From 961aaf367f539a4a30a77f7868c1df08d97d7c7c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 25 Oct 2010 20:30:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5132 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/neb.html | 25 ++++++------------------- 1 file changed, 6 insertions(+), 19 deletions(-) diff --git a/doc/neb.html b/doc/neb.html index 885b03fbbd..0fbf2edc6d 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -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 fix neb command.

-

In the second stage of NEB, the replica with the highest energy +

In the second stage of NEB, the replica nearest the top of the barrier 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 barrier-climbing calculation described in +the barrier, via the hill-climbing calculation described in (Henkelman2). As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced.

@@ -205,27 +205,14 @@ and restart files. this case), the print-out to the screen and master log.lammps file contains a line of output, printed once every Nevery timesteps. It contains the timestep, the maximum force per replica, the maximum -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 +force per atom (in any replica), 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 ftol 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 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. -

-

The "reaction coordinate" (RC) for each -replica is the two-norm of the 3N-length vector of distances between +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 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