matscipy.calculators.eam.io

Read and write tabulated EAM potentials

Functions

mix_eam(files, kind, method[, f, rep_ab, ...])

mix eam alloy files data set and compute the interspecies pair potential part using the mean geometric value from each pure species

read_eam(eam_file[, kind])

Read a tabulated EAM potential

write_eam(source, parameters, F, f, rep, ...)

Write an eam lammps format file

Classes

EAMParameters(symbols, atomic_numbers, ...)

Embedded Atom Method potential parameters
class matscipy.calculators.eam.io.EAMParameters(symbols, atomic_numbers, atomic_masses, lattice_constants, crystal_structures, number_of_density_grid_points, number_of_distance_grid_points, density_grid_spacing, distance_grid_spacing, cutoff)

Bases: EAMParameters

Embedded Atom Method potential parameters

Parameters:

  • symbols (array_like) – Symbols of the elements coverered by this potential (only for eam/alloy and eam/fs, EMPTY for eam

  • atomic_numbers (array_like) – Atomic numbers of the elements covered by this potential

  • atomic_masses (array_like) – Atomic masses of the elements covered by this potential

  • lattice_constants (array_like) – Lattice constant of a pure crystal with crystal structure as specified in crystal_structures

  • crystal_structures (array_like) – Crystal structure of the pure metal.

  • number_of_density_grid_points (int) – Number of grid points of the embedding energy functional

  • number_of_distance_grid_points (int) – Number of grid points of the electron density function and the pair potential

  • density_grid_spacing (float) – Grid spacing in electron density space

  • distance_grid_spacing (float) – Grid spacing in pair distance space

  • cutoff (float) – Cutoff distance of the potential

Attributes:
atomic_masses

Alias for field number 2

atomic_numbers

Alias for field number 1

crystal_structures

Alias for field number 4

cutoff

Alias for field number 9

density_grid_spacing

Alias for field number 7

distance_grid_spacing

Alias for field number 8

lattice_constants

Alias for field number 3

number_of_density_grid_points

Alias for field number 5

number_of_distance_grid_points

Alias for field number 6

symbols

Alias for field number 0

Methods

count(value, /)

Return number of occurrences of value.

index(value[, start, stop])

Return first index of value.
atomic_masses

Alias for field number 2

atomic_numbers

Alias for field number 1

count(value, /)

Return number of occurrences of value.

crystal_structures

Alias for field number 4

cutoff

Alias for field number 9

density_grid_spacing

Alias for field number 7

distance_grid_spacing

Alias for field number 8

index(value, start=0, stop=sys.maxsize, /)

Return first index of value.

Raises ValueError if the value is not present.

lattice_constants

Alias for field number 3

number_of_density_grid_points

Alias for field number 5

number_of_distance_grid_points

Alias for field number 6

symbols

Alias for field number 0

matscipy.calculators.eam.io.read_eam(eam_file, kind='eam/alloy')

Read a tabulated EAM potential

There are differnt flavors of EAM, with different storage formats. This function supports a subset of the formats supported by Lammps (http://lammps.sandia.gov/doc/pair_eam.html), * eam (DYNAMO funcfl format) * eam/alloy (DYNAMO setfl format) * eam/fs (DYNAMO setfl format)

Parameters:

  • eam_file (string) – eam alloy file name

  • kind ({'eam', 'eam/alloy', 'eam/fs'}) – kind of EAM file to read

Returns:

  • source (string) – Source informations or comment line for the file header

  • parameters (EAMParameters) – EAM potential parameters

  • F (array_like) – contain the tabulated values of the embedded functions shape = (nb elements, nb of data points)

  • f (array_like) – contain the tabulated values of the density functions shape = (nb elements, nb of data points)

  • rep (array_like) – contain the tabulated values of pair potential shape = (nb elements,nb elements, nb of data points)

matscipy.calculators.eam.io.mix_eam(files, kind, method, f=[], rep_ab=[], alphas=[], betas=[])

mix eam alloy files data set and compute the interspecies pair potential part using the mean geometric value from each pure species

Parameters:

  • files (array of strings) – Contain all the files to merge and mix

  • kind (string) – kinf of eam. Supported eam/alloy, eam/fs

  • method (string, {geometric, arithmetic, weighted, fitted}) – Method used to mix the pair interaction terms. The geometric, arithmetic, and weighted arithmetic average are available. The weighted arithmetic method is using the electron density function values of atom a and b to ponderate the pair potential between species a and \(b\), rep_ab = 0.5(fb/fa * rep_a + fa/fb * rep_b), see [1]. The fitted method is to be used if rep_ab has been previously fitted and is parse as \(rep_ab\) karg.

  • f (np.array) – fitted density term (for FS eam style)

  • rep_ab (np.array) – fitted rep_ab term

  • alphas (array) – fitted alpha values for the fine tuned mixing. rep_ab = alpha_a*rep_a+alpha_b*rep_b

  • betas (array) – fitted values for the fine tuned mixing. f_ab = beta_00*rep_a+beta_01*rep_b f_ba = beta_10*rep_a+beta_11*rep_b

Returns:

  • sources (string) – Source informations or comment line for the file header

  • parameters_mix (EAMParameters) – EAM potential parameters

  • F_ (array_like) – contain the tabulated values of the embedded functions shape = (nb elements, nb elements, nb of data points)

  • f_ (array_like) – contain the tabulated values of the density functions shape = (nb elements, nb elements, nb of data points)

  • rep_ (array_like) – contain the tabulated values of pair potential shape = (nb elements, nb elements, nb of data points)

References

      1. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, 144113 (2004)

matscipy.calculators.eam.io.write_eam(source, parameters, F, f, rep, out_file, kind='eam')

Write an eam lammps format file

There are differnt flavors of EAM, with different storage formats. This function supports a subset of the formats supported by Lammps (http://lammps.sandia.gov/doc/pair_eam.html), * eam (DYNAMO funcfl format) * eam/alloy (DYNAMO setfl format) * eam/fs (DYNAMO setfl format)

Parameters:

  • source (string) – Source information or comment line for the file header

  • parameters_mix (EAMParameters) – EAM potential parameters

  • F (array_like) – contain the tabulated values of the embedded functions shape = (nb of data points)

  • f (array_like) – contain the tabulated values of the density functions shape = (nb of data points)

  • rep (array_like) – contain the tabulated values of pair potential shape = (nb of data points)

  • out_file (string) – output file name for the eam alloy potential file

  • kind ({'eam', 'eam/alloy', 'eam/fs'}) – kind of EAM file to read

Return type:

None