Analyzing models using Atomes

Atomes can compute the following structural characteristics of a 3D structure model:

• Radial distribution functions g(r) (RDFs) [1] including \(^{\circ}\):

  • Total RDFs for neutrons and X-rays.

  • Partial RDFs.

  • Bhatia-Thornton RDFs [2]

  \(^{\circ}\) Radial distribution functions can be computed by i) direct real space calculation and/or ii) Fourier transforming of the structure factor calculated using the Debye formalism [3]

• Structure factors S(q) [3] including \(^{\circ\circ}\):

  • Total structure factors S(q) for neutrons and X-rays.

  • Total Q(q) [3], [4] for neutrons and X-rays.

  • Partial S(q):

    • Faber-Ziman [5] partial S(q)

    • Ashcroft-Langreth [6], [7], [8] partial S(q)

    • Bhatia-Thornton [9] partial S(q)

  \(^{\circ\circ}\) Structure factors can be computed by i) Fourier transforming of the radial distribution functions and/or ii) using the Debye formalism [3]

• Interatomic bond properties

  • Coordination numbers

  • Atomic near neighbor distribution

  • Fraction of links between tetrahedra

  • Fraction of tetrahedral units

  • Bond lengths distribution for the first coordination sphere

• Distribution of Bond angles

• Distribution of Dihedral angles

• Ring statistics, according to several definitions:

  • All closed paths (no rules)

  • King's rings [10], [11]

  • Guttman's rings [12]

  • Primitive rings [13], [14] (or Irreducible [15])

  • Strong rings [13], [14]

  And including options to:

  • search only for ABAB rings

  • exclude rings with homopolar bonds (A-A or B-B) from the analysis

  Ring statistics is presented according to the R.I.N.G.S. method [16].

• Chain statistics, including options to:

  • search only for AAAA chains

  • search only for ABAB chains

  • exclude chains with homopolar bonds (A-A or B-B) from the analysis

  • search only for 1-(2)\(_n\)-1 chains

• Spherical harmonics invariant, \(Q_l\), as local atomic ordering symmetry identifiers [17]

  • Average Q\(_l\) for each chemical species

  • Average Q\(_l\) for a user specified structural unit

• Mean Square Displacement of atoms (MSD)

  • Atomic species MSD

  • Directional MSD (x, y, z, xy, xz, yz)

  • Drift of the center of mass

See appendix 5 to learn more about the physics and the chemistry behind these calculations.

The calculations presented in this list can only be performed on the active project, ie. the project which name appears in the title bar of the Atomes program main window, in bold font in the Atomes workspace tree and in green bold font in the workspace information dialog [Fig. 1.1].
For more about running calculation using Atomes see chapter 4.

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