forked from lijiext/lammps
171 lines
6.5 KiB
Plaintext
171 lines
6.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style eim command :h3
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pair_style eim/omp command :h3
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[Syntax:]
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pair_style style :pre
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style = {eim} :ul
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[Examples:]
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pair_style eim
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pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
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pair_coeff * * Na Cl ffield.eim Na Na Na Cl
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pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na :pre
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[Description:]
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Style {eim} computes pairwise interactions for ionic compounds
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using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou. The
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energy of the system E is given by
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:c,image(Eqs/pair_eim1.jpg)
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The first term is a double pairwise sum over the J neighbors of all I
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atoms, where phi_ij is a pair potential. The second term sums over
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the embedding energy E_i of atom I, which is a function of its charge
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q_i and the electrical potential sigma_i at its location. E_i, q_i,
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and sigma_i are calculated as
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:c,image(Eqs/pair_eim2.jpg)
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where eta_ji is a pairwise function describing electron flow from atom
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I to atom J, and psi_ij is another pairwise function. The multi-body
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nature of the EIM potential is a result of the embedding energy term.
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A complete list of all the pair functions used in EIM is summarized
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below
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:c,image(Eqs/pair_eim3.jpg)
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Here E_b, r_e, r_(c,phi), alpha, beta, A_(psi), zeta, r_(s,psi),
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r_(c,psi), A_(eta), r_(s,eta), r_(c,eta), chi, and pair function type
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p are parameters, with subscripts ij indicating the two species of
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atoms in the atomic pair.
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IMPORTANT NOTE: Even though the EIM potential is treating atoms as
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charged ions, you should not use a LAMMPS "atom_style"_atom_style.html
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that stores a charge on each atom and thus requires you to assign a
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charge to each atom, e.g. the {charge} or {full} atom styles. This is
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because the EIM potential infers the charge on an atom from the
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equation above for q_i; you do not assign charges explicitly.
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:line
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All the EIM parameters are listed in a potential file which is
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specified by the "pair_coeff"_pair_coeff.html command. This is an
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ASCII text file in a format described below. The "ffield.eim" file
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included in the "potentials" directory of the LAMMPS distribution
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currently includes nine elements Li, Na, K, Rb, Cs, F, Cl, Br, and I.
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A system with any combination of these elements can be modeled. This
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file is parameterized in terms of LAMMPS "metal units"_units.html.
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Note that unlike other potentials, cutoffs for EIM potentials are not
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set in the pair_style or pair_coeff command; they are specified in the
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EIM potential file itself. Likewise, the EIM potential file lists
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atomic masses; thus you do not need to use the "mass"_mass.html
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command to specify them.
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Only a single pair_coeff command is used with the {eim} style which
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specifies an EIM potential file and the element(s) to extract
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information for. The EIM elements are mapped to LAMMPS atom types by
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specifying N additional arguments after the filename in the pair_coeff
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command, where N is the number of LAMMPS atom types:
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Elem1, Elem2, ...
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EIM potential file
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N element names = mapping of EIM elements to atom types :ul
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As an example like one of those above, suppose you want to model a
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system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
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types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
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use the following pair_coeff command:
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pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre
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The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The filename is the EIM potential file. The Na and Cl arguments
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(before the file name) are the two elements for which info will be
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extracted from the potentail file. The first three trailing Na
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arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
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final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.
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If a mapping value is specified as NULL, the mapping is not performed.
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This can be used when an {eim} potential is used as part of the
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{hybrid} pair style. The NULL values are placeholders for atom types
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that will be used with other potentials.
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The ffield.eim file in the {potentials} directory of the LAMMPS
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distribution is formated as follows:
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Lines starting with # are comments and are ignored by LAMMPS. Lines
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starting with "global:" include three global values. The first value
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divides the cations from anions, i.e., any elements with
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electronegativity above this value are viewed as anions, and any
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elements with electronegativity below this value are viewed as
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cations. The second and third values are related to the cutoff
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function - i.e. the 0.510204, 1.64498, and 0.010204 shown in the above
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equation can be derived from these values.
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Lines starting with "element:" are formatted as follows: name of
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element, atomic number, atomic mass, electronic negativity, atomic
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radius (LAMMPS ignores it), ionic radius (LAMMPS ignores it), cohesive
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energy (LAMMPS ignores it), and q0 (must be 0).
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Lines starting with "pair:" are entered as: element 1, element 2,
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r_(c,phi), r_(c,phi) (redundant for historical reasons), E_b, r_e,
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alpha, beta, r_(c,eta), A_(eta), r_(s,eta), r_(c,psi), A_(psi), zeta,
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r_(s,psi), and p.
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The lines in the file can be in any order; LAMMPS extracts the info it
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needs.
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This style is part of the MANYBODY package. It is only enabled if
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LAMMPS was built with that package (which it is by default).
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Zhou)
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[(Zhou)] Zhou, submitted for publication (2010). Please contact
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Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
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