ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
0d2f47ddd46907520a087ec0618734d82ae02d0f
lammps/doc/src/pair_eam.rst

551 lines
21 KiB
ReStructuredText
Raw Blame History

.. index:: pair_style eam
.. index:: pair_style eam/gpu
.. index:: pair_style eam/intel
.. index:: pair_style eam/kk
.. index:: pair_style eam/omp
.. index:: pair_style eam/opt
.. index:: pair_style eam/alloy
.. index:: pair_style eam/alloy/gpu
.. index:: pair_style eam/alloy/intel
.. index:: pair_style eam/alloy/kk
.. index:: pair_style eam/alloy/omp
.. index:: pair_style eam/alloy/opt
.. index:: pair_style eam/cd
.. index:: pair_style eam/cd/old
.. index:: pair_style eam/fs
.. index:: pair_style eam/fs/gpu
.. index:: pair_style eam/fs/intel
.. index:: pair_style eam/fs/kk
.. index:: pair_style eam/fs/omp
.. index:: pair_style eam/fs/opt
.. index:: pair_style eam/he
pair_style eam command
======================
Accelerator Variants: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt*
pair_style eam/alloy command
============================
Accelerator Variants: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt*
pair_style eam/cd command
=========================
pair_style eam/cd/old command
=============================
pair_style eam/fs command
=========================
pair_style eam/he command
=========================
Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
* style = *eam* or *eam/alloy* or *eam/cd* or *eam/cd/old* or *eam/fs* or *eam/he*
Examples
""""""""
.. code-block:: LAMMPS
pair_style eam
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
pair_style eam/alloy
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
pair_style eam/he
pair_coeff * * PdHHe.eam.he Pd H He
Description
"""""""""""
Style *eam* computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials :ref:`(Daw) <Daw>`. The total
energy Ei of an atom I is given by
.. math::
E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
\frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, and alpha
and beta are the element types of atoms I and J. The multi-body
nature of the EAM potential is a result of the embedding energy term.
Both summations in the formula are over all neighbors J of atom I
within the cutoff distance.
The cutoff distance and the tabulated values of the functionals F,
rho, and phi are listed in one or more files which are specified by
the :doc:`pair_coeff <pair_coeff>` command. These are ASCII text files
in a DYNAMO-style format which is described below. DYNAMO was the
original serial EAM MD code, written by the EAM originators. Several
DYNAMO potential files for different metals are included in the
"potentials" directory of the LAMMPS distribution. All of these files
are parameterized in terms of LAMMPS :doc:`metal units <units>`.
.. note::
The *eam* style reads single-element EAM potentials in the
DYNAMO *funcfl* format. Either single element or alloy systems can be
modeled using multiple *funcfl* files and style *eam*\ . For the alloy
case LAMMPS mixes the single-element potentials to produce alloy
potentials, the same way that DYNAMO does. Alternatively, a single
DYNAMO *setfl* file or Finnis/Sinclair EAM file can be used by LAMMPS
to model alloy systems by invoking the *eam/alloy* or *eam/cd* or
*eam/fs* or *eam/he* styles as described below. These files require no
mixing since they specify alloy interactions explicitly.
.. note::
Note that unlike for other potentials, cutoffs for EAM potentials are not
set in the pair_style or pair_coeff command; they are specified in the EAM
potential files themselves. Likewise, valid EAM potential files usually
contain atomic masses; thus you may not need to use the :doc:`mass <mass>`
command to specify them, unless the potential file uses a dummy value (e.g.
0.0). LAMMPS will print a warning, if this is the case.
There are web sites that distribute and document EAM potentials stored
in DYNAMO or other formats:
* https://www.ctcms.nist.gov/potentials
* https://openkim.org
These potentials should be usable with LAMMPS, though the alternate
formats would need to be converted to the DYNAMO format used by LAMMPS
and described on this page. The NIST site is maintained by Chandler
Becker (cbecker at nist.gov) who is good resource for info on
interatomic potentials and file formats.
The OpenKIM Project at
`https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
provides EAM potentials that can be used directly in LAMMPS with the
:doc:`kim command <kim_commands>` interface.
.. warning::
The EAM potential files tabulate the embedding energy as a function
of the local electron density :math:`\rho`. When atoms get too
close, this electron density may exceed the range for which the
embedding energy was tabulated for. To avoid crashes, LAMMPS will
assume a linearly increasing embedding energy for electron densities
beyond the maximum tabulated value. LAMMPS will print a warning when
this happens. It may be acceptable at the beginning of an
equilibration (e.g. when using randomized coordinates) but would be a
big concern for accuracy if it happens during production runs. The
EAM potential file triggering the warning during production is thus
not a good choice, and the EAM model in general not likely a good
model for the kind of system under investigation.
----------
For style *eam*, potential values are read from a file that is in the
DYNAMO single-element *funcfl* format. If the DYNAMO file was created
by a Fortran program, it cannot have "D" values in it for exponents.
C only recognizes "e" or "E" for scientific notation.
For style *eam* a potential file must be assigned to each I,I pair of
atom types by using one or more pair_coeff commands, each with a
single argument:
* filename
Thus the following command
.. code-block:: LAMMPS
pair_coeff *2 1*2 cuu3.eam
will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). See the :doc:`pair_coeff <pair_coeff>` doc
page for alternate ways to specify the path for the potential file.
In effect, this makes atom types 1 and 2 in LAMMPS be Cu atoms.
Different single-element files can be assigned to different atom types
to model an alloy system. The mixing to create alloy potentials for
type pairs with I != J is done automatically the same way that the
serial DYNAMO code originally did it; you do not need to specify
coefficients for these type pairs.
*Funcfl* files in the *potentials* directory of the LAMMPS
distribution have an ".eam" suffix. 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
On line 2, all values but the mass are ignored by LAMMPS. The mass is
in mass :doc:`units <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 used by LAMMPS 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,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
by LAMMPS to compute the pair potential term in the EAM energy
expression as r\*phi, in units of eV-Angstroms, via the formula
.. math::
r \cdot \phi = 27.2 \cdot 0.529 \cdot Z_i \cdot Z_j
where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
----------
Style *eam/alloy* computes pairwise interactions using the same
formula as style *eam*\ . However the associated
:doc:`pair_coeff <pair_coeff>` command reads a DYNAMO *setfl* file
instead of a *funcfl* file. *Setfl* files can be used to model a
single-element or alloy system. In the alloy case, as explained
above, *setfl* files contain explicit tabulated values for alloy
interactions. Thus they allow more generality than *funcfl* files for
modeling alloys.
For style *eam/alloy*, potential values are read from a file that is
in the DYNAMO multi-element *setfl* format, except that element names
(Ni, Cu, etc) are added to one of the lines in the file. If the
DYNAMO file was created by a Fortran program, it cannot have "D"
values in it for exponents. C only recognizes "e" or "E" for
scientific notation.
Only a single pair_coeff command is used with the *eam/alloy* style
which specifies a DYNAMO *setfl* file, which contains information for
M elements. These are mapped to LAMMPS atom types by specifying N
additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
* filename
* N element names = mapping of *setfl* elements to atom types
As an example, the potentials/NiAlH_jea.eam.alloy file is a *setfl*
file which has tabulated EAM values for 3 elements and their alloy
interactions: Ni, Al, and H. See the :doc:`pair_coeff <pair_coeff>` doc
page for alternate ways to specify the path for the potential file.
If your LAMMPS simulation has 4 atoms types and you want the first 3 to
be Ni, and the fourth to be Al, you would use the following pair_coeff
command:
.. code-block:: LAMMPS
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the *setfl* file. The final Al argument maps LAMMPS atom
type 4 to the Al element in the *setfl* file. Note that there is no
requirement that your simulation use all the elements specified by the
*setfl* file.
If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an *eam/alloy* potential is used as part of the
*hybrid* pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
*Setfl* files in the *potentials* directory of the LAMMPS distribution
have an ".eam.alloy" suffix. 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. For LAMMPS, the element name (Ni, Cu,
etc) of each element must be added to 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)
As with the *funcfl* files, only the mass (in mass :doc:`units <units>`,
e.g. mass number or grams/mole for metal units) is used by LAMMPS from
the first line. 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.
----------
Style *eam/cd* is similar to the *eam/alloy* style, except that it
computes alloy pairwise interactions using the concentration-dependent
embedded-atom method (CD-EAM). This model can reproduce the enthalpy
of mixing of alloys over the full composition range, as described in
:ref:`(Stukowski) <Stukowski>`. Style *eam/cd/old* is an older, slightly
different and slower two-site formulation of the model :ref:`(Caro) <Caro>`.
The pair_coeff command is specified the same as for the *eam/alloy*
style. However the DYNAMO *setfl* file must has two
lines added to it, at the end of the file:
* line 1: Comment line (ignored)
* line 2: N Coefficient0 Coefficient1 ... CoefficientN
The last line begins with the degree *N* of the polynomial function
*h(x)* that modifies the cross interaction between A and B elements.
Then *N+1* coefficients for the terms of the polynomial are then
listed.
Modified EAM *setfl* files used with the *eam/cd* style must contain
exactly two elements, i.e. in the current implementation the *eam/cd*
style only supports binary alloys. The first and second elements in
the input EAM file are always taken as the *A* and *B* species.
*CD-EAM* files in the *potentials* directory of the LAMMPS
distribution have a ".cdeam" suffix.
----------
Style *eam/fs* computes pairwise interactions for metals and metal
alloys using a generalized form of EAM potentials due to Finnis and
Sinclair :ref:`(Finnis) <Finnis1>`. Style *eam/he* is similar to
*eam/fs* except that it allows for negative electron density in
order to capture the behavior of helium in metals :ref:`(Zhou6) <Zhou6>`.
The total energy Ei of an atom I is given by
.. math::
E_i = F_\alpha \left(\sum_{j \neq i}\
\rho_{\alpha\beta} (r_{ij})\right) +
\frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
where :math:`\rho_{\alpha\beta}` refers to the density contributed
by a neighbor atom J of element :math:`\beta` at the site of atom I
of element :math:`\alpha`.
This has the same form as the EAM formula above, except that rho is
now a functional specific to the elements of both atoms I and J,
so that different elements can contribute differently to the total
electron density at an atomic site depending on the identity of the
element at that atomic site.
The associated :doc:`pair_coeff <pair_coeff>` command for style *eam/fs*
or *eam/he* reads a DYNAMO *setfl* file that has been extended to include
additional :math:`\rho_{\alpha\beta}` arrays of tabulated values. A
discussion of how FS EAM differs from conventional EAM alloy potentials is
given in :ref:`(Ackland1) <Ackland1>`. An example of such a potential is the
same author's Fe-P FS potential :ref:`(Ackland2) <Ackland2>`. Note that while
FS potentials always specify the embedding energy with a square root
dependence on the total density, the implementation in LAMMPS does not
require that; the user can tabulate any functional form desired in the
FS potential files.
For style *eam/fs* and *eam/he* the form of the pair_coeff command is exactly
the same as for style *eam/alloy*, e.g.
.. code-block:: LAMMPS
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
with N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the :doc:`pair_coeff <pair_coeff>`
doc page for alternate ways to specify the path for the potential
file. The N values determine the mapping of LAMMPS atom types to EAM
elements in the file, as described above for style *eam/alloy*\ . As
with *eam/alloy*, if a mapping value is NULL, the mapping is not
performed. This can be used when an *eam/fs* or *eam/he* potential is
used as part of a *hybrid* pair style. The NULL values are used as
placeholders for atom types that will be used with other potentials.
FS EAM and HE EAM files include more information than the DYNAMO *setfl*
format files read by *eam/alloy*, in that i,j density functionals for
all pairs of elements are included as needed by the Finnis/Sinclair
formulation of the EAM.
FS EAM files in the *potentials* directory of the LAMMPS distribution
have an ".eam.fs" suffix. They are formatted as follows:
* 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 :math:`\beta`,
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 :math:`\rho_{1\beta} (r)` for element :math:`\beta` at element 1 (Nr values)
* density function :math:`\rho_{2\beta} (r)` for element :math:`\beta` at element 2
* ...
* density function :math:`\rho_{N_{elem}\beta} (r)` for element :math:`\beta` at element :math:`N_{elem}`
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 (:math:`\rho_{\alpha\beta} (r) \neq \rho_{\beta\alpha} (r)` )
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.
HE EAM files in the *potentials* directory of the LAMMPS distribution
have an ".eam.he" suffix. They are formatted as follows:
* lines 1,2,3 = comments (ignored)
* line 4: Nelements Element1 Element2 ... ElementN
* line 5: Nrho, drho, Nr, dr, cutoff, rhomax
The 5-line header section is identical to an FS EAM file
except that line 5 lists an additional value, rhomax. Unlike in FS EAM
files where embedding energies F(rho) are always defined between rho = 0
and rho = (Nrho -1)drho, F(rho) in HE EAM files are defined between
rho = rhomin and rho = rhomax. Since drho = (rhomax - rhomin)/(Nrho - 1),
rhomin = rhomax - (Nrho - 1)drho. The embedding energies F(rho) are
listed for rho = rhomin, rhomin + drho, rhomin + 2drho, ..., rhomax.
This gives users additional flexibility to define a negative rhomin and
therefore an embedding energy function that works for both positive and
negative electron densities. The format and units of these sections are
identical to the FS EAM files (see above).
----------
.. versionadded:: 3Nov2022
The *eam*, *eam/alloy*, *eam/fs*, and *eam/he* pair styles support
extraction of two per-atom quantities by the :doc:`fix pair <fix_pair>`
command. This allows the quantities to be output to files by the
:doc:`dump <dump>` or otherwise processed by other LAMMPS commands.
The names of the two quantities are "rho" and "fp" for the density and
derivative of the embedding energy for each atom. Neither quantity
needs to be triggered by the :doc:`fix pair <fix_pair>` command in order
for these pair styles to calculate it.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam styles.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
The eam pair styles do not write their information to :doc:`binary
restart files <restart>`, since it is stored in tabulated potential
files. Thus, you need to re-specify the pair_style and pair_coeff
commands in an input script that reads a restart file.
The eam pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
All of these styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
Default
"""""""
none
----------
.. _Ackland1:
**(Ackland1)** Ackland, Condensed Matter (2005).
.. _Ackland2:
**(Ackland2)** Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
of Physics: Condensed Matter, 16, S2629 (2004).
.. _Daw:
**(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
.. _Finnis1:
**(Finnis)** Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
.. _Zhou6:
**(Zhou6)** Zhou, Bartelt, Sills, Physical Review B, 103, 014108 (2021).
.. _Stukowski:
**(Stukowski)** Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
Materials Science & Engineering, 7, 075005 (2009).
.. _Caro:
**(Caro)** A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
Reference in New Issue View Git Blame Copy Permalink