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Chapter 7
INPUT FILES

7.1 Condition Files

  • *.eris: An input file storing all the conditions of MEM calculations.
  • *.prf: An input file of PRIMA storing conditions of MEM calculations. This file keeps backward compatibility with PRIMA while some new parameters are added for new features in Dysnomia and ERIS.
  • *.alb: An input file of ALBA storing conditions of MEM calculations.

7.2 Intensity Files

  • *.fcf, *.cif: Standard CIF file format.
  • *.fos: Powder diffraction data generated by RIETAN-FP [6].
  • *.mem: (a) Single-crystal data or (b) powder data where standard uncertainties of observed structure factors are given.
  • *.baymem: .
  • *.ffo: Powder diffraction data generated by RIETAN-FP [6].
  • *.hkl: .

7.3 File format of *.eris

7.3.1 title

  • Value: string of characters up to 80 characters long
  • Default: none
  • Description: Title of the calculation.

7.3.2 algorithm

  • Value: 0/1
  • Default: 1

  • Description: Switch algorithm of MEM calculation.

    1. ZSPA algorithm.
    2. L-BFGS algorithm.

7.3.3 beam_source

  • Value: 0/1
  • Default: 0

  • Description: From which experiment was the diffraction data obtained? This keyword only affects on the Wilson plot performed to calculate scale factor in the MEP analysis.

    1. X-ray diffraction data.
    2. Neutron diffraction data.

7.3.4 cell

  • Value: a b c \(\alpha \) \(\beta \) \(\gamma \)
  • Default: none
  • Description: Gives unit cell parameters for input data *.hkl, *.ffo, in which unit cell parameters are not recorded.

7.3.5 data

  • Value: filename
  • Default: compulsory keyword – no default
  • Description: Gives the name of diffraction data file. It can be specified as a relative path from the place of *.eris file.

7.3.6 delta_d

  • Value: positive real number
  • Default: 0
  • Description: Maximum difference in d/Angstrom in grouped reflections. Reflections with the d-spacing closer than delta_d will be considered as overlapped and treated as grouped reflections.

7.3.7 elements

  • Value: positive integer, followed by a pair of element name and real number in each line
  • Default: 0
  • Description: Number of chemical species in the unit cell. It is followed by lines of equal numbers, each line describing a pair of element names and amounts in the unit cell. These data are used for the Wilson plot performed to calculate scale factor in the MEP analysis.

7.3.8 epsilon

  • Value: positive real number
  • Default: 0
  • Description: A small value \(\varepsilon \), used as a criterion for convergence of optimization. The convergence of the L-BFGS algorithm is judged by \begin {equation} \sqrt { \sum _{k=1}^{N_\mathrm {V}} \rho _k \left ( \frac {\partial Q}{\partial \rho _k} \right )^2 } < \varepsilon \left \langle \frac {\partial S}{\partial \rho _k} \right \rangle , \end {equation}

7.3.9 lambda

  • Value: positive real number
  • Default: automatically determined
  • Description: The initial Lagrangian multiplier \(\lambda \) used in the ZSPA algorithm. This keyword has no effect on the use of the L-BFGS algorithm.

7.3.10 lambda_coef

  • Value: positive real number
  • Default: 0.05
  • Description: A coefficient t, to adjust Lagrangian multiplier \(\lambda \). This keyword is used only in the ZSPA algorithm and has no effect on the use of the L-BFGS algorithm.

7.3.11 max_cycles

  • Value: positive integer
  • Default: 10000
  • Description: Maximum number of MEM cycles.

7.3.12 resolution

  • Value: positive real number
  • Default: 0.1
  • Description: Resolution of real space voxels in angstrom.

7.3.13 restart

  • Value: 0/1
  • Default: 0

  • Description: From which densities will you start the calculation?

    1. Start from flat (or prior) density.
    2. Start from the results of previous run stored in *.pgrid file.

7.3.14 scale_sigma

  • Value: real value
  • Default: 1
  • Description: Scale input \(\sigma (F)\) as \(\sigma (F)' = \textrm {scale\_sigma} \times \sigma (F)\).

7.3.15 space_group

  • Value: [space group number] [setting number]
  • Default: 1 1
  • Description: Gives the space group number and setting number.

7.3.16 scio

  • Value: real value
  • Default: 1
  • Description: Scale input \(\sigma (F)\) as \(\sigma (F)' = \sigma (F) / \sqrt { \textrm {scio} }\).

7.3.17 use_prior

  • Value: 0/1
  • Default: 0

  • Description: Which prior densities will you use?

    1. Flat density.
    2. Prior density recorded in *_prior.pgrid file.

7.3.18 weight_cn

  • Value: eight real numbers
  • Default: 1 0 0 0 0 0 0 0
  • Description: Fractions of lambda for generalized constraints.

7.3.19 weight_m

  • Value: real number
  • Default: 0
  • Description: Scale input \(\sigma (F)\) as \(\sigma (F)' = c \times \sigma (F) / \sqrt { m }\), where \(m\) is multiplicity of the reflection \(F\) and \(c\) is a constant value automatically determined so as not to change total scale of \(\langle \sigma (F)\rangle \). See section 4.4 for more detail.

7.3.20 weight_d

  • Value: [auto/exp/power] [real number]
  • Default: auto
  • Description: Weighting of observed reflections based on lattice-plane spacing \(d\).

7.4 File format of *.prf

The content of *.prf storing various flags and specifications for MEM analysis is described in 6.2.1, and execution of ERIS and the subsequent input of *.prf in 6.2.2.

7.5 File format of *.alb

7.6 File format of *.mem

A line to give values (POP1, POP2, IPTYP, JPH, JPK, and JPL) related to preferred orientation is currently a dummy one. Never analyze powder diffraction data where preferred orientation was observed.

Grid numbers along \(a\), \(b\), and \(c\) axes should be selected in such a way that symmetry elements such as mirrors, rotation axes, and inversion centers coincide with intersections of grid lines. In addition, the grid numbers must be appropriately set by considering lattice parameters, \(a\), \(b\), and \(c\). On the use of FFT, the best performance is achieved when division number along each axis is represented as \begin {equation*} 2^p \times 3^q \times 4^r \times 5^s \times 7^t \times 11^u \times 13^v , \end {equation*} where \(p\), \(q\), \(r\), \(s\), \(t\), \(u\), and \(v\) are integers equal to or larger than 0. Any other integers are also allowed; the calculation time is proportional to \(N \log N\) even for prime numbers of \(N\).

Beware that the sum, \(T^-\), of negative \(b_\mathrm {c}\)’s in the unit cell should be set at 0.0 even if the sample contains no element with a negative \(b_\mathrm {c}\) value, e.g., H, Li, Ti, or Mn.

In a solid solution where two or more elements occupy the same site, a special procedure is required for calculating the sum, \(T^+\), of positive \(b_\mathrm {c}\)’s and/or the sum, \(T^-\), of negative \(b_\mathrm {c}\)’s in the unit cell [26]. Suppose a virtual chemical species with an average coherent-scattering length, \(\bar {b}_\mathrm {c}\), calculated from the occupancies of the constituent elements. Then, add \(\bar {b}_\mathrm {c}\) multiplied by the number of the virtual chemical species in the unit cell to \(T^+\) if \(\bar {b}_\mathrm {c} > 0\) or \(T^-\) if \(\bar {b}_\mathrm {c} < 0\).

7.7 File format of *.fos

With Alchemy [24], text files with the following two formats can be obtained from output files, *.lst, of GSAS:

*.fos


Regardless of ID(neg.), both positive and negative values of total scattering amplitudes are always input. If ID(neg.) = 0, the second amplitude must be 0.0 (dummy).

*.mem


If ID(neg.) = 0, only a positive total scattering amplitude is input, followed by \(\lambda \) in the same line. If ID(neg.) = 1, both positive and negative values of total scattering amplitudes are input, followed by \(\lambda \) as well.

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