2006-09-22 00:22:34 +08:00
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>pair_style eam command
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</H3>
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2007-02-13 02:36:07 +08:00
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<H3>pair_style eam/opt command
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</H3>
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2006-09-22 00:22:34 +08:00
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<H3>pair_style eam/alloy command
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</H3>
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2007-02-13 02:36:07 +08:00
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<H3>pair_style eam/alloy/opt command
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</H3>
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2006-09-22 00:22:34 +08:00
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<H3>pair_style eam/fs command
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</H3>
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2007-02-13 02:36:07 +08:00
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<H3>pair_style eam/fs/opt command
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</H3>
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2006-09-22 00:22:34 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style style
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</PRE>
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2007-02-10 05:40:32 +08:00
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<UL><LI>style = <I>eam</I> or <I>eam/alloy</I> or <I>eam/fs</I> or <I>eam/opt</I> or <I>eam/alloy/opt</I> or <I>eam/fs/opt</I>
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2006-09-22 00:22:34 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style eam
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2007-02-10 05:40:32 +08:00
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pair_style eam/opt
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pair_coeff * * cuu3
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2006-11-02 07:01:32 +08:00
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pair_coeff 1*3 1*3 niu3.eam
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</PRE>
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<PRE>pair_style eam/alloy
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2007-02-10 05:40:32 +08:00
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pair_style eam/alloy/opt
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pair_coeff * * ../potentials/nialhjea.eam.alloy Ni Al Ni Ni
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</PRE>
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<PRE>pair_style eam/fs
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2007-02-10 05:40:32 +08:00
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pair_style eam/fs/opt
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2006-11-02 07:01:32 +08:00
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pair_coeff * * nialhjea.eam.fs Ni Al Ni Ni
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Style <I>eam</I> computes pairwise interactions for metals and metal alloys
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using embedded-atom method (EAM) potentials <A HREF = "#Daw">(Daw)</A>. The total
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energy Ei of an atom I is given by
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</P>
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<CENTER><IMG SRC = "Eqs/pair_eam.jpg">
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</CENTER>
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<P>where F is the embedding energy which is a function of the atomic
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electron density rho, phi is a pair potential interaction, and alpha
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and beta are the element types of atoms I and J. The multi-body
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nature of the EAM potential is a result of the embedding energy term.
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Both summations in the formula are over all neighbors J of atom I
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within the cutoff distance.
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</P>
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2007-02-10 05:40:32 +08:00
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<P>Style <I>eam/opt</I> is an optimized version of style <I>eam</I> that should
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give identical answers. Depending on system size and the processor
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you are running on, it may be 5-25% faster (for the pairwise portion
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of the run time).
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</P>
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2006-09-22 00:22:34 +08:00
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<P>The cutoff distance and the tabulated values of the functionals F,
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rho, and phi are listed in one or more files which are specified by
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the <A HREF = "pair_coeff.html">pair_coeff</A> command. These are ASCII text files
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2007-01-30 07:28:45 +08:00
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in a DYNAMO-style format which is described below. DYNAMO is a serial
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MD code. Several DYNAMO potential files for different metals are
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included in the "potentials" directory of the LAMMPS distribution.
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2007-02-23 00:52:24 +08:00
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All of these files are parameterized in terms of LAMMPS <A HREF = "units.html">metal
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2007-01-30 07:28:45 +08:00
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units</A>.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>IMPORTANT NOTE: The <I>eam</I> style reads single-element EAM potentials in
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2006-09-28 03:12:31 +08:00
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the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
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2006-11-02 07:01:32 +08:00
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can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>. For the
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alloy case LAMMPS mixes the single-element potentials to produce alloy
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potentials, the same way that DYNAMO does. Alternatively, a single
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2007-03-08 09:01:08 +08:00
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DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
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2006-11-02 07:01:32 +08:00
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to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/fs</I> styles
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as described below. These files require no mixing since they specify
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alloy interactions explicitly.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>For style <I>eam</I>, potential values are read from a file that is in the
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DYNAMO single-element <I>funcfl</I> format. If the DYNAMO file was created
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by a Fortran program, it cannot have "D" values in it for exponents.
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C only recognizes "e" or "E" for scientific notation.
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</P>
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2006-11-02 07:01:32 +08:00
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<P>Note that unlike for other potentials, cutoffs for EAM potentials are
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not set in the pair_style or pair_coeff command; they are specified in
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the EAM potential files themselves.
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2006-09-22 00:22:34 +08:00
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</P>
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2006-11-02 07:01:32 +08:00
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<P>For style <I>eam</I> a potential file must be assigned to each I,I pair of
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atom types by using one or more pair_coeff commands, each with a
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single argument:
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2006-09-22 00:22:34 +08:00
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</P>
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<UL><LI>filename
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</UL>
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<P>Thus the following command
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</P>
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2006-11-02 07:01:32 +08:00
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<PRE>pair_coeff *2 1*2 cuu3.eam
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P>will read the cuu3 potential file and use the tabulated Cu values for
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F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
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1,2 and 2,1 are ignored). In effect, this makes atom types 1 and 2 in
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LAMMPS be Cu atoms. Different single-element files can be assigned to
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different atom types to model an alloy system. The mixing to create
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alloy potentials for type pairs with I != J is done automatically the
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same way that the serial DYANMO code originally did it; you do not
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need to specify coefficients for these type pairs.
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</P>
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2006-11-04 04:18:04 +08:00
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<P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
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distribution have an ".eam" suffix. A DYNAMO single-element <I>funcfl</I>
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file is formatted as follows:
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</P>
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<UL><LI>line 1: comment (ignored)
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<LI>line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
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<LI>line 3: Nrho, drho, Nr, dr, cutoff
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</UL>
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<P>On line 2, all values but the mass are ignored by LAMMPS. The mass is
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2007-06-20 20:56:17 +08:00
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in mass <A HREF = "units.html">units</A> (e.g. mass number or grams/mole for metal
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units). The cubic lattice constant is in Angstroms. On line 3, Nrho
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and Nr are the number of tabulated values in the subsequent arrays,
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drho and dr are the spacing in density and distance space for the
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values in those arrays, and the specified cutoff becomes the pairwise
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cutoff used by LAMMPS for the potential. The units of dr are
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Angstroms; I'm not sure of the units for drho - some measure of
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electron density.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>Following the 3 header lines are 3 arrays of tabulated values:
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</P>
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<UL><LI>embedding function F(rho) (Nrho values)
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<LI>effective charge function Z(r) (Nr values)
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<LI>density function rho(r) (Nr values)
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</UL>
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<P>The values for each array can be listed as multiple values per line,
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so long as each array starts on a new line. For example, the
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individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
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</P>
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<P>The units for the embedding function F are eV. The units for the
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density function rho are the same as for drho (see above, electron
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density). The units for the effective charge Z are "atomic charge" or
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sqrt(Hartree * Bohr-radii). For 2 interacting atoms i,j this is used
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by LAMMPS to compute the pair potential term in the EAM energy
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expression as r*phi, in units of eV-Angstroms, via the formula
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</P>
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<PRE>r*phi = 27.2 * 0.529 * Zi * Zj
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</PRE>
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<P>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
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2006-09-22 00:22:34 +08:00
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</P>
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<HR>
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<P>Style <I>eam/alloy</I> computes pairwise interactions using the same
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formula as style <I>eam</I>. However the associated
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<A HREF = "pair_coeff.html">pair_coeff</A> command reads a DYNAMO <I>setfl</I> file
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instead of a <I>funcfl</I> file. <I>Setfl</I> files can be used to model a
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single-element or alloy system. In the alloy case, as explained
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above, <I>setfl</I> files contain explicit tabulated values for alloy
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interactions. Thus they allow more generality than <I>funcfl</I> files for
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modeling alloys.
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</P>
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2007-02-10 05:40:32 +08:00
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<P>Style <I>eam/alloy/opt</I> is an optimized version of style <I>eam/alloy</I>
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that should give identical answers. Depending on system size and the
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processor you are running on, it may be 5-25% faster (for the pairwise
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portion of the run time).
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</P>
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2006-09-22 00:22:34 +08:00
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<P>For style <I>eam/alloy</I>, potential values are read from a file that is
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2006-11-02 07:01:32 +08:00
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in the DYNAMO multi-element <I>setfl</I> format, except that element names
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(Ni, Cu, etc) are added to one of the lines in the file. If the
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DYNAMO file was created by a Fortran program, it cannot have "D"
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values in it for exponents. C only recognizes "e" or "E" for
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scientific notation.
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</P>
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2006-11-04 01:09:44 +08:00
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<P>Only a single pair_coeff command is used with the <I>eam/alloy</I> style
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which specifies a DYNAMO <I>setfl</I> file, which contains information for
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M elements. These are mapped to LAMMPS atom types by specifying N
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additional arguments after the filename in the pair_coeff command,
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where N is the number of LAMMPS atom types:
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</P>
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<UL><LI>filename
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<LI>N element names = mapping of <I>setfl</I> elements to atom types
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</UL>
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2006-11-04 01:09:44 +08:00
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<P>As an example, the potentials/nialhjea <I>setfl</I> file has tabulated EAM
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values for 3 elements and their alloy interactions: Ni, Al, and H. If
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your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be
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Ni, and the 4th to be Al, you would use the following pair_coeff
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command:
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2006-09-22 00:22:34 +08:00
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</P>
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<PRE>pair_coeff * * nialhjea.eam.alloy Ni Ni Ni Al
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</PRE>
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<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
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The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
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element in the <I>setfl</I> file. The final Al argument maps LAMMPS atom
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2006-11-04 01:09:44 +08:00
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type 4 to the Al element in the <I>setfl</I> file. Note that there is no
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requirement that your simulation use all the elements specified by the
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<I>setfl</I> file.
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</P>
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<P>If a mapping value is specified as NULL, the mapping is not performed.
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This can be used when an <I>eam/alloy</I> potential is used as part of the
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<I>hybrid</I> 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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2006-09-28 03:12:31 +08:00
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</P>
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<P><I>Setfl</I> files in the <I>potentials</I> directory of the LAMMPS distribution
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have an ".eam.alloy" suffix. A DYNAMO multi-element <I>setfl</I> file is
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formatted as follows:
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</P>
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<UL><LI>lines 1,2,3 = comments (ignored)
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<LI>line 4: Nelements Element1 Element2 ... ElementN
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<LI>line 5: Nrho, drho, Nr, dr, cutoff
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</UL>
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2006-11-02 07:01:32 +08:00
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<P>In a DYNAMO <I>setfl</I> file, line 4 only lists Nelements = the # of
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elements in the <I>setfl</I> file. For LAMMPS, the element name (Ni, Cu,
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etc) of each element must be added to the line, in the order the
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elements appear in the file.
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</P>
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<P>The meaning and units of the values in line 5 is the same as for the
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<I>funcfl</I> file described above. Note that the cutoff (in Angstroms) is
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a global value, valid for all pairwise interactions for all element
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pairings.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>Following the 5 header lines are Nelements sections, one for each
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element, each with the following format:
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</P>
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<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
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<LI>embedding function F(rho) (Nrho values)
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<LI>density function rho(r) (Nr values)
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</UL>
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2006-11-02 07:01:32 +08:00
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<P>As with the <I>funcfl</I> files, only the mass (g/cm^3) is used by LAMMPS
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from the 1st line. The cubic lattice constant is in Angstroms. The F
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and rho arrays are unique to a single element and have the same format
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and units as in a <I>funcfl</I> file.
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</P>
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<P>Following the Nelements sections, Nr values for each pair potential
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phi(r) array are listed for all i,j element pairs in the same format
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as other arrays. Since these interactions are symmetric (i,j = j,i)
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only phi arrays with i >= j are listed, in the following order: i,j =
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(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
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Nelements). Unlike the effective charge array Z(r) in <I>funcfl</I> files,
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the tabulated values for each phi function are listed in <I>setfl</I> files
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directly as r*phi (in units of eV-Angstroms), since they are for atom
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pairs.
|
2006-09-22 00:22:34 +08:00
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</P>
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<HR>
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<P>Style <I>eam/fs</I> computes pairwise interactions for metals and metal
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alloys using a generalized form of EAM potentials due to Finnis and
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Sinclair <A HREF = "#Finnis">(Finnis)</A>. The total energy Ei of an atom I is
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given by
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</P>
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<CENTER><IMG SRC = "Eqs/pair_eam_fs.jpg">
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</CENTER>
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<P>This has the same form as the EAM formula above, except that rho is
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now a functional specific to the atomic types of both atoms I and J,
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so that different elements can contribute differently to the total
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electron density at an atomic site depending on the identity of the
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element at that atomic site.
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</P>
|
2007-02-10 05:40:32 +08:00
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<P>Style <I>eam/fs/opt</I> is an optimized version of style <I>eam/fs</I> that
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should give identical answers. Depending on system size and the
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processor you are running on, it may be 5-25% faster (for the pairwise
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portion of the run time).
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</P>
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2006-09-22 00:22:34 +08:00
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<P>The associated <A HREF = "pair_coeff.html">pair_coeff</A> command for style <I>eam/fs</I>
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reads a DYNAMO <I>setfl</I> file that has been extended to include
|
2006-11-04 04:18:04 +08:00
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additional rho_alpha_beta arrays of tabulated values. A discussion of
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how FS EAM differs from conventional EAM alloy potentials is given in
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<A HREF = "#Ackland1">(Ackland1)</A>. An example of such a potential is the same
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author's Fe-P FS potential <A HREF = "#Ackland2">(Ackland2)</A>. Note that while FS
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potentials always specify the embedding energy with a square root
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dependence on the total density, the implementation in LAMMPS does not
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require that; the user can tabulate any functional form desired in the
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FS potential files.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>For style <I>eam/fs</I>, the form of the pair_coeff command is exactly the
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same as for style <I>eam/alloy</I>, e.g.
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</P>
|
2006-11-02 07:01:32 +08:00
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<PRE>pair_coeff * * nialhjea.eam.fs Ni Ni Ni Al
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P>where there are N additional arguments after the filename, where N is
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the number of LAMMPS atom types. The N values determine the mapping
|
2006-09-28 03:12:31 +08:00
|
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of LAMMPS atom types to EAM elements in the file, as described above
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for style <I>eam/alloy</I>. As with <I>eam/alloy</I>, if a mapping value is
|
2006-11-02 07:01:32 +08:00
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NULL, the mapping is not performed. This can be used when an <I>eam/fs</I>
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potential is used as part of the <I>hybrid</I> pair style. The NULL values
|
2006-09-28 03:12:31 +08:00
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are used as placeholders for atom types that will be used with other
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potentials.
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</P>
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<P>FS EAM files include more information than the DYNAMO <I>setfl</I> format
|
2006-11-02 07:01:32 +08:00
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files read by <I>eam/alloy</I>, in that i,j density functionals for all
|
2006-09-28 03:12:31 +08:00
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pairs of elements are included as needed by the Finnis/Sinclair
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formulation of the EAM.
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</P>
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<P>FS EAM files in the <I>potentials</I> directory of the LAMMPS distribution
|
2006-11-02 07:01:32 +08:00
|
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have an ".eam.fs" suffix. They are formatted as follows:
|
2006-09-22 00:22:34 +08:00
|
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</P>
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<UL><LI>lines 1,2,3 = comments (ignored)
|
2006-11-02 07:01:32 +08:00
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<LI>line 4: Nelements Element1 Element2 ... ElementN
|
2006-09-22 00:22:34 +08:00
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<LI>line 5: Nrho, drho, Nr, dr, cutoff
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</UL>
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<P>The 5-line header section is identical to an EAM <I>setfl</I> file.
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</P>
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<P>Following the header are Nelements sections, one for each element I,
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each with the following format:
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</P>
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<UL><LI>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)
|
2006-11-02 07:01:32 +08:00
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<LI>embedding function F(rho) (Nrho values)
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<LI>density function rho(r) for element I at element 1 (Nr values)
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<LI>density function rho(r) for element I at element 2
|
2006-09-22 00:22:34 +08:00
|
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<LI>...
|
2006-11-02 07:01:32 +08:00
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<LI>density function rho(r) for element I at element Nelement
|
2006-09-22 00:22:34 +08:00
|
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</UL>
|
2006-11-02 07:01:32 +08:00
|
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|
<P>The units of these quantities in line 1 are the same as for <I>setfl</I>
|
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|
files. Note that the rho(r) arrays in Finnis/Sinclair can be
|
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|
|
asymmetric (i,j != j,i) so there are Nelements^2 of them listed in the
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|
file.
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|
</P>
|
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<P>Following the Nelements sections, Nr values for each pair potential
|
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|
phi(r) array are listed in the same manner (r*phi, units of
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|
eV-Angstroms) as in EAM <I>setfl</I> files. Note that in Finnis/Sinclair,
|
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|
the phi(r) arrays are still symmetric, so only phi arrays for i >= j
|
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|
are listed.
|
2006-09-22 00:22:34 +08:00
|
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|
</P>
|
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|
<HR>
|
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|
2007-10-04 08:21:14 +08:00
|
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|
<P><B>Mixing, shift, table, tail correction, per-atom energy/stress,
|
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|
|
|
restart, rRESPA info</B>:
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P>For atom type pairs I,J and I != J, where types I and J correspond to
|
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|
|
|
two different element types, mixing is performed by LAMMPS as
|
2007-06-25 22:36:36 +08:00
|
|
|
described above with the individual styles. You never need to specify
|
|
|
|
|
a pair_coeff command with I != J arguments for the eam styles.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
|
2007-06-26 08:03:39 +08:00
|
|
|
shift, table, and tail options.
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
|
|
|
|
<P>All of the eam pair styles can calculate per-atom energy and stress,
|
|
|
|
|
as used by the <A HREF = "compute_epair_atom.html">compute epair/atom</A>, <A HREF = "compute_stress_atom.html">compute
|
|
|
|
|
stress/atom</A>, and <A HREF = "dump.html">dump custom</A>
|
|
|
|
|
commands. These quantities include the contribution from the
|
|
|
|
|
embedding term in the EAM formulas.
|
|
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P>The eam pair styles do not write their information to <A HREF = "restart.html">binary restart
|
|
|
|
|
files</A>, since it is stored in potential files. Thus, you
|
|
|
|
|
need to re-specify the pair_style and pair_coeff commands in an input
|
|
|
|
|
script that reads a restart file.
|
2007-06-25 22:36:36 +08:00
|
|
|
</P>
|
2007-10-04 08:21:14 +08:00
|
|
|
<P>The eam pair styles can only be used via the <I>pair</I> keyword of the
|
|
|
|
|
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
|
2007-10-12 07:09:49 +08:00
|
|
|
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
|
2007-10-04 08:21:14 +08:00
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-02-10 05:40:32 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P>All of these styles except those ending in <I>opt</I> are part of the
|
|
|
|
|
"manybody" package. They are only enabled if LAMMPS was built with
|
|
|
|
|
that package (which it is by default). The styles ending in <I>opt</I> are
|
|
|
|
|
part of the "opt" package and also require the "manybody" package.
|
|
|
|
|
They are only enabled if LAMMPS was built with those packages. See
|
|
|
|
|
the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "pair_coeff.html">pair_coeff</A>
|
|
|
|
|
</P>
|
2007-09-20 01:16:54 +08:00
|
|
|
<P>Here are several WWW sites that discuss EAM potentials stored in
|
|
|
|
|
either the original DYNAMO or other formats:
|
2007-02-23 00:52:24 +08:00
|
|
|
</P>
|
|
|
|
|
<PRE>http://www.ims.uconn.edu/centers/simul/pot
|
2007-09-20 01:16:54 +08:00
|
|
|
http://cst-www.nrl.navy.mil/ccm6/ap
|
|
|
|
|
http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
|
2007-02-23 00:52:24 +08:00
|
|
|
</PRE>
|
2007-09-20 01:16:54 +08:00
|
|
|
<P>In principle, these potentials could be used with LAMMPS, though the
|
|
|
|
|
alternate formats would need to be converted to the DYNAMO format used
|
|
|
|
|
by LAMMPS and described above.
|
2007-02-23 00:52:24 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Ackland1"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Ackland1)</B> Ackland, Condensed Matter (2005).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Ackland2"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Ackland2)</B> Ackland, Mendelev, Srolovitz, Han and Barashev, Journal
|
|
|
|
|
of Physics: Condensed Matter, 16, S2629 (2004).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Daw"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Daw)</B> Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
|
|
|
|
|
Daw, Baskes, Phys Rev B, 29, 6443 (1984).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Finnis"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Finnis)</B> Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
