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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<div class="section" id="neb-command">
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<span id="index-0"></span><h1>neb command<a class="headerlink" href="#neb-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>neb etol ftol N1 N2 Nevery file-style arg
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</pre></div>
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</div>
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<ul class="simple">
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<li>etol = stopping tolerance for energy (energy units)</li>
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<li>ftol = stopping tolerance for force (force units)</li>
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<li>N1 = max # of iterations (timesteps) to run initial NEB</li>
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<li>N2 = max # of iterations (timesteps) to run barrier-climbing NEB</li>
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<li>Nevery = print replica energies and reaction coordinates every this many timesteps</li>
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<li>file-style= <em>final</em> or <em>each</em> or <em>none</em></li>
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</ul>
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<pre class="literal-block">
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<em>final</em> arg = filename
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filename = file with initial coords for final replica
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coords for intermediate replicas are linearly interpolated between first and last replica
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<em>each</em> arg = filename
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filename = unique filename for each replica (except first) with its initial coords
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<em>none</em> arg = no argument
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all replicas assumed to already have their initial coords
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>neb 0.1 0.0 1000 500 50 final coords.final
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neb 0.0 0.001 1000 500 50 each coords.initial.$i
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neb 0.0 0.001 1000 500 50 none
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Perform a nudged elastic band (NEB) calculation using multiple
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replicas of a system. Two or more replicas must be used; the first
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and last are the end points of the transition path.</p>
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<p>NEB is a method for finding both the atomic configurations and height
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of the energy barrier associated with a transition state, e.g. for an
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atom to perform a diffusive hop from one energy basin to another in a
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coordinated fashion with its neighbors. The implementation in LAMMPS
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follows the discussion in these 3 papers: <a class="reference internal" href="#henkelman1"><span>(Henkelman1)</span></a>,
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<a class="reference internal" href="#henkelman2"><span>(Henkelman2)</span></a>, and <a class="reference internal" href="#nakano"><span>(Nakano)</span></a>.</p>
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<p>Each replica runs on a partition of one or more processors. Processor
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partitions are defined at run-time using the -partition command-line
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switch; see <a class="reference internal" href="Section_start.html#start-7"><span>Section_start 7</span></a> of the
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manual. Note that if you have MPI installed, you can run a
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multi-replica simulation with more replicas (partitions) than you have
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physical processors, e.g you can run a 10-replica simulation on just
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one or two processors. You will simply not get the performance
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speed-up you would see with one or more physical processors per
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replica. See <a class="reference internal" href="Section_howto.html#howto-5"><span>this section</span></a> of the manual
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for further discussion.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">The current NEB implementation in LAMMPS only allows
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there to be one processor per replica.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">As explained below, a NEB calculation perfoms a damped
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dynamics minimization across all the replicas. The mimimizer uses
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whatever timestep you have defined in your input script, via the
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<a class="reference internal" href="timestep.html"><em>timestep</em></a> command. Often NEB will converge more
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quickly if you use a timestep about 10x larger than you would normally
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use for dynamics simulations.</p>
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</div>
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<p>When a NEB calculation is performed, it is assumed that each replica
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is running the same system, though LAMMPS does not check for this.
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I.e. the simulation domain, the number of atoms, the interaction
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potentials, and the starting configuration when the neb command is
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issued should be the same for every replica.</p>
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<p>In a NEB calculation each atom in a replica is connected to the same
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atom in adjacent replicas by springs, which induce inter-replica
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forces. These forces are imposed by the <a class="reference internal" href="fix_neb.html"><em>fix neb</em></a>
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command, which must be used in conjunction with the neb command. The
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group used to define the fix neb command defines the NEB atoms which
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are the only ones that inter-replica springs are applied to. If the
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group does not include all atoms, then non-NEB atoms have no
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inter-replica springs and the forces they feel and their motion is
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computed in the usual way due only to other atoms within their
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replica. Conceptually, the non-NEB atoms provide a background force
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field for the NEB atoms. They can be allowed to move during the NEB
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minimiation procedure (which will typically induce different
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coordinates for non-NEB atoms in different replicas), or held fixed
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using other LAMMPS commands such as <a class="reference external" href="fix_setforce">fix setforce</a>. Note
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that the <a class="reference internal" href="partition.html"><em>partition</em></a> command can be used to invoke a
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command on a subset of the replicas, e.g. if you wish to hold NEB or
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non-NEB atoms fixed in only the end-point replicas.</p>
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<p>The initial atomic configuration for each of the replicas can be
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specified in different manners via the <em>file-style</em> setting, as
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discussed below. Only atoms whose initial coordinates should differ
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from the current configuration need be specified.</p>
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<p>Conceptually, the initial configuration for the first replica should
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be a state with all the atoms (NEB and non-NEB) having coordinates on
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one side of the energy barrier. A perfect energy minimum is not
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required, since atoms in the first replica experience no spring forces
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from the 2nd replica. Thus the damped dynamics minimizaiton will
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drive the first replica to an energy minimum if it is not already
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there. However, you will typically get better convergence if the
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initial state is already at a minimum. For example, for a system with
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a free surface, the surface should be fully relaxed before attempting
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a NEB calculation.</p>
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<p>Likewise, the initial configuration of the final replica should be a
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state with all the atoms (NEB and non-NEB) on the other side of the
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energy barrier. Again, a perfect energy minimum is not required,
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since the atoms in the last replica also experience no spring forces
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from the next-to-last replica, and thus the damped dynamics
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minimization will drive it to an energy minimum.</p>
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<p>As explained below, the initial configurations of intermediate
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replicas can be atomic coordinates interpolated in a linear fashion
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between the first and last replicas. This is often adequate state for
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simple transitions. For more complex transitions, it may lead to slow
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convergence or even bad results if the minimum energy path (MEP, see
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below) of states over the barrier cannot be correctly converged to
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from such an initial configuration. In this case, you will want to
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generate initial states for the intermediate replicas that are
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geometrically closer to the MEP and read them in.</p>
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<hr class="docutils" />
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<p>For a <em>file-style</em> setting of <em>final</em>, a filename is specified which
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contains atomic coordinates for zero or more atoms, in the format
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described below. For each atom that appears in the file, the new
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coordinates are assigned to that atom in the final replica. Each
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intermediate replica also assigns a new position to that atom in an
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interpolated manner. This is done by using the current position of
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the atom as the starting point and the read-in position as the final
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point. The distance between them is calculated, and the new position
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is assigned to be a fraction of the distance. E.g. if there are 10
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replicas, the 2nd replica will assign a position that is 10% of the
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distance along a line between the starting and final point, and the
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9th replica will assign a position that is 90% of the distance along
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the line. Note that this procedure to produce consistent coordinates
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across all the replicas, the current coordinates need to be the same
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in all replicas. LAMMPS does not check for this, but invalid initial
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configurations will likely result if it is not the case.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The “distance” between the starting and final point is
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calculated in a minimum-image sense for a periodic simulation box.
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This means that if the two positions are on opposite sides of a box
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(periodic in that dimension), the distance between them will be small,
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because the periodic image of one of the atoms is close to the other.
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Similarly, even if the assigned position resulting from the
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interpolation is outside the periodic box, the atom will be wrapped
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back into the box when the NEB calculation begins.</p>
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</div>
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<p>For a <em>file-style</em> setting of <em>each</em>, a filename is specified which is
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assumed to be unique to each replica. This can be done by
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using a variable in the filename, e.g.</p>
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<div class="highlight-python"><div class="highlight"><pre>variable i equal part
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neb 0.0 0.001 1000 500 50 each coords.initial.$i
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</pre></div>
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</div>
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<p>which in this case will substitute the partition ID (0 to N-1) for the
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variable I, which is also effectively the replica ID. See the
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<a class="reference internal" href="variable.html"><em>variable</em></a> command for other options, such as using
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world-, universe-, or uloop-style variables.</p>
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<p>Each replica (except the first replica) will read its file, formatted
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as described below, and for any atom that appears in the file, assign
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the specified coordinates to its atom. The various files do not need
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to contain the same set of atoms.</p>
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<p>For a <em>file-style</em> setting of <em>none</em>, no filename is specified. Each
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replica is assumed to already be in its initial configuration at the
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time the neb command is issued. This allows each replica to define
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its own configuration by reading a replica-specific data or restart or
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dump file, via the <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or <a class="reference internal" href="read_dump.html"><em>read_dump</em></a>
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commands. The replica-specific names of these files can be specified
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as in the discussion above for the <em>each</em> file-style. Also see the
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section below for how a NEB calculation can produce restart files, so
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that a long calculation can be restarted if needed.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">None of the <em>file-style</em> settings change the initial
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configuration of any atom in the first replica. The first replica
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must thus be in the correct initial configuration at the time the neb
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command is issued.</p>
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</div>
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<hr class="docutils" />
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<p>A NEB calculation proceeds in two stages, each of which is a
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minimization procedure, performed via damped dynamics. To enable
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this, you must first define a damped dynamics
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<a class="reference internal" href="min_style.html"><em>min_style</em></a>, such as <em>quickmin</em> or <em>fire</em>. The <em>cg</em>,
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<em>sd</em>, and <em>hftn</em> styles cannot be used, since they perform iterative
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line searches in their inner loop, which cannot be easily synchronized
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across multiple replicas.</p>
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<p>The minimizer tolerances for energy and force are set by <em>etol</em> and
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<em>ftol</em>, the same as for the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command.</p>
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<p>A non-zero <em>etol</em> means that the NEB calculation will terminate if the
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energy criterion is met by every replica. The energies being compared
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to <em>etol</em> do not include any contribution from the inter-replica
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forces, since these are non-conservative. A non-zero <em>ftol</em> means
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that the NEB calculation will terminate if the force criterion is met
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by every replica. The forces being compared to <em>ftol</em> include the
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inter-replica forces between an atom and its images in adjacent
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replicas.</p>
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<p>The maximum number of iterations in each stage is set by <em>N1</em> and
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<em>N2</em>. These are effectively timestep counts since each iteration of
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damped dynamics is like a single timestep in a dynamics
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<a class="reference internal" href="run.html"><em>run</em></a>. During both stages, the potential energy of each
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replica and its normalized distance along the reaction path (reaction
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coordinate RD) will be printed to the screen and log file every
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<em>Nevery</em> timesteps. The RD is 0 and 1 for the first and last replica.
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For intermediate replicas, it is the cumulative distance (normalized
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by the total cumulative distance) between adjacent replicas, where
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“distance” is defined as the length of the 3N-vector of differences in
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atomic coordinates, where N is the number of NEB atoms involved in the
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transition. These outputs allow you to monitor NEB’s progress in
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finding a good energy barrier. <em>N1</em> and <em>N2</em> must both be multiples
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of <em>Nevery</em>.</p>
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<p>In the first stage of NEB, the set of replicas should converge toward
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the minimum energy path (MEP) of conformational states that transition
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over the barrier. The MEP for a barrier is defined as a sequence of
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3N-dimensional states that cross the barrier at its saddle point, each
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of which has a potential energy gradient parallel to the MEP itself.
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The replica states will also be roughly equally spaced along the MEP
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due to the inter-replica spring force added by the <a class="reference internal" href="fix_neb.html"><em>fix neb</em></a> command.</p>
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<p>In the second stage of NEB, the replica with the highest energy
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is selected and the inter-replica forces on it are converted to a
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force that drives its atom coordinates to the top or saddle point of
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the barrier, via the barrier-climbing calculation described in
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<span class="xref std std-ref">(Henkelman2)</span>. As before, the other replicas rearrange
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themselves along the MEP so as to be roughly equally spaced.</p>
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<p>When both stages are complete, if the NEB calculation was successful,
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one of the replicas should be an atomic configuration at the top or
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saddle point of the barrier, the potential energies for the set of
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replicas should represent the energy profile of the barrier along the
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MEP, and the configurations of the replicas should be a sequence of
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configurations along the MEP.</p>
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<hr class="docutils" />
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<p>A few other settings in your input script are required or advised to
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perform a NEB calculation. See the IMPORTANT NOTE about the choice of
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timestep at the beginning of this doc page.</p>
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<p>An atom map must be defined which it is not by default for <a class="reference internal" href="atom_style.html"><em>atom_style atomic</em></a> problems. The <a class="reference internal" href="atom_modify.html"><em>atom_modify map</em></a> command can be used to do this.</p>
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<p>The “atom_modify sort 0 0.0” command should be used to turn off atom
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sorting.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">This sorting restriction will be removed in a future version of
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NEB in LAMMPS.</p>
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</div>
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<p>The minimizers in LAMMPS operate on all atoms in your system, even
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non-NEB atoms, as defined above. To prevent non-NEB atoms from moving
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during the minimization, you should use the <a class="reference internal" href="fix_setforce.html"><em>fix setforce</em></a> command to set the force on each of those
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atoms to 0.0. This is not required, and may not even be desired in
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some cases, but if those atoms move too far (e.g. because the initial
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state of your system was not well-minimized), it can cause problems
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for the NEB procedure.</p>
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<p>The damped dynamics <a class="reference internal" href="min_style.html"><em>minimizers</em></a>, such as <em>quickmin</em>
|
|
and <em>fire</em>), adjust the position and velocity of the atoms via an
|
|
Euler integration step. Thus you must define an appropriate
|
|
<a class="reference internal" href="timestep.html"><em>timestep</em></a> to use with NEB. As mentioned above, NEB
|
|
will often converge more quickly if you use a timestep about 10x
|
|
larger than you would normally use for dynamics simulations.</p>
|
|
<hr class="docutils" />
|
|
<p>Each file read by the neb command containing atomic coordinates used
|
|
to initialize one or more replicas must be formatted as follows.</p>
|
|
<p>The file can be ASCII text or a gzipped text file (detected by a .gz
|
|
suffix). The file can contain initial blank lines or comment lines
|
|
starting with “#” which are ignored. The first non-blank, non-comment
|
|
line should list N = the number of lines to follow. The N successive
|
|
lines contain the following information:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID1 x1 y1 z1
|
|
ID2 x2 y2 z2
|
|
...
|
|
IDN xN yN zN
|
|
</pre></div>
|
|
</div>
|
|
<p>The fields are the the atom ID, followed by the x,y,z coordinates.
|
|
The lines can be listed in any order. Additional trailing information
|
|
on the line is OK, such as a comment.</p>
|
|
<p>Note that for a typical NEB calculation you do not need to specify
|
|
initial coordinates for very many atoms to produce differing starting
|
|
and final replicas whose intermediate replicas will converge to the
|
|
energy barrier. Typically only new coordinates for atoms
|
|
geometrically near the barrier need be specified.</p>
|
|
<p>Also note there is no requirement that the atoms in the file
|
|
correspond to the NEB atoms in the group defined by the <a class="reference internal" href="fix_neb.html"><em>fix neb</em></a> command. Not every NEB atom need be in the file,
|
|
and non-NEB atoms can be listed in the file.</p>
|
|
<hr class="docutils" />
|
|
<p>Four kinds of output can be generated during a NEB calculation: energy
|
|
barrier statistics, thermodynamic output by each replica, dump files,
|
|
and restart files.</p>
|
|
<p>When running with multiple partitions (each of which is a replica in
|
|
this case), the print-out to the screen and master log.lammps file
|
|
contains a line of output, printed once every <em>Nevery</em> timesteps. It
|
|
contains the timestep, the maximum force per replica, the maximum
|
|
force per atom (in any replica), potential gradients in the initial,</p>
|
|
<blockquote>
|
|
<div>final, and climbing replicas,</div></blockquote>
|
|
<p>the forward and backward energy barriers,
|
|
the total reaction coordinate (RDT), and
|
|
the normalized reaction coordinate and potential energy of each replica.</p>
|
|
<p>The “maximum force per replica” is
|
|
the two-norm of the 3N-length force vector for the atoms in each
|
|
replica, maximized across replicas, which is what the <em>ftol</em> setting
|
|
is checking against. In this case, N is all the atoms in each
|
|
replica. The “maximum force per atom” is the maximum force component
|
|
of any atom in any replica. The potential gradients are the two-norm
|
|
of the 3N-length force vector solely due to the interaction potential i.e.
|
|
without adding in inter-replica forces. Note that inter-replica forces
|
|
are zero in the initial and final replicas, and only affect
|
|
the direction in the climbing replica. For this reason, the “maximum
|
|
force per replica” is often equal to the potential gradient in the
|
|
climbing replica. In the first stage of NEB, there is no climbing
|
|
replica, and so the potential gradient in the highest energy replica
|
|
is reported, since this replica will become the climbing replica
|
|
in the second stage of NEB.</p>
|
|
<p>The “reaction coordinate” (RD) for each
|
|
replica is the two-norm of the 3N-length vector of distances between
|
|
its atoms and the preceding replica’s atoms, added to the RD of the
|
|
preceding replica. The RD of the first replica RD1 = 0.0;
|
|
the RD of the final replica RDN = RDT, the total reaction coordinate.
|
|
The normalized RDs are divided by RDT,
|
|
so that they form a monotonically increasing sequence
|
|
from zero to one. When computing RD, N only includes the atoms
|
|
being operated on by the fix neb command.</p>
|
|
<p>The forward (reverse) energy barrier is the potential energy of the highest
|
|
replica minus the energy of the first (last) replica.</p>
|
|
<p>When running on multiple partitions, LAMMPS produces additional log
|
|
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
|
NEB calculation, these contain the thermodynamic output for each
|
|
replica.</p>
|
|
<p>If <a class="reference internal" href="dump.html"><em>dump</em></a> commands in the input script define a filename
|
|
that includes a <em>universe</em> or <em>uloop</em> style <a class="reference internal" href="variable.html"><em>variable</em></a>,
|
|
then one dump file (per dump command) will be created for each
|
|
replica. At the end of the NEB calculation, the final snapshot in
|
|
each file will contain the sequence of snapshots that transition the
|
|
system over the energy barrier. Earlier snapshots will show the
|
|
convergence of the replicas to the MEP.</p>
|
|
<p>Likewise, <a class="reference internal" href="restart.html"><em>restart</em></a> filenames can be specified with a
|
|
<em>universe</em> or <em>uloop</em> style <a class="reference internal" href="variable.html"><em>variable</em></a>, to generate
|
|
restart files for each replica. These may be useful if the NEB
|
|
calculation fails to converge properly to the MEP, and you wish to
|
|
restart the calculation from an intermediate point with altered
|
|
parameters.</p>
|
|
<p>There are 2 Python scripts provided in the tools/python directory,
|
|
neb_combine.py and neb_final.py, which are useful in analyzing output
|
|
from a NEB calculation. Assume a NEB simulation with M replicas, and
|
|
the NEB atoms labelled with a specific atom type.</p>
|
|
<p>The neb_combine.py script extracts atom coords for the NEB atoms from
|
|
all M dump files and creates a single dump file where each snapshot
|
|
contains the NEB atoms from all the replicas and one copy of non-NEB
|
|
atoms from the first replica (presumed to be identical in other
|
|
replicas). This can be visualized/animated to see how the NEB atoms
|
|
relax as the NEB calculation proceeds.</p>
|
|
<p>The neb_final.py script extracts the final snapshot from each of the M
|
|
dump files to create a single dump file with M snapshots. This can be
|
|
visualized to watch the system make its transition over the energy
|
|
barrier.</p>
|
|
<p>To illustrate, here are images from the final snapshot produced by the
|
|
neb_combine.py script run on the dump files produced by the two
|
|
example input scripts in examples/neb. Click on them to see a larger
|
|
image.</p>
|
|
<a data-lightbox="group-default"
|
|
href="_images/hop1.jpg"
|
|
class=""
|
|
title=""
|
|
data-title=""
|
|
><img src="_images/hop1.jpg"
|
|
class=""
|
|
width="25%"
|
|
height="auto"
|
|
alt=""/>
|
|
</a><a data-lightbox="group-default"
|
|
href="_images/hop2.jpg"
|
|
class=""
|
|
title=""
|
|
data-title=""
|
|
><img src="_images/hop2.jpg"
|
|
class=""
|
|
width="25%"
|
|
height="auto"
|
|
alt=""/>
|
|
</a></div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>This command can only be used if LAMMPS was built with the REPLICA
|
|
package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
|
|
for more info on packages.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="prd.html"><em>prd</em></a>, <a class="reference internal" href="temper.html"><em>temper</em></a>, <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>, <a class="reference internal" href="fix_viscous.html"><em>fix viscous</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="henkelman1"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>
|
|
<p id="henkelman2"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
|
|
9901-9904 (2000).</p>
|
|
<p id="nakano"><strong>(Nakano)</strong> Nakano, Comp Phys Comm, 178, 280-289 (2008).</p>
|
|
</div>
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