mirror of https://github.com/lammps/lammps.git
126 lines
4.1 KiB
Plaintext
126 lines
4.1 KiB
Plaintext
.. index:: fix neb
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fix neb command
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===============
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID neb Kspring
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* neb = style name of this fix command
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* Kspring = inter-replica spring constant (force/distance units)
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Examples
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""""""""
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.. parsed-literal::
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fix 1 active neb 10.0
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Description
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"""""""""""
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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 :doc:`neb <neb>` 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 :doc:`neb <neb>` command and in
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:ref:`Section_howto 5 <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 :ref:`(Henkelman1) <Henkelman1>` paper, to become:
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.. parsed-literal::
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Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That
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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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:ref:`(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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:ref:`(Henkelman2) <Henkelman2>` paper, and become:
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.. parsed-literal::
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Fi = -Grad(V) + 2 (Grad(V) dot That) That
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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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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` 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 :ref:`output commands <howto_15>`. No parameter of this fix can
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be used with the *start/stop* keywords of the :doc:`run <run>` 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 :doc:`minimize <minimize>` command via the
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:doc:`neb <neb>` command.
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Restrictions
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""""""""""""
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This command can only be used if LAMMPS was built with the REPLICA
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package. See the :ref:`Making LAMMPS <start_3>` section
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for more info on packages.
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Related commands
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""""""""""""""""
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:doc:`neb <neb>`
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**Default:** none
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.. _Henkelman:
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**(Henkelman1)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
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.. _Henkelman:
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**(Henkelman2)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
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9901-9904 (2000).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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