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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5474 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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327 lines
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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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</CENTER>
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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
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method requires two or more partitions to perform NEB transition
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state searches.
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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
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generate results at a specified lower temperature.
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A good
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overview of accelerated dynamics methods for such systems is given in
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<A HREF = "#Voter2">this review 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 system is
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is confined to low energy basins for long periods,
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punctuated by brief, randomly-occurring transitions to adjacent basins.
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TAD is suitable for
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infrequent-event systems, where in addition, the transition
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kinetics are well-approximated
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by harmonic transition state theory (hTST). In hTST, the temperature
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dependence of transition rates follows the Arrhenius relation.
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As a consequence a set of event times generated in a high-temperature
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simulation can be mapped to a set of much longer estimated times
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in the low-temperature system. However, because this mapping involves
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the energy barrier of the transition event, which is different for each event,
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the first event at the high temperature may not be the earliest event at the
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low temperature. TAD handles this by first generating
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a set of possible events from the current basin. After each event,
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the simulation is reflected backwards into the current basin.
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This is repeated until the stopping criterion is satisfied,
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at which point the event with the earliest
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low-temperature occurrence time is selected.
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The stopping criterion is that the confidence measure
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be greater than 1-<I>delta</I>. The confidence measure is
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the probability that no earlier low-temperature
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event will occur at some later time
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in the high-temperature simulation.
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hTST provides an lower bound for this probability,
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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
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TAD method invokes the <A HREF = "neb.html">NEB</A> method. Each NEB
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replica runs on a partition of processors. The current
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NEB implementation in LAMMPS restricts you to having
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exactly one processor per replica. For more information,
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see the documentation for the <A HREF = "neb.html">neb</A> command.
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In the current LAMMPS implementation of TAD, all the non-NEB
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TAD operations are performed on the first partition, while the
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other partitions remain idle. Processor partitions are
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defined at run-time using the -partition command-line
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switch.
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</P>
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<P>A TAD run has several stages,
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which are repeated each time an event
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is performed. The logic for a TAD
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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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perform earliest event
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</PRE>
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<P>Before this outer loop begins,
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the initial potential energy basin is identified by
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quenching (an energy minimization, see below) the initial state and
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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
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every <I>t_event</I> steps to check if a transition event has occurred.
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This check is performed by quenching the system and comparing the
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resulting 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
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need to perform a highly-converged minimization to detect a transition
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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> command,
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except that the final state is generated internally, instead of being read
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in from a file. The TAD implementation provides default values
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for the NEB settings, which can be overridden using the <I>neb</I> and <I>neb_style</I>
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keywords.
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</P>
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<HR>
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<P>A key aspect of the TAD method is setting the stopping criterion appropriately.
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If this criterion is
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too conservative, then many events must be generated before one is finally performed.
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Conversely, if this criterion is too aggressive, high-entropy high-barrier events will
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be over-sampled, while low-entropy low-barrier events will be under-sampled. If the lowest
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pre-exponential factor is known fairly accurately, then it can be used to estimate <I>tmax</I>,
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and the value of <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 are not well
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characterized (the most common case), it will be necessary to experiment with the values
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of <I>delta</I> and <I>tmax</I> to get a good trade-off between accuracy and performance. To aid
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with this, for each new event that is detected, a line is printed to the
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screen and log output for the first partition, as follows:
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</P>
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<PRE>New event: t_hi = 1950 ievent = 2 eb = 2.97066 dt_lo = 114049 dt_hi/t_stop = 0.610293
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</PRE>
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<P><I>t_hi</I> is the timestep on which the event occurrred.
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<I>ievent</I> is the event index, zero for the first event in each basin.
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<I>eb</I> is the energy barrier for the event.
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<I>dt_lo</I> is the low-temperature time since entering the basin.
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<I>dt_hi/t_stop</I> is a measure of how close the stopping criterion is to
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being met (if > 1.0, then the criterion is met).
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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 increases
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the rate at which new events are generated.
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However, too 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 necessary
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to determine the best value of <I>t_hi</I>.
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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,
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dump 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
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file each time an event is performed. The quantities are the timestep,
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CPU time, clock, and event number.
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The timestep is the usual LAMMPS
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timestep, which corresponds to
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the high-temperature time at which the event was detected,
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in units of timestep.
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The CPU time is the total processor
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time since the start of the TAD run.
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The clock is the low-temperature
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event time, in units of timestep.
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Each clock interval is equal to the timestep interval
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between events scaled by an exponential factor that depends on
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the hi/lo temperature ratio and the energy barrier for that event.
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The event number is a counter that increments with each performed
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event.
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</P>
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<P>The NEB statistics are written to the file specified
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by the <I>neb_log</I> keyword. If the keyword value is "none",
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then no NEB statistics are printed out. The statistics
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are written every <I>Nevery</I> timesteps.
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See the <A HREF = "neb.html">neb</A> command for a full description of
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the NEB statistics. When invoked from TAD, NEB statistics are
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never printed to the screen.
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</P>
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<P>Because the NEB calculation must run on multiple partitions,
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LAMMPS produces additional screen and log
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files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For
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the TAD command, these contain the thermodynamic output of each
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NEB replica. In addition, the log file for the first partition,
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log.lammps.0, will contain thermodynamic output from short runs and
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minimizations corresponding to the dynamics and quench operations, as
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well as a line for each new 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
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written to during a TAD run at timesteps when an event
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is performed. This means the the requested dump
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frequency in the <A HREF = "dump.html">dump</A> command is ignored. There will be
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one dump file (per dump command) created for all partitions.
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The atom coordinates of the dump snapshot are those of the minimum
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energy configuration resulting from quenching following the
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performed event.
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The timesteps written into the dump files correspond to the
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timestep at which the event occurred and NOT the clock. A dump
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snapshot corresponding to the initial minimum state used for event
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detection is written to the dump file at the beginning of each TAD
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run.
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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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continued by a new input script in the usual manner.
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The restart file is generated after an event is performed. The restart
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file contains a snapshot of the system in the new quenched state,
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including the event number and the low-temperature time.
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The restart frequency specified in the <A HREF = "restart.html">restart</A> command
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is interpreted differently when performing a TAD run. It does not
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mean the timestep interval between restart files. Instead it means an
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event interval for performed events. Thus a frequency of 1 means
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write a restart file every time an event is performed. A
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frequency of 10 means write a restart file every 10th performed
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event.
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When an input script reads a restart file from a previous TAD run, the
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new script can be run on a different number of replicas or processors.
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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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the stopping criterionis satisfied.
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When the event is eventually performed,
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the timestep counter is reset to the
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value when the event was detected. Similarly, after each quench
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and NEB minimization,
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the timestep counter is reset to the value at the start of the
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minimization. This means that the timesteps listed in the replica log
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files do not always increase monotonically. However,
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the timestep values printed to the master log file, dump files, and
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restart files are always monotonically increasing.
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</P>
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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>
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<P><I>N</I> setting must be integer multiple of
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<I>t_event</I>.
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</P>
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<P>Runs restarted from restart files written during a TAD run will only
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produce identical results if the user-specified integrator
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supports exact restarts. So <A HREF = "fix_nh.html">fix nvt</A> will produce an exact restart,
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but <A HREF = "fix_langevin.html">fix langevin</A> will not.
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</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>,
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<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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<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>
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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 10,
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<I>min_style</I> = <I>cg</I>, <I>neb_style</I> = <I>quickmin</I>,
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and <I>neb_log</I> = "none"
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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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Research 32, 321 (2002).
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</P>
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</HTML>
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