forked from lijiext/lammps
199 lines
8.3 KiB
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199 lines
8.3 KiB
HTML
<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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<H3>pair_style comb command
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</H3>
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<H3>pair_style comb/omp command
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</H3>
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<H3>pair_style comb3 command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style comb
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pair_style comb3 keyword
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</PRE>
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<PRE>keyword = <I>polar</I>
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<I>polar</I> value = <I>polar_on</I> or <I>polar_off</I> = whether or not to include atomic polarization
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</PRE>
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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 comb
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pair_coeff * * ../potentials/ffield.comb Si
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pair_coeff * * ../potentials/ffield.comb Hf Si O
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</PRE>
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<PRE>pair_style comb3 polar_off
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pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
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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>comb</I> computes the second-generation variable charge COMB
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(Charge-Optimized Many-Body) potential. Style <I>comb3</I> computes the
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third-generation COMB potential. These COMB potentials are described
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in <A HREF = "#COMB">(COMB)</A> and <A HREF = "#COMB3">(COMB3)</A>. Briefly, the total energy
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<I>E<sub>T</sub></I> of a system of atoms is given by
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</P>
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<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
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</CENTER>
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<P>where <I>E<sub>i</sub><sup>self</sup></I> is the self-energy of atom <I>i</I>
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(including atomic ionization energies and electron affinities),
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<I>E<sub>ij</sub><sup>short</sup></I> is the bond-order potential between
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atoms <I>i</I> and <I>j</I>,
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<I>E<sub>ij</sub><sup>Coul</sup></I> is the Coulomb interactions,
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<I>E<sup>polar</sup></I> is the polarization term for organic systems
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(style <I>comb3</I> only),
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<I>E<sup>vdW</sup></I> is the van der Waals energy (style <I>comb3</I> only),
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<I>E<sup>barr</sup></I> is a charge barrier function, and
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<I>E<sup>corr</sup></I> are angular correction terms.
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</P>
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<P>The COMB potentials (styles <I>comb</I> and <I>comb3</I>) are variable charge
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potentials. The equilibrium charge on each atom is calculated by the
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electronegativity equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for
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further details. This is implemented by the <A HREF = "fix_qeq_comb.html">fix
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qeq/comb</A> command, which should normally be
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specified in the input script when running a model with the COMB
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potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command has options
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that determine how often charge equilibration is performed, its
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convergence criterion, and which atoms are included in the
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calculation.
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</P>
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<P>Only a single pair_coeff command is used with the <I>comb</I> and <I>comb3</I>
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styles which specifies the COMB potential file with parameters for all
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needed elements. These are mapped to LAMMPS atom types by specifying
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N additional arguments after the potential file in the pair_coeff
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command, where N is the number of LAMMPS atom types.
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</P>
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<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
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HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
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last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
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use the following pair_coeff command:
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</P>
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<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
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</PRE>
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<P>The first two arguments must be * * so as to span all LAMMPS atom
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types. The first and last Si arguments map LAMMPS atom types 1 and 4
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to the Si element in the <I>ffield.comb</I> file. The second Hf argument
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maps LAMMPS atom type 2 to the Hf element, and the third O argument
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maps LAMMPS atom type 3 to the O element in the potential file. If a
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mapping value is specified as NULL, the mapping is not performed.
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This can be used when a <I>comb</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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</P>
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<P>For style <I>comb</I>, the provided potential file <I>ffield.comb</I> contains
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all currently-available 2nd generation COMB parameterizations: for Si,
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Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
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<I>comb3</I>, the potential file <I>ffield.comb3</I> contains all
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currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
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H, Ti and Zn. The status of the optimization of the compounds, for
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example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
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following table:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
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</CENTER>
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<P>For style <I>comb3</I>, in addition to ffield.comb3, a special parameter
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file, <I>lib.comb3</I>, that is exclusively used for C/O/H systems, will be
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automatically loaded if carbon atom is detected in LAMMPS input
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structure. Keyword <I>polar</I> indicates whether the force field includes
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the atomic polarization. Since the equilibration of the polarization
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has not yet been implemented, it can only set polar_off at present.
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</P>
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<P>IMPORTANT NOTE: You can not use potential file <I>ffield.comb</I> with
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style <I>comb3</I>, nor file <I>ffield.comb3</I> with style <I>comb</I>.
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</P>
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<HR>
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> 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 <A HREF = "Section_accelerate.html">Section_accelerate</A> 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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</P>
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<P>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 <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<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
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described above from values in the potential file.
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</P>
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<P>These pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
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shift, table, and tail options.
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</P>
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<P>These pair styles do not write its information to <A HREF = "restart.html">binary restart
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files</A>, since it is stored in potential files. Thus, you
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need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
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qeq/comb</A> commands in an input script that reads a
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restart file.
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</P>
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<P>These pair styles can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. It does not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>These pair styles are part of the MANYBODY package. It is only enabled
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if LAMMPS was built with that package (which it is by default). See
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the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
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</P>
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<P>These pair styles requires the <A HREF = "newton.html">newton</A> setting to be "on"
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for pair interactions.
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</P>
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<P>The COMB potentials in the <I>ffield.comb</I> and <I>ffield.comb3</I> files provided
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with LAMMPS (see the potentials directory) are parameterized for metal
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<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
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units, but you would need to create your own COMB potential file with
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coefficients listed in the appropriate units if your simulation
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doesn't use "metal" units.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
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<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "COMB"></A>
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<P><B>(COMB)</B> S. R. Phillpot and S. B. Sinnott, Science 325, 1634-1635 (2009)
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</P>
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<A NAME = "COMB3"></A>
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<P><B>(COMB3)</B> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
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Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R,
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in press (DOI: 10.1016/j.mser.2013.07.001)
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</P>
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<A NAME = "Rick"></A>
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<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
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(1994).
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</P>
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</HTML>
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