PyhCha

Atomic Polyhedra Chains

The scripts and code to build atomic polyhedra chains and calculate pair radial distribution functions (PDF, RDF, etc) for them.

• Atomic Simulation Environment (ASE) https://wiki.fysik.dtu.dk/ase/ is inheritely used.

  A.H. Larsen, J.J. Mortensen, J. Blomqvist, I.E. Castelli, R. Christensen, M. Dułak, J. Friis, M.N. Groves, B. Hammer, C. Hargus, E.D. Hermes, P.C. Jennings, P.B. Jensen, J. Kermode, J.R. Kitchin, E.L. Kolsbjerg, J. Kubal, K. Kaasbjerg, S. Lysgaard, J.B. Maronsson, T. Maxson, T. Olsen, L. Pastewka, A. Peterson, C. Rostgaard, J. Schiøtz, O. Schütt, M. Strange, K.S. Thygesen, T. Vegge, L. Vilhelmsen, M. Walter, Z. Zeng, K.W. Jacobsen The atomic simulation environment - a Python library for working with atoms J. Phys.: Condens. Matter, 2017, 29, 273002

• Polyhedra data are from:

  Arrangement of n points on a sphere in 3 dimensions so as to maximize the volume of the convex hull [1994 by R. H. Hardin, N. J. A. Sloane & W. D. Smith] http://neilsloane.com/maxvolumes

• PDF calculation code is adapted from C++ code of PDFgui https://github.com/diffpy/diffpy.pdffit2 (file diffpy.pdffit2/libpdffit2/pdf.cc)

  C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin, J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals, J. Phys.: Condens. Matter 19, 335219 (2007)

Example

Create chain of 3 segments of BaO6 octavedra.

from gen_AOn_chain import gen_polyhedra_chain

atoms = gen_polyhedra_chain(n_verteces=6, n_segments=3,
                            R=2.75, phi1=30, theta=120, 
                            phi2=30, A='Ba')

print(atoms)

Output:

Atoms(symbols='BaO6BaO5BaO5', pbc=False)

Acknowledgments

The work was financially supported by a Russian Science Foundation, grant # 22-12-00106.

Cite

If the code is used in academic publications please cite the following article:

Glass and Ceramics, 2023, 80, 85-90 doi: 10.1007/s10717-023-00562-0