forked from lijiext/lammps
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194 lines
8.8 KiB
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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>fix atom_swap command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID atom_swap N X seed T keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>atom_swap = style name of this fix command
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<LI>N = invoke this fix every N steps
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<LI>X = number of swaps to attempt every N steps
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<LI>seed = random # seed (positive integer)
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<LI>T = scaling temperature of the MC swaps (temperature units)
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<LI>one or more keyword/value pairs may be appended to args
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<LI>keyword = <I>types</I> or <I>delta_mu</I> or <I>ke</I> or <I>semi-grand</I> or <I>region</I>
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<PRE> <I>types</I> values = two or more atom types
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<I>delta_mu</I> values = number_of_types-1 relative chemical potentials (energy units)
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<I>ke</I> value = <I>no</I> or <I>yes</I>
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<I>no</I> = no conservation of kinetic energy after atom swaps
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<I>yes</I> = kinetic energy is conserved after atom swaps
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<I>semi-grand</I> value = <I>no</I> or <I>yes</I>
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<I>no</I> = particle type counts and fractions conserved
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<I>yes</I> = semi-grand canonical ensemble, particle fractions not conserved
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<I>region</I> value = region-ID
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region-ID = ID of region to use as an exchange/move volume
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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>fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
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fix atom_swap_fix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
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fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 delta_mu 4.3 -5.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix performs Monte Carlo swaps of atoms of one given atom type with atoms
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of the other given atom types. The specified T is used in the Metropolis criterion
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dictating swap probabilities.
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</P>
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<P>Perform X swaps of atoms of one type with atoms of another type according to a
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Monte Carlo probability. Swap candidates must be in the fix group, must be in
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the region (if specified), and must be of one of the listed types. Swaps are
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attempted between candidates that are chosen randomly with equal probability
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among the candidate atoms. Swaps are not attempted between atoms of the same
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type since nothing would happen.
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</P>
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<P>All atoms in the simulation domain can be moved using regular time
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integration displacements, e.g. via <A HREF = "fix_nvt.html">fix_nvt</A>, resulting
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in a hybrid MC+MD simulation. A smaller-than-usual timestep size
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may be needed when running such a hybrid simulation, especially if
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the swapped atoms are not well equilibrated.
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</P>
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<P>The <I>types</I> keyword is required. At least two atom types must be specified.
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</P>
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<P>The <I>ke</I> keyword can be set to <I>no</I> to turn off kinetic energy conservation
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for swaps. The default is <I>yes</I>, which means that swapped atoms have their
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velocities scaled by the ratio of the masses of the swapped atom types. This
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ensures that the kinetic energy of each atom is the same after the swap as it
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was before the swap, even though the atom masses have changed.
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</P>
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<P>The <I>semi-grand</I> keyword can be set to <I>yes</I> to switch to the semi-grand
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canonical ensemble as discussed in <A HREF = "#Sadigh">(Sadigh)</A>. This means that the
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total number of each particle type does not need to be conserved. The default
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is <I>no</I>, which means that the only kind of swap allowed exchanges an atom of
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one type with an atom of a different given type. In other words, the relative
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mole fractions of the swapped atoms remains constant. Whereas in the
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semi-grand canonical ensemble, the composition of the system can change. Note
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that when using <I>semi-grand</I>, all atoms in the fix group are eligible for
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attempted conversion to one of the given types, even if its current type is
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not one of the given types. An attempt is made to switch the selected atom to
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one of the listed <I>types</I> with equal probability. Acceptance of each attempt
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depends upon the Metropolis criterion.
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</P>
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<P>The <I>delta_mu</I> keyword allows users to specify non-zero chemical potentials
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for each of the atom types. All chemical potentials are relative to the first
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atom type, so no value is given for the first atom type. These parameters are
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useful for semi-grand canonical ensemble simulations where it may be
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desirable to actively control the composition of the system. When given,
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there must be ntypes-1 values given, where ntypes is the number of atom
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types in the simulated system. Note that a value for delta_mu is required for
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all atom types when using <I>semi-grand</I>, even for atom types not listed
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following the <I>types</I> keyword. This is because when using <I>semi-grand</I>, it is
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possible that any of the atom types in the system could be part of the fix
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group and therefore are eligible for swapping to one of the listed atom types.
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</P>
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<P>This command may optionally use the <I>region</I> keyword to define
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swap volume. The specified region must have been
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previously defined with a <A HREF = "region.html">region</A> command. It must be
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defined with side = <I>in</I>. Swap attempts occur only between atoms that
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are both within the specified region. Swaps are not otherwise attempted.
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</P>
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<P>You should ensure you do not swap atoms belonging to a molecule, or
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LAMMPS will soon generate an error when it tries to find those atoms.
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LAMMPS will warn you if any of the atoms eligible for swapping have a
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non-zero molecule ID, but does not check for this at the time of
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swapping.
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</P>
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<P>This fix checks to ensure all atoms of the given types have the same
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atomic charge. LAMMPS doesn't enforce this in general, but it is
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needed for this fix to simplify the swapping procedure. Successful swaps
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will swap the atom type and charge of the swapped atoms.
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</P>
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<P>Since this fix computes total potential energies before and after
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proposed swaps, so even complicated potential energy calculations are
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OK, including the following:
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</P>
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<UL><LI> long-range electrostatics (kspace)
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<LI> many body pair styles
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<LI> hybrid pair styles
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<LI> eam pair styles
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<LI> triclinic systems
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<LI> need to include potential energy contributions from other fixes
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</UL>
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<P>Some fixes have an associated potential energy. Examples of such fixes
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include: <A HREF = "fix_efield.html">efield</A>, <A HREF = "fix_gravity.html">gravity</A>,
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<A HREF = "fix_addforce.html">addforce</A>, <A HREF = "fix_langevin.html">langevin</A>,
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<A HREF = "fix_restrain.html">restrain</A>, <A HREF = "fix_temp_berendsen.html">temp/berendsen</A>,
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<A HREF = "fix_temp_rescale.html">temp/rescale</A>, and <A HREF = "fix_wall.html">wall fixes</A>.
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For that energy to be included in the total potential energy of the
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system (the quantity used when performing GCMC moves),
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you MUST enable the <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for
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that fix. The doc pages for individual <A HREF = "fix.html">fix</A> commands
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specify if this should be done.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the state of the fix to <A HREF = "restart.html">binary restart
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files</A>. This includes information about the random
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number generator seed, the next timestep for MC exchanges, etc. See
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the <A HREF = "read_restart.html">read_restart</A> command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
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fix.
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</P>
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<P>This fix computes a global vector of length 2, which can be accessed
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by various <A HREF = "Section_howto.html#howto_15">output commands</A>. The vector
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values are the following global cumulative quantities:
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</P>
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<UL><LI>1 = swap attempts
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<LI>2 = swap successes
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</UL>
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<P>The vector values calculated by this fix are "extensive".
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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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 = "fix_nvt.html">fix_nvt</A>, <A HREF = "neighbor.html">neighbor</A>,
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<A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_evaporate.html">fix_evaporate</A>,
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<A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "fix_gcmc.html">fix_gcmc</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are ke = yes, semi-grand = no, delta_mu = 0.0 for
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all atom types.
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</P>
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<HR>
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<A NAME = "Sadigh"></A>
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<P><B>(Sadigh)</B> B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
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L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
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</P>
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</HTML>
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