2011-01-05 07:39:13 +08:00
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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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<HR>
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<H3>tad command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>tad N t_event T_lo T_hi delta tmax compute-ID seed keyword value ...
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</PRE>
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<UL><LI>N = # of timesteps to run (not including dephasing/quenching)
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<LI>t_event = timestep interval between event checks
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<LI>T_lo = temperature at which event times are desired
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<LI>T_hi = temperature at which MD simulation is performed
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<LI>delta = desired confidence level for stopping criterion
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<LI>tmax = reciprocal of lowest expected preexponential factor (time units)
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<LI>compute-ID = ID of the compute used for event detection
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>min</I> or <I>neb</I> or <I>min_style</I> or <I>neb_style</I> or <I>neb_log</I>
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<PRE> <I>min</I> 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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<I>neb</I> 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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<I>min_style</I> value = <I>cg</I> or <I>hftn</I> or <I>sd</I> or <I>quickmin</I> or <I>fire</I>
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<I>neb_style</I> value = <I>quickmin</I> or <I>fire</I>
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<I>neb_log</I> value = file where NEB statistics are printed
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>tad 2000 50 1800 2300 0.01 0.01 event 54985
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tad 2000 50 1800 2300 0.01 0.01 event 54985 &
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min 1e-05 1e-05 100 100 &
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neb 0.0 0.01 200 200 20 &
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min_style cg &
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neb_style fire &
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neb_log log.neb
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</PRE>
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<P><B>Description:</B>
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</P>
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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.
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2011-01-05 07:39:13 +08:00
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</P>
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<P>TAD is described in <A HREF = "#Voter">this paper</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 HREF = "#Voter2">this review
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paper</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-<I>delta</I>. 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 <I>tmax</I>).
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</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 HREF = "neb.html">NEB</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 HREF = "neb.html">neb</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 HREF = "Section_howto.html#4_5">this
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section</A> of the manual for further discussion
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of multi-replica simulations.
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</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:
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</P>
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<PRE>while (time remains):
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while (time < tstop):
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until (event occurs):
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run dynamics for t_event steps
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quench
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run neb calculation using all replicas
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compute tlo from energy barrier
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update earliest event
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update tstop
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reflect back into current basin
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execute earliest event
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</PRE>
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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.
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</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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<I>t_event</I> 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.
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</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 <I>min</I> and <I>min_style</I> keywords or
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their default values. Note that typically, you do not need to perform
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a highly-converged minimization to detect a transition event.
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</P>
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<P>The event check is performed by a compute with the specified
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<I>compute-ID</I>. Currently there is only one compute that works with the
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TAD commmand, which is the <A HREF = "compute_event_displace.html">compute
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event/displace</A> command. Other
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event-checking computes may be added. <A HREF = "compute_event_displace.html">Compute
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event/displace</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.
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</P>
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<P>The neb calculation is similar to that invoked by the <A HREF = "neb.html">neb</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 TAD implementation provides default
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values for the NEB settings, which can be overridden using the <I>neb</I>
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and <I>neb_style</I> keywords.
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2011-01-05 07:39:13 +08:00
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</P>
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<HR>
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2011-01-05 23:43:09 +08:00
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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 <I>tmax</I>, and the value of
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<I>delta</I> can be set to the desired confidence level e.g. <I>delta</I> = 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 <I>delta</I> and <I>tmax</I> to get a
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good trade-off between accuracy and performance.
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</P>
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<P>A second key aspect is the choice of <I>t_hi</I>. 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 <I>t_hi</I>.
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2011-01-05 07:39:13 +08:00
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</P>
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<HR>
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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.
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</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 <I>N</I>, local event number <I>M</I>,
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event status, energy barrier, time margin, <I>t_lo</I> and <I>delt_lo</I>.
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The timestep is the usual LAMMPS
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timestep, which corresponds to the high-temperature time at which the
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event was detected, in units of timestep. The CPU time is the total
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processor time since the start of the TAD run.
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The global event number <I>N</I> is a counter
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that increments with each executed event. The local event number <I>M</I>
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is a counter that resets to zero upon entering each new basin.
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The event status is <I>E</I> when an event is executed, and
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is <I>D</I> for an event that is detected, while <I>DF</I> is for a detected
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event that is also the earliest (first) event at the low temperature.
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</P>
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<P>The time margin is the ratio of the high temperature time in the current
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basin to the stopping time. This last number can be used to judge
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whether the stopping time is too short or too long (see above).
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</P>
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<P><I>t_lo</I> is the low-temperature event time when the current basin was entered,
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in units of timestep. del<I>t_lo</I> is the time of each detected
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event, measured relative to <I>t_lo</I>. <I>delt_lo</I>
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is equal to the high-temperature time since entering the current
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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.
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</P>
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<P>On lines for executed events, with status <I>E</I>, the global event number is
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incremented by one, and the timestep, local event number,
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energy barrier, <I>t_lo</I>, and <I>delt_lo</I> match the last event with status <I>DF</I> in the
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immediately preceding block of detected events.
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</P>
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<P>The NEB statistics are written to the file specified by the <I>neb_log</I>
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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 <I>Nevery</I> timesteps. See
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the <A HREF = "neb.html">neb</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.
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</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.
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</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).
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</P>
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<P>Any <A HREF = "dump.html">dump files</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 HREF = "dump.html">dump</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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2011-01-05 23:43:09 +08:00
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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.
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2011-01-05 07:39:13 +08:00
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</P>
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<P>If the <A HREF = "restart.html">restart</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
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2011-01-05 23:43:09 +08:00
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continued by a new input script in the usual manner. The restart file
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2011-01-22 09:03:17 +08:00
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is generated after an event is executed. The restart file contains a
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2011-01-05 23:43:09 +08:00
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snapshot of the system in the new quenched state, including the event
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number and the low-temperature time. The restart frequency specified
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in the <A HREF = "restart.html">restart</A> command is interpreted differently when
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performing a TAD run. It does not mean the timestep interval between
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2011-01-22 09:03:17 +08:00
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restart files. Instead it means an event interval for executed
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2011-01-05 23:43:09 +08:00
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events. Thus a frequency of 1 means write a restart file every time
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2011-01-22 09:03:17 +08:00
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an event is executed. A frequency of 10 means write a restart file
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every 10th executed event. When an input script reads a restart file
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2011-01-05 23:43:09 +08:00
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from a previous TAD run, the new script can be run on a different
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number of replicas or processors.
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2011-01-05 07:39:13 +08:00
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</P>
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<P>Note that within a single state, the dynamics will typically
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temporarily continue beyond the event that is ultimately chosen, until
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2011-01-05 23:43:09 +08:00
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the stopping criterionis satisfied. When the event is eventually
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2011-01-22 09:03:17 +08:00
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executed, the timestep counter is reset to the value when the event
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2011-01-05 23:43:09 +08:00
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was detected. Similarly, after each quench and NEB minimization, the
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timestep counter is reset to the value at the start of the
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2011-01-05 07:39:13 +08:00
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minimization. This means that the timesteps listed in the replica log
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2011-01-05 23:43:09 +08:00
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files do not always increase monotonically. However, the timestep
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values printed to the master log file, dump files, and restart files
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are always monotonically increasing.
|
2011-01-05 07:39:13 +08:00
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</P>
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2011-01-05 23:43:09 +08:00
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<HR>
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|
2011-01-05 07:39:13 +08:00
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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>
|
2011-01-05 23:43:09 +08:00
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<P><I>N</I> setting must be integer multiple of <I>t_event</I>.
|
2011-01-05 07:39:13 +08:00
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</P>
|
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<P>Runs restarted from restart files written during a TAD run will only
|
2011-01-05 23:43:09 +08:00
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|
produce identical results if the user-specified integrator supports
|
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|
exact restarts. So <A HREF = "fix_nh.html">fix nvt</A> will produce an exact
|
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|
restart, but <A HREF = "fix_langevin.html">fix langevin</A> will not.
|
2011-01-05 07:39:13 +08:00
|
|
|
|
</P>
|
|
|
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|
<P>This command cannot be used when any fixes are defined that keep track
|
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|
|
of elapsed time to perform time-dependent operations. Examples
|
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|
include the "ave" fixes such as <A HREF = "fix_ave_spatial.html">fix
|
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|
|
ave/spatial</A>. Also <A HREF = "fix_dt_reset.html">fix
|
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|
dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
|
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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 = "compute_event_displace.html">compute event/displace</A>,
|
|
|
|
|
|
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
|
|
|
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|
|
<A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
|
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|
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|
|
<A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>,
|
|
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|
|
<A HREF = "prd.html">prd</A>
|
|
|
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|
|
</P>
|
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|
<P><B>Default:</B>
|
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|
|
</P>
|
2011-01-05 23:43:09 +08:00
|
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|
<P>The option defaults are <I>min</I> = 0.1 0.1 40 50, <I>neb</I> = 0.01 100 100
|
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|
|
10, <I>min_style</I> = <I>cg</I>, <I>neb_style</I> = <I>quickmin</I>, and <I>neb_log</I> =
|
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|
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|
|
"none"
|
2011-01-05 07:39:13 +08:00
|
|
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|
</P>
|
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|
<HR>
|
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|
|
<A NAME = "Voter"></A>
|
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|
<P><B>(Voter)</B> S<>rensen and Voter, J Chem Phys, 112, 9599 (2000)
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</P>
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|
<A NAME = "Voter2"></A>
|
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|
<P><B>(Voter2)</B> Voter, Montalenti, Germann, Annual Review of Materials
|
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|
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|
|
Research 32, 321 (2002).
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</P>
|
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</HTML>
|
