mirror of https://github.com/lammps/lammps.git
110 lines
4.2 KiB
HTML
110 lines
4.2 KiB
HTML
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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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</CENTER>
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<HR>
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<H3>fix neb 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 neb kspring
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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>neb = style name of this fix command
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<LI>kspring = inter-replica spring constant
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 active neb 10.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Add inter-replica forces to atoms in the group for a multi-partition
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simulation run via the <A HREF = "neb.html">neb</A> command to perform a nudged
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elastic band (NEB) calculation for transition state finding. Hi-level
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explanations of NEB are given with the <A HREF = "neb.html">neb</A> command and in
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<A HREF = "Section_howto.html#neb">this section</A> of the doc pages. The fix neb
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command is used to define how inter-replica forces are computed.
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</P>
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<P>Atoms in the two end-point replicas do not experience inter-replica
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forces, but those in intermediate replicas do. The 3N-length vector
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of interatomic forces Fi = -Grad(V) acting on the atoms of each
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intermediate replica I is altered to become:
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</P>
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<PRE>Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
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</PRE>
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<P>Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
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coordinates of its neighbor replicas. That (t with a hat over it) is
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the unit "tangent" vector for replica I which is a function of Ri,
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Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
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roughly in the direction of (Ri+i - Ri-1). The first two terms in the
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above equation are the component of the interatomic forces
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perpendicular to the tangent vector. The last term is a spring force
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between replica I and its neighbors, parallel to the tangent vector
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direction with the specified spring constant.
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</P>
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<P>NOTE: That is defined in what papers?
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</P>
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<P>The effect of the first two terms is to push the atoms of each replica
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toward the minimum energy path (MEP) of conformational states that
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transition over the energy barrier. The MEP for an energy barrier is
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defined as a sequence of 3N-dimensional states which cross the barrier
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at its saddle point, each of which has a potential energy gradient
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parallel to the MEP itself.
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</P>
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<P>The effect of the last term is to push each replica away from its two
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neighbors in a direction along the MEP, so that the final set of
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states are equidistant from each other.
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</P>
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<P>A NEB calculation is performed in two stages, as described by the neb
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command. In the second stage, the forces on atoms in the replica
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nearest the top of the energy barrier are altered so that it climbs to
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the top of the barrier and finds the saddle point. The forces on
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atoms in this replica become:
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</P>
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<PRE>Fi = -Grad(V) + 2 (Grad(V) dot that) that
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</PRE>
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<P>The inter-replica forces for the other replicas are unchanged from the
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first equation.
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</P>
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<P>NOTE: discuss how to do NEB on a subset of atoms - group ID of fix neb
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command.
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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>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various <A HREF = "Section_howto.html#4_15">output
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commands</A>. No parameter of this fix can be
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used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy 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 command can only be used if LAMMPS was built with the "replica"
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package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for
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more info on packages.
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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 = "neb.html">neb</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<A NAME = "HJ1"></A>
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<P><B>(Henkelman1)</B> Henkelman and Jonsson, J Phys Chem, 113, 9978-9985 (2000).
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</P>
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<A NAME = "HJ2"></A>
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<P><B>(Henkelman2)</B> Henkelman and Jonsson, J Phys Chem, 113, 99019904 (2000).
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</P>
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</HTML>
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