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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4972 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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36
doc/neb.html
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@ -13,10 +13,9 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>neb etol ftol N1 N2 Nevery filename
<PRE>neb ftol N1 N2 Nevery filename
</PRE>
<UL><LI>etol = stopping tolerance for energy (unitless)
<LI>ftol = stopping tolerance for force (force units)
<UL><LI>ftol = stopping tolerance for force (force units)
<LI>N1 = max # of iterations (timesteps) to run initial NEB
<LI>N2 = max # of iterations (timesteps) to run barrier-climbing NEB
<LI>Nevery = print replica energies and reaction coordinates every this many timesteps
@ -106,19 +105,24 @@ first define an appropriate <A HREF = "min_style.html">min_style</A>, such as
used, since they perform iterative line searches in their inner loop,
which cannot be easily synchronized across multiple replicas.
</P>
<P>The minimizer tolerances for energy and force are set by <I>etol</I> and
<I>ftol</I>, the same as for the <A HREF = "minimize.html">minimize</A> command. The
maximum number of iterations in each stage is set by <I>N1</I> and <I>N2</I>.
These are effectively timestep counts since each iteration of damped
dynamics is like a single timestep in a dynamics <A HREF = "run.html">run</A>.
During both stages, the potential energy of each replica and its
normalized distance along the reaction path (reaction coordinate RD)
will be printed to the screen and log file every <I>Nevery</I> timesteps.
The RD is 0 and 1 for the first and last replica. For intermediate
replicas, it is the cummulative distance (normalized by the total
cummulative distance) between adjacent replicas, where "distance" is
defined as the length of the 3N-vector of differences in atomic
coordinates, where N is the number of NEB atoms involved in the
<P>The minimizer tolerances for force is set by <I>ftol</I>, the same as for
the <A HREF = "minimize.html">minimize</A> command. In this case a non-zero <I>ftol</I>
means that the <I>ftol</I> criterion must be met by every replica in order
for the NEB calculation to converge. The forces being compared to
<I>ftol</I> include the inter-replica forces between an atom and its images
in adjacent replicas.
</P>
<P>The maximum number of iterations in each stage is set by <I>N1</I> and
<I>N2</I>. These are effectively timestep counts since each iteration of
damped dynamics is like a single timestep in a dynamics
<A HREF = "run.html">run</A>. During both stages, the potential energy of each
replica and its normalized distance along the reaction path (reaction
coordinate RD) will be printed to the screen and log file every
<I>Nevery</I> timesteps. The RD is 0 and 1 for the first and last replica.
For intermediate replicas, it is the cummulative distance (normalized
by the total cummulative distance) between adjacent replicas, where
"distance" is defined as the length of the 3N-vector of differences in
atomic coordinates, where N is the number of NEB atoms involved in the
transition. These outputs allow you to monitor NEB's progress in
finding a good energy barrier. <I>N1</I> and <I>N2</I> must both be multiples
of <I>Nevery</I>.

34
doc/neb.txt
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@ -10,9 +10,8 @@ neb command :h3
[Syntax:]
neb etol ftol N1 N2 Nevery filename :pre
neb ftol N1 N2 Nevery filename :pre
etol = stopping tolerance for energy (unitless)
ftol = stopping tolerance for force (force units)
N1 = max # of iterations (timesteps) to run initial NEB
N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@ -103,19 +102,24 @@ first define an appropriate "min_style"_min_style.html, such as
used, since they perform iterative line searches in their inner loop,
which cannot be easily synchronized across multiple replicas.
The minimizer tolerances for energy and force are set by {etol} and
{ftol}, the same as for the "minimize"_minimize.html command. The
maximum number of iterations in each stage is set by {N1} and {N2}.
These are effectively timestep counts since each iteration of damped
dynamics is like a single timestep in a dynamics "run"_run.html.
During both stages, the potential energy of each replica and its
normalized distance along the reaction path (reaction coordinate RD)
will be printed to the screen and log file every {Nevery} timesteps.
The RD is 0 and 1 for the first and last replica. For intermediate
replicas, it is the cummulative distance (normalized by the total
cummulative distance) between adjacent replicas, where "distance" is
defined as the length of the 3N-vector of differences in atomic
coordinates, where N is the number of NEB atoms involved in the
The minimizer tolerances for force is set by {ftol}, the same as for
the "minimize"_minimize.html command. In this case a non-zero {ftol}
means that the {ftol} criterion must be met by every replica in order
for the NEB calculation to converge. The forces being compared to
{ftol} include the inter-replica forces between an atom and its images
in adjacent replicas.
The maximum number of iterations in each stage is set by {N1} and
{N2}. These are effectively timestep counts since each iteration of
damped dynamics is like a single timestep in a dynamics
"run"_run.html. During both stages, the potential energy of each
replica and its normalized distance along the reaction path (reaction
coordinate RD) will be printed to the screen and log file every
{Nevery} timesteps. The RD is 0 and 1 for the first and last replica.
For intermediate replicas, it is the cummulative distance (normalized
by the total cummulative distance) between adjacent replicas, where
"distance" is defined as the length of the 3N-vector of differences in
atomic coordinates, where N is the number of NEB atoms involved in the
transition. These outputs allow you to monitor NEB's progress in
finding a good energy barrier. {N1} and {N2} must both be multiples
of {Nevery}.