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This directory contains an EAM Model Driver which reads Dynamo setfl, funcfl,
and setfl Finnis Sinclair table files. The driver is written in C++. The
driver is designed to mimic/reproduce the behavior of LAMMPS's eam, eam/alloy,
and eam/fs pair_styles. The type of table file provided is automatically
detected. However, note that the spline algorithms used are cubic natrual
splines.
This Model Driver supports optional computation of `partialEnergy',
`partialForces', `partialParticleEnergy', `ProcessDeDrTerm', and
`ProcessD2EDr2Term'. When the number of table files provided to the Model
Driver is greater than one, the Model Driver expects each table file to be a
funcfl file. These are, together, are used to define a multi-species Model.
When only one table file is provided, the Model Driver determines the type of
provided table file by the file's contents.
The format of the Dynamo files supported by this Model Driver follows the LAMMPS
format. (NOTE an exception: To facilitate auto-detection of table file type,
all floating point values are expected to be proper floating point numbers, with
at least a decimal point. This is required in order to distinguish them from
integer values.) The LAMMPS format is described below (adapted from the LAMMPS
documentation as of 2013-11-19):
This Model Driver computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials (Daw). The total energy Ei of an
atom I is given by
E_i = F_\alpha( \sum_{j\neq i} \rho_\beta(r_{ij})) + (1/2)\sum_{j\neq i}
\phi_{\alpha \beta}(r_{ij})
A DYNAMO single-element funcfl file is formatted as follows:
* line 1: comment (ignored)
* line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
* line 3: Nrho, drho, Nr, dr, cutoff
The mass is in mass units, e.g. mass number or grams/mole for metal units. The
cubic lattice constant is in Angstroms. On line 3, Nrho and Nr are the number
of tabulated values in the subsequent arrays, drho and dr are the spacing in
density and distance space for the values in those arrays, and the specified
cutoff becomes the pairwise cutoff for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of electron
density.
Following the three header lines are three arrays of tabulated values:
* embedding function F(rho) (Nrho values)
* effective charge function Z(r) (Nr values)
* density function rho(r) (Nr values)
The values for each array can be listed as multiple values per line, so long as
each array starts on a new line. For example, the individual Z(r) values are
for r = 0.0,dr,2*dr, ... (Nr-1)*dr.
The units for the embedding function F are eV. The units for the density
function rho are the same as for drho (see above, electron density). The units
for the effective charge Z are "atomic charge" or sqrt(Hartree * Bohr-radii).
For two interacting atoms i,j this is used to compute the pair potential term in
the EAM energy expression as r*phi, in units of eV-Angstroms, via the formula
r*phi = 27.2 * 0.529 * Zi * Zj where 1 Hartree = 27.2 eV and 1 Bohr = 0.529
Angstroms.
A DYNAMO multi-element setfl file is formatted as follows:
* lines 1,2,3 = comments (ignored)
* line 4: Nelements Element1 Element2 ... ElementN
* line 5: Nrho, drho, Nr, dr, cutoff
In a DYNAMO setfl file, line 4 only lists Nelements = the # of elements in the
setfl file. The element name (Ni, Cu, etc) of each element must be included on
the line, in the order the elements appear in the file.
The meaning and units of the values in line 5 is the same as for the funcfl file
described above. Note that the cutoff (in Angstroms) is a global value, valid
for all pairwise interactions for all element pairings.
Following the 5 header lines are Nelements sections, one for each element, each
with the following format:
* line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
* embedding function F(rho) (Nrho values)
* density function rho(r) (Nr values)
The cubic lattice constant is in Angstroms. The F and rho arrays are unique to a
single element and have the same format and units as in a funcfl file.
Following the Nelements sections, Nr values for each pair potential phi(r) array
are listed for all i,j element pairs in the same format as other arrays. Since
these interactions are symmetric (i,j = j,i) only phi arrays with i >= j are
listed, in the following order: i,j = (1,1), (2,1), (2,2), (3,1), (3,2), (3,3),
(4,1), ..., (Nelements, Nelements). Unlike the effective charge array Z(r) in
funcfl files, the tabulated values for each phi function are listed in setfl
files directly as r*phi (in units of eV-Angstroms), since they are for atom
pairs.
A DYNAMO Finnis Sinclair setfl file is formatted as follows:
In this case the Model Driver computes pairwise interactions for metals and
metal alloys using a generalized form of EAM potentials due to Finnis and
Sinclair (Finnis). The total energy Ei of an atom I is given by
E_i = F_\alpha( \sum_{j\neq i} \rho_{\alpha \beta}(r_{ij})) +
(1/2)\sum_{j\neq i} \phi_{\alpha \beta}(r_{ij})
These files include more information than the DYNAMO setfl format files
described above, in that i,j density functionals for all pairs of elements are
included as needed by the Finnis/Sinclair formulation of the EAM.
* lines 1,2,3 = comments (ignored)
* line 4: Nelements Element1 Element2 ... ElementN
* line 5: Nrho, drho, Nr, dr, cutoff
The 5-line header section is identical to an EAM setfl file.
Following the header are Nelements sections, one for each element I, each with
the following format:
* line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
* embedding function F(rho) (Nrho values)
* density function rho(r) for element I at element 1 (Nr values)
* density function rho(r) for element I at element 2
* ...
* density function rho(r) for element I at element Nelement
The units of these quantities in line 1 are the same as for setfl files. Note
that the rho(r) arrays in Finnis/Sinclair can be asymmetric (i,j != j,i) so
there are Nelements^2 of them listed in the file.
Following the Nelements sections, Nr values for each pair potential phi(r) array
are listed in the same manner (r*phi, units of eV-Angstroms) as in EAM setfl
files. Note that in Finnis/Sinclair, the phi(r) arrays are still symmetric, so
only phi arrays for i >= j are listed.
Natural cubic spline is used to interpolate the tabulated potential data. This
spline requires second derivatives at both ends to be zero, and first and second
derivatives to be continuous at each internal knot.