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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_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</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_tools.html">9. Additional tools</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 role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="tad-command">
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<span id="index-0"></span><h1>tad command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="n">N</span> <span class="n">t_event</span> <span class="n">T_lo</span> <span class="n">T_hi</span> <span class="n">delta</span> <span class="n">tmax</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>N = # of timesteps to run (not including dephasing/quenching)</li>
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<li>t_event = timestep interval between event checks</li>
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<li>T_lo = temperature at which event times are desired</li>
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<li>T_hi = temperature at which MD simulation is performed</li>
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<li>delta = desired confidence level for stopping criterion</li>
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<li>tmax = reciprocal of lowest expected preexponential factor (time units)</li>
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<li>compute-ID = ID of the compute used for event detection</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>min</em> or <em>neb</em> or <em>min_style</em> or <em>neb_style</em> or <em>neb_log</em></li>
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</ul>
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<pre class="literal-block">
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<em>min</em> values = etol ftol maxiter maxeval
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etol = stopping tolerance for energy (energy units)
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ftol = stopping tolerance for force (force units)
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maxiter = max iterations of minimize
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maxeval = max number of force/energy evaluations
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<em>neb</em> values = ftol N1 N2 Nevery
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etol = stopping tolerance for energy (energy units)
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ftol = stopping tolerance for force (force units)
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N1 = max # of iterations (timesteps) to run initial NEB
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N2 = max # of iterations (timesteps) to run barrier-climbing NEB
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Nevery = print NEB statistics every this many timesteps
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<em>neb_style</em> value = <em>quickmin</em> or <em>fire</em>
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<em>neb_step</em> value = dtneb
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dtneb = timestep for NEB damped dynamics minimization
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<em>neb_log</em> value = file where NEB statistics are printed
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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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span>
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<span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span> <span class="o">&</span>
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<span class="nb">min</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">100</span> <span class="mi">100</span> <span class="o">&</span>
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<span class="n">neb</span> <span class="mf">0.0</span> <span class="mf">0.01</span> <span class="mi">200</span> <span class="mi">200</span> <span class="mi">20</span> <span class="o">&</span>
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<span class="n">min_style</span> <span class="n">cg</span> <span class="o">&</span>
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<span class="n">neb_style</span> <span class="n">fire</span> <span class="o">&</span>
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<span class="n">neb_log</span> <span class="n">log</span><span class="o">.</span><span class="n">neb</span>
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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</h2>
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<p>Run a temperature accelerated dynamics (TAD) simulation. This method
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requires two or more partitions to perform NEB transition state
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searches.</p>
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<p>TAD is described in <a class="reference internal" href="#voter"><span class="std std-ref">this paper</span></a> by Art Voter. It is a method
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that uses accelerated dynamics at an elevated temperature to generate
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results at a specified lower temperature. A good overview of
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accelerated dynamics methods for such systems is given in <a class="reference internal" href="#voter2"><span class="std std-ref">this review paper</span></a> from the same group. In general, these methods assume
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that the long-time dynamics is dominated by infrequent events i.e. the
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system is is confined to low energy basins for long periods,
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punctuated by brief, randomly-occurring transitions to adjacent
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basins. TAD is suitable for infrequent-event systems, where in
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addition, the transition kinetics are well-approximated by harmonic
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transition state theory (hTST). In hTST, the temperature dependence of
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transition rates follows the Arrhenius relation. As a consequence a
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set of event times generated in a high-temperature simulation can be
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mapped to a set of much longer estimated times in the low-temperature
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system. However, because this mapping involves the energy barrier of
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the transition event, which is different for each event, the first
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event at the high temperature may not be the earliest event at the low
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temperature. TAD handles this by first generating a set of possible
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events from the current basin. After each event, the simulation is
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reflected backwards into the current basin. This is repeated until
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the stopping criterion is satisfied, at which point the event with the
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earliest low-temperature occurrence time is selected. The stopping
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criterion is that the confidence measure be greater than
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1-<em>delta</em>. The confidence measure is the probability that no earlier
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low-temperature event will occur at some later time in the
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high-temperature simulation. hTST provides an lower bound for this
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probability, based on the user-specified minimum pre-exponential
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factor (reciprocal of <em>tmax</em>).</p>
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<p>In order to estimate the energy barrier for each event, the TAD method
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invokes the <a class="reference internal" href="neb.html"><span class="doc">NEB</span></a> method. Each NEB replica runs on a
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partition of processors. The current NEB implementation in LAMMPS
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restricts you to having exactly one processor per replica. For more
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information, see the documentation for the <a class="reference internal" href="neb.html"><span class="doc">neb</span></a> command. In
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the current LAMMPS implementation of TAD, all the non-NEB TAD
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operations are performed on the first partition, while the other
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partitions remain idle. See <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">Section_howto 5</span></a> of the manual for further discussion of
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multi-replica simulations.</p>
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<p>A TAD run has several stages, which are repeated each time an event is
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performed. The logic for a TAD run is as follows:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="n">remains</span><span class="p">):</span>
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<span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="o"><</span> <span class="n">tstop</span><span class="p">):</span>
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<span class="n">until</span> <span class="p">(</span><span class="n">event</span> <span class="n">occurs</span><span class="p">):</span>
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<span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_event</span> <span class="n">steps</span>
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<span class="n">quench</span>
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<span class="n">run</span> <span class="n">neb</span> <span class="n">calculation</span> <span class="n">using</span> <span class="nb">all</span> <span class="n">replicas</span>
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<span class="n">compute</span> <span class="n">tlo</span> <span class="kn">from</span> <span class="nn">energy</span> <span class="n">barrier</span>
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<span class="n">update</span> <span class="n">earliest</span> <span class="n">event</span>
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<span class="n">update</span> <span class="n">tstop</span>
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<span class="n">reflect</span> <span class="n">back</span> <span class="n">into</span> <span class="n">current</span> <span class="n">basin</span>
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<span class="n">execute</span> <span class="n">earliest</span> <span class="n">event</span>
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</pre></div>
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</div>
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<p>Before this outer loop begins, the initial potential energy basin is
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identified by quenching (an energy minimization, see below) the
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initial state and storing the resulting coordinates for reference.</p>
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<p>Inside the inner loop, dynamics is run continuously according to
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whatever integrator has been specified by the user, stopping every
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<em>t_event</em> steps to check if a transition event has occurred. This
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check is performed by quenching the system and comparing the resulting
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atom coordinates to the coordinates from the previous basin.</p>
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<p>A quench is an energy minimization and is performed by whichever
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algorithm has been defined by the <a class="reference internal" href="min_style.html"><span class="doc">min_style</span></a> command;
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its default is the CG minimizer. The tolerances and limits for each
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quench can be set by the <em>min</em> keyword. Note that typically, you do
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not need to perform a highly-converged minimization to detect a
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transition event.</p>
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<p>The event check is performed by a compute with the specified
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<em>compute-ID</em>. Currently there is only one compute that works with the
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TAD commmand, which is the <a class="reference internal" href="compute_event_displace.html"><span class="doc">compute event/displace</span></a> command. Other
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event-checking computes may be added. <a class="reference internal" href="compute_event_displace.html"><span class="doc">Compute event/displace</span></a> checks whether any atom in
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the compute group has moved further than a specified threshold
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distance. If so, an “event” has occurred.</p>
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<p>The NEB calculation is similar to that invoked by the <a class="reference internal" href="neb.html"><span class="doc">neb</span></a>
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command, except that the final state is generated internally, instead
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of being read in from a file. The style of minimization performed by
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NEB is determined by the <em>neb_style</em> keyword and must be a damped
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dynamics minimizer. The tolerances and limits for each NEB
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calculation can be set by the <em>neb</em> keyword. As discussed on the
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<a class="reference internal" href="neb.html"><span class="doc">neb</span></a>, it is often advantageous to use a larger timestep for
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NEB than for normal dyanmics. Since the size of the timestep set by
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the <a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a> command is used by TAD for performing
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dynamics, there is a <em>neb_step</em> keyword which can be used to set a
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larger timestep for each NEB calculation if desired.</p>
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<hr class="docutils" />
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<p>A key aspect of the TAD method is setting the stopping criterion
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appropriately. If this criterion is too conservative, then many
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events must be generated before one is finally executed. Conversely,
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if this criterion is too aggressive, high-entropy high-barrier events
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will be over-sampled, while low-entropy low-barrier events will be
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under-sampled. If the lowest pre-exponential factor is known fairly
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accurately, then it can be used to estimate <em>tmax</em>, and the value of
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<em>delta</em> can be set to the desired confidence level e.g. <em>delta</em> = 0.05
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corresponds to 95% confidence. However, for systems where the dynamics
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are not well characterized (the most common case), it will be
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necessary to experiment with the values of <em>delta</em> and <em>tmax</em> to get a
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good trade-off between accuracy and performance.</p>
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<p>A second key aspect is the choice of <em>t_hi</em>. A larger value greatly
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increases the rate at which new events are generated. However, too
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large a value introduces errors due to anharmonicity (not accounted
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for within hTST). Once again, for any given system, experimentation is
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necessary to determine the best value of <em>t_hi</em>.</p>
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<hr class="docutils" />
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<p>Five kinds of output can be generated during a TAD run: event
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statistics, NEB statistics, thermodynamic output by each replica, dump
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files, and restart files.</p>
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<p>Event statistics are printed to the screen and master log.lammps file
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each time an event is executed. The quantities are the timestep, CPU
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time, global event number <em>N</em>, local event number <em>M</em>, event status,
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energy barrier, time margin, <em>t_lo</em> and <em>delt_lo</em>. The timestep is
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the usual LAMMPS timestep, which corresponds to the high-temperature
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time at which the event was detected, in units of timestep. The CPU
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time is the total processor time since the start of the TAD run. The
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global event number <em>N</em> is a counter that increments with each
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executed event. The local event number <em>M</em> is a counter that resets to
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zero upon entering each new basin. The event status is <em>E</em> when an
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event is executed, and is <em>D</em> for an event that is detected, while
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<em>DF</em> is for a detected event that is also the earliest (first) event
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at the low temperature.</p>
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<p>The time margin is the ratio of the high temperature time in the
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current basin to the stopping time. This last number can be used to
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judge whether the stopping time is too short or too long (see above).</p>
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<p><em>t_lo</em> is the low-temperature event time when the current basin was
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entered, in units of timestep. del<em>t_lo</em> is the time of each detected
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event, measured relative to <em>t_lo</em>. <em>delt_lo</em> is equal to the
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high-temperature time since entering the current basin, scaled by an
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exponential factor that depends on the hi/lo temperature ratio and the
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energy barrier for that event.</p>
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<p>On lines for executed events, with status <em>E</em>, the global event number
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is incremented by one,
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the local event number and time margin are reset to zero,
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while the global event number, energy barrier, and
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<em>delt_lo</em> match the last event with status <em>DF</em>
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in the immediately preceding block of detected events.
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The low-temperature event time <em>t_lo</em> is incremented by <em>delt_lo</em>.</p>
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<p>NEB statistics are written to the file specified by the <em>neb_log</em>
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keyword. If the keyword value is “none”, then no NEB statistics are
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printed out. The statistics are written every <em>Nevery</em> timesteps. See
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the <a class="reference internal" href="neb.html"><span class="doc">neb</span></a> command for a full description of the NEB
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statistics. When invoked from TAD, NEB statistics are never printed to
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the screen.</p>
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<p>Because the NEB calculation must run on multiple partitions, LAMMPS
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produces additional screen and log files for each partition,
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e.g. log.lammps.0, log.lammps.1, etc. For the TAD command, these
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contain the thermodynamic output of each NEB replica. In addition, the
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log file for the first partition, log.lammps.0, will contain
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thermodynamic output from short runs and minimizations corresponding
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to the dynamics and quench operations, as well as a line for each new
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detected event, as described above.</p>
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<p>After the TAD command completes, timing statistics for the TAD run are
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printed in each replica’s log file, giving a breakdown of how much CPU
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time was spent in each stage (NEB, dynamics, quenching, etc).</p>
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<p>Any <a class="reference internal" href="dump.html"><span class="doc">dump files</span></a> defined in the input script will be written
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to during a TAD run at timesteps when an event is executed. This
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means the the requested dump frequency in the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command
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is ignored. There will be one dump file (per dump command) created
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for all partitions. The atom coordinates of the dump snapshot are
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those of the minimum energy configuration resulting from quenching
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following the executed event. The timesteps written into the dump
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files correspond to the timestep at which the event occurred and NOT
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the clock. A dump snapshot corresponding to the initial minimum state
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used for event detection is written to the dump file at the beginning
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of each TAD run.</p>
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<p>If the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> command is used, a single restart file
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for all the partitions is generated, which allows a TAD run to be
|
|
continued by a new input script in the usual manner. The restart file
|
|
is generated after an event is executed. The restart file contains a
|
|
snapshot of the system in the new quenched state, including the event
|
|
number and the low-temperature time. The restart frequency specified
|
|
in the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> command is interpreted differently when
|
|
performing a TAD run. It does not mean the timestep interval between
|
|
restart files. Instead it means an event interval for executed
|
|
events. Thus a frequency of 1 means write a restart file every time
|
|
an event is executed. A frequency of 10 means write a restart file
|
|
every 10th executed event. When an input script reads a restart file
|
|
from a previous TAD run, the new script can be run on a different
|
|
number of replicas or processors.</p>
|
|
<p>Note that within a single state, the dynamics will typically
|
|
temporarily continue beyond the event that is ultimately chosen, until
|
|
the stopping criterionis satisfied. When the event is eventually
|
|
executed, the timestep counter is reset to the value when the event
|
|
was detected. Similarly, after each quench and NEB minimization, the
|
|
timestep counter is reset to the value at the start of the
|
|
minimization. This means that the timesteps listed in the replica log
|
|
files do not always increase monotonically. However, the timestep
|
|
values printed to the master log file, dump files, and restart files
|
|
are always monotonically increasing.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section
|
|
for more info on packages.</p>
|
|
<p><em>N</em> setting must be integer multiple of <em>t_event</em>.</p>
|
|
<p>Runs restarted from restart files written during a TAD run will only
|
|
produce identical results if the user-specified integrator supports
|
|
exact restarts. So <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> will produce an exact
|
|
restart, but <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> will not.</p>
|
|
<p>This command cannot be used when any fixes are defined that keep track
|
|
of elapsed time to perform time-dependent operations. Examples
|
|
include the “ave” fixes such as <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a>.
|
|
Also <a class="reference internal" href="fix_dt_reset.html"><span class="doc">fix dt/reset</span></a> and <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_event_displace.html"><span class="doc">compute event/displace</span></a>,
|
|
<a class="reference internal" href="min_modify.html"><span class="doc">min_modify</span></a>, <a class="reference internal" href="min_style.html"><span class="doc">min_style</span></a>,
|
|
<a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>, <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a>,
|
|
<a class="reference internal" href="temper.html"><span class="doc">temper</span></a>, <a class="reference internal" href="neb.html"><span class="doc">neb</span></a>,
|
|
<a class="reference internal" href="prd.html"><span class="doc">prd</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are <em>min</em> = 0.1 0.1 40 50, <em>neb</em> = 0.01 100 100
|
|
10, <em>neb_style</em> = <em>quickmin</em>, <em>neb_step</em> = the same timestep set by
|
|
the <a class="reference internal" href="timestep.html"><span class="doc">timestep</span></a> command, and <em>neb_log</em> = “none”.</p>
|
|
<hr class="docutils" />
|
|
<p id="voter"><strong>(Voter)</strong> Sorensen and Voter, J Chem Phys, 112, 9599 (2000)</p>
|
|
<p id="voter2"><strong>(Voter2)</strong> Voter, Montalenti, Germann, Annual Review of Materials
|
|
Research 32, 321 (2002).</p>
|
|
</div>
|
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