Diffraction Data ◽  
Distribution Maps ◽  
Structure Solution ◽  
Population Genetic Algorithm

The paper describes an approach for automated crystal structure solution from powder diffraction data using the multi-population genetic algorithm (MPGA). The advantage of using co-evolution with the best individual exchange, compared with the using of the evolution with a single genetic algorithm without interpopulation exchange, is shown. As an example, the paper describes the use of MPGA for solving the [Pt(NH3)5Cl]Br3 crystal structure, having the tetragonal I41/a space group [a = 17.2587(5) Å, c = 15.1164(3) Å, Z = 16, unit-cell volume V = 4502.61(10) Å3]. The MPGA convergence charts and the atomic positions distribution maps of the MPGA populations are given. The description of the final structure solution is also shown.

scholarly journals Solving molecular crystal structures from laboratory X-ray powder diffraction data withDASH: the state of the art and challenges

2005 ◽  
Vol 38 (2) ◽  
pp. 249-259 ◽  
Author(s):  
Alastair J. Florence ◽  
Norman Shankland ◽  
Kenneth Shankland ◽  
William I. F. David ◽  
Elna Pidcock ◽  
...  
Keyword(s):  
Global Optimization ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Search Space ◽  
Powder Diffraction Data ◽  
Multi Centre Study ◽  
X Ray ◽  
Structure Solution

The crystal structures of 35 molecular compounds have been redetermined from laboratory monochromatic capillary transmission X-ray powder diffraction data using the simulated-annealing approach embodied within theDASHstructure solution package. The compounds represent industrially relevant areas (pharmaceuticals; metal coordination compounds; nonlinear optical materials; dyes) in which the research groups in this multi-centre study are active. The molecules were specifically selected to form a series within which the degree of structural complexity (i.e. degrees of freedom in the global optimization) increased systematically, the degrees of freedom increasing with increasing number of optimizable torsion angles in the structural model and with the inclusion of positional disorder or multiple fragments (counterions; crystallization solvent;Z′ > 1). At the lower end of the complexity scale, the structure was solved with excellent reproducibility and high accuracy. At the opposite end of the scale, the more complex search space offered a significant challenge to the global optimization procedure and it was demonstrated that the inclusion of modal torsional constraints, derived from the Cambridge Structural Database, offered significant benefits in terms of increasing the frequency of successful structure solution by restricting the magnitude of the search space in the global optimization.

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>

Structure solution of zeolites from powder diffraction data

2004 ◽  
Vol 219 (12) ◽  
Author(s):  
Allen W. Burton
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structure Elucidation ◽  
Model Building ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
Zeolite Structure ◽  
Structure Solution

AbstractThis article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.

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
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