EAM¶
Introduction¶
The Embedded Atom Method (EAM) [1] is a classical potential which is good for modelling metals, particularly fcc materials. Because it is an equiaxial potential the EAM does not model directional bonds well. However, the Angular Dependent Potential (ADP) [2] which is an extended version of EAM is able to model directional bonds and is also included in the EAM calculator.
Generally all that is required to use this calculator is to supply a potential file or as a set of functions that describe the potential. The files containing the potentials for this calculator are not included but many suitable potentials can be downloaded from The Interatomic Potentials Repository Project at https://www.ctcms.nist.gov/potentials/
Theory¶
A single element EAM potential is defined by three functions: the embedded energy, electron density and the pair potential. A two element alloy contains the individual three functions for each element plus cross pair interactions. The ADP potential has two additional sets of data to define the dipole and quadrupole directional terms for each alloy and their cross interactions.
The total energy \(E_{\rm tot}\) of an arbitrary arrangement of atoms is given by the EAM potential as
and
where \(F\) is an embedding function, namely the energy to embed an atom \(i\) in the combined electron density \(\bar\rho_i\) which is contributed from each of its neighbouring atoms \(j\) by an amount \(\rho(r_{ij})\), \(\phi(r_{ij})\) is the pair potential function representing the energy in bond \(ij\) which is due to the shortrange electrostatic interaction between atoms, and \(r_{ij}\) is the distance between an atom and its neighbour for that bond.
The ADP potential is defined as
where \(\mu_i^\alpha\) is the dipole vector, \(\lambda_i^{\alpha\beta}\) is the quadrupole tensor and \(\nu_i\) is the trace of \(\lambda_i^{\alpha\beta}\).
The fs potential is defined as
where \(\alpha\) and \(\beta\) are element types of atoms. This form is similar to original EAM formula above, except that \(\rho\) and \(\phi\) are determined by element types.
Running the Calculator¶
EAM calculates the cohesive atom energy and forces. Internally the
potential functions are defined by splines which may be directly
supplied or created by reading the spline points from a data file from
which a spline function is created. The LAMMPS compatible .alloy
, .fs
and .adp
formats are supported. The LAMMPS .eam
format is
slightly different from the .alloy
format and is currently not
supported.
For example:
from ase.calculators.eam import EAM
mishin = EAM(potential='Al99.eam.alloy')
mishin.write_potential('new.eam.alloy')
mishin.plot()
slab.calc = mishin
slab.get_potential_energy()
slab.get_forces()
The breakdown of energy contribution from the indvidual components are
stored in the calculator instance .results['energy_components']
Arguments¶
Keyword 
Description 


file of potential in 

array of N element abbreviations 

arrays of embedded energy functions 

arrays of electron density functions 

arrays of pair potential functions 

arrays of derivative embedded energy functions 

arrays of derivative electron density functions 

arrays of derivative pair potentials functions 

ADP dipole and quadrupole function 

ADP dipole and quadrupole derivative functions 

skin distance passed to NeighborList(). If no atom
has moved more than the skindistance since the last
call to the 

the form of the potential

Additional parameters for writing potential files¶
The following parameters are only required for writing a potential in
.alloy
, .adp
or fs
format file.
Keyword 
Description 


Three line text header. Default is standard message. 

Array of atomic number of each element 

Atomic mass of each element 

Array of lattice parameters for each element 

Lattice type 

No. of rho samples along embedded energy curve 

Increment for sampling density 

No. of radial points along density and pair potential curves 

Increment for sampling radius 
Special features¶
.plot()
Plots the individual functions. This may be called from multiple EAM potentials to compare the shape of the individual curves. This function requires the installation of the Matplotlib libraries.
Notes/Issues¶
Although currently not fast, this calculator can be good for trying small calculations or for creating new potentials by matching baseline data such as from DFT results. The format for these potentials is compatible with LAMMPS and so can be used either directly by LAMMPS or with the ASE LAMMPS calculator interface.
Supported formats are the LAMMPS
.alloy
and.adp
. The.eam
format is currently not supported. The form of the potential will be determined from the file suffix.Any supplied values will override values read from the file.
The derivative functions, if supplied, are only used to calculate forces.
There is a bug in early versions of scipy that will cause eam.py to crash when trying to evaluate splines of a potential with one neighbor such as caused by evaluating a dimer.
Example:¶
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline as spline
from ase.build import bulk
from ase.calculators.eam import EAM
def test_eam(testdir):
# test to generate an EAM potential file using a simplified
# approximation to the Mishin potential Al99.eam.alloy data
cutoff = 6.28721
n = 21
rs = np.arange(0, n) * (cutoff / n)
rhos = np.arange(0, 2, 2. / n)
# generated from
# mishin = EAM(potential='../potentials/Al99.eam.alloy')
# m_density = mishin.electron_density[0](rs)
# m_embedded = mishin.embedded_energy[0](rhos)
# m_phi = mishin.phi[0,0](rs)
m_density = np.array([2.78589606e01, 2.02694937e01, 1.45334053e01,
1.06069912e01, 8.42517168e02, 7.65140344e02,
7.76263116e02, 8.23214224e02, 8.53322309e02,
8.13915861e02, 6.59095390e02, 4.28915711e02,
2.27910928e02, 1.13713167e02, 6.05020311e03,
3.65836583e03, 2.60587564e03, 2.06750708e03,
1.48749693e03, 7.40019174e04, 6.21225205e05])
m_embedded = np.array([1.04222211e10, 1.04142633e+00, 1.60359806e+00,
1.89287637e+00, 2.09490167e+00, 2.26456628e+00,
2.40590322e+00, 2.52245359e+00, 2.61385603e+00,
2.67744693e+00, 2.71053295e+00, 2.71110418e+00,
2.69287013e+00, 2.68464527e+00, 2.69204083e+00,
2.68976209e+00, 2.66001244e+00, 2.60122024e+00,
2.51338548e+00, 2.39650817e+00, 2.25058831e+00])
m_phi = np.array([6.27032242e+01, 3.49638589e+01, 1.79007014e+01,
8.69001383e+00, 4.51545250e+00, 2.83260884e+00,
1.93216616e+00, 1.06795515e+00, 3.37740836e01,
1.61087890e02, 6.20816372e02, 6.51314297e02,
5.35210341e02, 5.20950200e02, 5.51709524e02,
4.89093894e02, 3.28051688e02, 1.13738785e02,
2.33833655e03, 4.19132033e03, 1.68600692e04])
m_densityf = spline(rs, m_density)
m_embeddedf = spline(rhos, m_embedded)
m_phif = spline(rs, m_phi)
a = 4.05 # Angstrom lattice spacing
al = bulk('Al', 'fcc', a=a)
mishin_approx = EAM(
elements=['Al'], embedded_energy=np.array([m_embeddedf]),
electron_density=np.array([m_densityf]),
phi=np.array([[m_phif]]), cutoff=cutoff, form='alloy',
# the following terms are only required to write out a file
Z=[13], nr=n, nrho=n, dr=cutoff / n, drho=2. / n,
lattice=['fcc'], mass=[26.982], a=[a])
al.calc = mishin_approx
mishin_approx_energy = al.get_potential_energy()
mishin_approx.write_potential('Al99test.eam.alloy')
mishin_check = EAM(potential='Al99test.eam.alloy')
al.calc = mishin_check
mishin_check_energy = al.get_potential_energy()
print('Cohesive Energy for Al = ', mishin_approx_energy, ' eV')
error = (mishin_approx_energy  mishin_check_energy) / mishin_approx_energy
print('read/write check error = ', error)
assert abs(error) < 1e4