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@ -68,6 +68,11 @@ a minimization.
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<P>Either the <I>quickmin</I> and <I>fire</I> styles are useful in the context of
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nudged elastic band (NEB) calculations via the <A HREF = "neb.html">neb</A> command.
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</P>
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<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
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you have defined via the <A HREF = "timestep.html">timestep</A> command. Often they
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will converge more quickly if you use a timestep about 10x larger than
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you would normally use for dynamics simulations.
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</P>
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<P>IMPORTANT NOTE: The <I>quickmin</I> and <I>fire</I> styles do not yet support
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the use of the <A HREF = "fix_box_relax.html">fix box/relax</A> command or
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minimizations involving the electron radius in <A HREF = "pair_eff.html">eFF</A>
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@ -64,6 +64,11 @@ a minimization.
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Either the {quickmin} and {fire} styles are useful in the context of
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nudged elastic band (NEB) calculations via the "neb"_neb.html command.
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IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
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you have defined via the "timestep"_timestep.html command. Often they
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will converge more quickly if you use a timestep about 10x larger than
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you would normally use for dynamics simulations.
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IMPORTANT NOTE: The {quickmin} and {fire} styles do not yet support
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the use of the "fix box/relax"_fix_box_relax.html command or
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minimizations involving the electron radius in "eFF"_pair_eff.html
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@ -63,12 +63,18 @@ Optimization (Procedure 3.1 on p 41).
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</P>
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<P>The <A HREF = "min_style.html">minimization styles</A> <I>quickmin</I> and <I>fire</I> perform
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damped dynamics using an Euler integration step. Thus they require a
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<A HREF = "timestep.html">timestep</A> be defined, typically the same value used for
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<A HREF = "run.html">running dynamics</A> with the system, though it may be more
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efficient to use a larger timestep.
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<A HREF = "timestep.html">timestep</A> be defined.
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</P>
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<P>The objective function being minimized is the total potential energy
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of the system as a function of the N atom coordinates:
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<P>IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
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you have defined via the <A HREF = "timestep.html">timestep</A> command. Often they
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will converge more quickly if you use a timestep about 10x larger than
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you would normally use for dynamics simulations.
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</P>
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<HR>
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<P>In all cases, the objective function being minimized is the total
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potential energy of the system as a function of the N atom
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coordinates:
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</P>
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<CENTER><IMG SRC = "Eqs/min_energy.jpg">
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</CENTER>
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@ -60,12 +60,18 @@ Optimization (Procedure 3.1 on p 41).
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The "minimization styles"_min_style.html {quickmin} and {fire} perform
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damped dynamics using an Euler integration step. Thus they require a
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"timestep"_timestep.html be defined, typically the same value used for
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"running dynamics"_run.html with the system, though it may be more
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efficient to use a larger timestep.
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"timestep"_timestep.html be defined.
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The objective function being minimized is the total potential energy
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of the system as a function of the N atom coordinates:
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IMPORTANT NOTE: The damped dynamic minimizers use whatever timestep
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you have defined via the "timestep"_timestep.html command. Often they
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will converge more quickly if you use a timestep about 10x larger than
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you would normally use for dynamics simulations.
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:line
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In all cases, the objective function being minimized is the total
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potential energy of the system as a function of the N atom
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coordinates:
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:c,image(Eqs/min_energy.jpg)
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10
doc/neb.html
10
doc/neb.html
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@ -70,12 +70,12 @@ for further discussion.
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<P>IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
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there to be one processor per replica.
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</P>
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<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
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damped-dynamics minimization across all the replicas. This will use
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<P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped
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dynamics minimization across all the replicas. The mimimizer uses
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whatever timestep you have defined in your input script, via the
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<A HREF = "timestep.html">timestep</A> command. You may get faster convergence for
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a NEB calculation if you use a larger timestep than you would normally
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use for dynamics with the same system.
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<A HREF = "timestep.html">timestep</A> command. Often NEB will converge more
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quickly if you use a timestep about 10x larger than you would normally
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use for dynamics simulations.
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</P>
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<P>When a NEB calculation is performed, it is assumed that each replica
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is running the same system, though LAMMPS does not check for this.
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10
doc/neb.txt
10
doc/neb.txt
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@ -60,12 +60,12 @@ for further discussion.
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IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
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there to be one processor per replica.
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IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
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damped-dynamics minimization across all the replicas. This will use
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IMPORTANT NOTE: As explained below, a NEB calculation perfoms a damped
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dynamics minimization across all the replicas. The mimimizer uses
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whatever timestep you have defined in your input script, via the
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"timestep"_timestep.html command. You may get faster convergence for
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a NEB calculation if you use a larger timestep than you would normally
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use for dynamics with the same system.
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"timestep"_timestep.html command. Often NEB will converge more
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quickly if you use a timestep about 10x larger than you would normally
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use for dynamics simulations.
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When a NEB calculation is performed, it is assumed that each replica
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is running the same system, though LAMMPS does not check for this.
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31
doc/tad.html
31
doc/tad.html
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@ -44,8 +44,9 @@
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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_step</I> value = dtneb
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dtneb = timestep for NEB damped dynamics minimization
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<I>neb_log</I> value = file where NEB statistics are printed
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</PRE>
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@ -132,9 +133,11 @@ 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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algorithm has been defined by the <A HREF = "min_style.html">min_style</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 <I>min</I> 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.
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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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@ -145,11 +148,17 @@ 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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<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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of being read in from a file. The style of minimization performed by
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NEB is determined by the <I>neb_style</I> 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 <I>neb</I> keyword. As discussed on the
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<A HREF = "neb.html">neb</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 HREF = "timestep.html">timestep</A> command is used by TAD for performing
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dynamics, there is a <I>neb_step</I> keyword which can be used to set a
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larger timestep for each NEB calculation if desired.
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</P>
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<HR>
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@ -211,7 +220,7 @@ while the global event number, energy barrier, and
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in the immediately preceding block of detected events.
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The low-temperature event time <I>t_lo</I> is incremented by <I>delt_lo</I>.
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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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<P>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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@ -301,8 +310,8 @@ dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
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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
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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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"none"
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10, <I>neb_style</I> = <I>quickmin</I>, <I>neb_step</I> = the same timestep set by
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the <A HREF = "timestep.html">timestep</A> command, and <I>neb_log</I> = "none".
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</P>
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<HR>
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33
doc/tad.txt
33
doc/tad.txt
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@ -33,8 +33,9 @@ keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l
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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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{min_style} value = {cg} or {hftn} or {sd} or {quickmin} or {fire}
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{neb_style} value = {quickmin} or {fire}
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{neb_step} value = dtneb
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dtneb = timestep for NEB damped dynamics minimization
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{neb_log} value = file where NEB statistics are printed :pre
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:ule
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@ -95,7 +96,6 @@ partitions remain idle. See "Section_howto
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5"_Section_howto.html#howto_5 of the manual for further discussion of
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multi-replica simulations.
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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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@ -122,9 +122,11 @@ 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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A quench is an energy minimization and is performed by whichever
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algorithm has been defined by the {min} and {min_style} 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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algorithm has been defined by the "min_style"_min_style.html 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 {min} 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.
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The event check is performed by a compute with the specified
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{compute-ID}. Currently there is only one compute that works with the
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@ -135,11 +137,17 @@ event/displace"_compute_event_displace.html 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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The neb calculation is similar to that invoked by the "neb"_neb.html
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The NEB calculation is similar to that invoked by the "neb"_neb.html
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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 {neb}
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and {neb_style} keywords.
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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 {neb_style} 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 {neb} keyword. As discussed on the
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"neb"_neb.html, 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 "timestep"_timestep.html command is used by TAD for performing
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dynamics, there is a {neb_step} keyword which can be used to set a
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larger timestep for each NEB calculation if desired.
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:line
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@ -201,8 +209,7 @@ while the global event number, energy barrier, and
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in the immediately preceding block of detected events.
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The low-temperature event time {t_lo} is incremented by {delt_lo}.
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The NEB statistics are written to the file specified by the {neb_log}
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NEB statistics are written to the file specified by the {neb_log}
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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 {Nevery} timesteps. See
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the "neb"_neb.html command for a full description of the NEB
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@ -292,8 +299,8 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
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[Default:]
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The option defaults are {min} = 0.1 0.1 40 50, {neb} = 0.01 100 100
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10, {min_style} = {cg}, {neb_style} = {quickmin}, and {neb_log} =
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"none"
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10, {neb_style} = {quickmin}, {neb_step} = the same timestep set by
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the "timestep"_timestep.html command, and {neb_log} = "none".
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:line
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