forked from lijiext/lammps
107 lines
4.0 KiB
Plaintext
107 lines
4.0 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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fix neb command :h3
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[Syntax:]
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fix ID group-ID neb Kspring :pre
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ID, group-ID are documented in "fix"_fix.html command
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neb = style name of this fix command
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Kspring = inter-replica spring constant (force/distance units) :ul
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[Examples:]
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fix 1 active neb 10.0 :pre
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[Description:]
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Add inter-replica forces to atoms in the group for a multi-replica
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simulation run via the "neb"_neb.html 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 "neb"_neb.html command and in
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"Section_howto 5"_Section_howto.html#howto_5 of the manual. The fix
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neb command must be used with the "neb" command to define how
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inter-replica forces are computed.
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Only the N atoms in the fix group experience inter-replica forces.
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Atoms in the two end-point replicas do not experience these forces,
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but those in intermediate replicas do. During the initial stage of
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NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
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on the atoms of each intermediate replica I is altered, as described
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in the "(Henkelman1)"_#Henkelman1 paper, to become:
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Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That :pre
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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); see the
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"(Henkelman1)"_#Henkelman1 paper for details.
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The first two terms in the above equation are the component of the
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interatomic forces perpendicular to the tangent vector. The last term
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is a spring force between replica I and its neighbors, parallel to the
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tangent vector direction with the specified spring constant {Kspring}.
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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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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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During the second stage of NEB, the forces on the N atoms in the
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replica nearest the top of the energy barrier are altered so that it
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climbs to the top of the barrier and finds the saddle point. The
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forces on atoms in this replica are described in the
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"(Henkelman2)"_#Henkelman2 paper, and become:
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Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
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The inter-replica forces for the other replicas are unchanged from the
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first equation.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html 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 "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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The forces due to this fix are imposed during an energy minimization,
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as invoked by the "minimize"_minimize.html command via the
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"neb"_neb.html command.
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[Restrictions:]
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This command can only be used if LAMMPS was built with the REPLICA
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package. See the "Making LAMMPS"_Section_start.html#start_3 section
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for more info on packages.
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[Related commands:]
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"neb"_neb.html
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[Default:] none
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:link(Henkelman)
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[(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
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:link(Henkelman)
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[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
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9901-9904 (2000).
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