Identifying duplicate crystal structures: XtalComp, an open-source solution

We describe the implementation of XtalComp, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the “real-world” difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html.

[1]  E. Parthé,et al.  The standardization of inorganic crystal-structure data , 1984 .

[2]  Ho,et al.  Molecular geometry optimization with a genetic algorithm. , 1995, Physical review letters.

[3]  David C. Lonie,et al.  XtalOpt version r7: An open-source evolutionary algorithm for crystal structure prediction , 2011, Comput. Phys. Commun..

[4]  Alex Zunger,et al.  Finding the lowest-energy crystal structure starting from randomly selected lattice vectors and atomic positions: first-principles evolutionary study of the Au–Pd, Cd–Pt, Al–Sc, Cu–Pd, Pd–Ti, and Ir–N binary systems , 2008 .

[5]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[6]  P D Adams,et al.  Numerically stable algorithms for the computation of reduced unit cells. , 2004, Acta crystallographica. Section A, Foundations of crystallography.

[7]  Donald G. Truhlar,et al.  Structures, Rugged Energetic Landscapes, and Nanothermodynamics of Aln (2 ≤ n ≤ 65) Particles , 2007 .

[8]  S. Woodley,et al.  Structure prediction of titania phases : Implementation of Darwinian versus Lamarckian concepts in an Evolutionary Algorithm , 2009 .

[9]  E. Parthé,et al.  STRUCTURE TIDY– a computer program to standardize crystal structure data , 1987 .

[10]  Thirring.  Handbuch der Experimentalphysik , 1928, Nature.

[11]  I. Křivý,et al.  A unified algorithm for determining the reduced (Niggli) cell , 1976 .

[12]  J. C. Schön,et al.  CMPZ– an algorithm for the efficient comparison of periodic structures , 2006 .

[13]  B. Gruber.  The relationship between reduced cells in a general Bravais lattice , 1973 .

[14]  Mario Valle,et al.  How to quantify energy landscapes of solids. , 2009, The Journal of chemical physics.

[15]  A. Oganov,et al.  Crystal fingerprint space--a novel paradigm for studying crystal-structure sets. , 2010, Acta crystallographica. Section A, Foundations of crystallography.

[16]  N. L. Abraham,et al.  Improved real-space genetic algorithm for crystal structure and polymorph prediction , 2008 .

[17]  A. V. Dzyabchenko.  Method of crystal-structure similarity searching , 1994 .

[18]  Mario Valle,et al.  How to predict very large and complex crystal structures , 2010, Comput. Phys. Commun..

[19]  P Verwer,et al.  Method for the computational comparison of crystal structures. , 2005, Acta crystallographica. Section B, Structural science.

[20]  H. Burzlaff,et al.  On quantitative relations among crystal structures , 1992 .

[21]  R. Johnston.  Evolving better nanoparticles: Genetic algorithms for optimising cluster geometries , 2003 .

[22]  James A. Chisholm,et al.  COMPACK: a program for identifying crystal structure similarity using distances , 2005 .

[23]  David C. Lonie,et al.  XtalOpt: An open-source evolutionary algorithm for crystal structure prediction , 2011, Comput. Phys. Commun..