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Added potential gradient columns 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5116 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps 2010-10-23 00:02:42 +00:00
parent 5f9d2ec85e
commit 3d4e086b2d
1 changed files with 19 additions and 6 deletions
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@ -136,10 +136,10 @@ The replica states will also be roughly equally spaced along the MEP
due to the inter-replica spring force added by the <A HREF = "fix_neb.html">fix
neb</A> command.
</P>
<P>In the second stage of NEB, the replica nearest the top of the barrier
<P>In the second stage of NEB, the replica with the highest energy
is selected and the inter-replica forces on it are converted to a
force that drives its atom coordinates to the top or saddle point of
the barrier, via the hill-climbing calculation described in
the barrier, via the barrier-climbing calculation described in
<A HREF = "#Hinkelman2">(Henkelman2)</A>. As before, the other replicas rearrange
themselves along the MEP so as to be roughly equally spaced.
</P>
@ -205,14 +205,27 @@ and restart files.
this case), the print-out to the screen and master log.lammps file
contains a line of output, printed once every <I>Nevery</I> timesteps. It
contains the timestep, the maximum force per replica, the maximum
force per atom (in any replica), and the reaction coordinate and
potential energy of each replica. The "maximum force per replica" is
force per atom (in any replica), potential gradients in the initial,
final, and climbing replicas, and
the reaction coordinate and potential energy of each replica.
The "maximum force per replica" is
the two-norm of the 3N-length force vector for the atoms in each
replica, maximized across replicas, which is what the <I>ftol</I> setting
is checking against. In this case, N is all the atoms in each
replica. The "maximum force per atom" is the maximum force component
of any atom in any replica. The "reaction coordinate" (RC) for each
replica is the length of the 3N-length vector of the distances between
of any atom in any replica. The potential gradients are the two-norm
of the 3N-length force vector solely due to the interaction potential i.e.
without adding in inter-replica forces. Note that inter-replica forces
are zero in the initial and final replicas, and only affect
the direction in the climbing replica. For this reason, the "maximum
force per replica" is often equal to the potential gradient in the
climbing replica. In the first stage of NEB, there is no climbing
replica, and so the potential gradient in the highest energy replica
is reported, since this replica will become the climbing replica
in the second stage of NEB.
</P>
<P>The "reaction coordinate" (RC) for each
replica is the two-norm of the 3N-length vector of distances between
its atoms and the preceding replica's atoms, added to the RC of the
preceding replica. The RC of the first replica = 0.0; the remaining
RCs are normalized so that the RC of the last replica = 1.0. In this