From fcb4b75589fe5e38204cff4c4dfc6ad4a0a4b701 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 8 Apr 2019 07:24:18 -0600 Subject: [PATCH] Commit JT 040819 - improved documentation neb/spin --- doc/src/neb_spin.txt | 38 ++++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/doc/src/neb_spin.txt b/doc/src/neb_spin.txt index 965414c3a1..83c98eef20 100644 --- a/doc/src/neb_spin.txt +++ b/doc/src/neb_spin.txt @@ -187,8 +187,6 @@ means that the GNEB calculation will terminate if the torque criterion is met by every replica. The torques being compared to {ftol} include the inter-replica nudging forces. -################################################################### - 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 @@ -196,37 +194,41 @@ damped dynamics is like a single timestep in a dynamics 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 cumulative distance (normalized -by the total cumulative 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 +For intermediate replicas, it is the cumulative angular distance +(normalized by the total cumulative angular distance) between adjacent +replicas, where "distance" is defined as the length of the 3N-vector of +the geodesic distances in spin coordinates, with N the number of +GNEB spinsi involved (see equation (13) in "(Bessarab)"_#Bessarab). +These outputs allow you to monitor NEB's progress in finding a good energy barrier. {N1} and {N2} must both be multiples of {Nevery}. -In the first stage of NEB, the set of replicas should converge toward +In the first stage of GNEB, the set of replicas should converge toward a minimum energy path (MEP) of conformational states that transition over a barrier. The MEP for a transition is defined as a sequence of -3N-dimensional states, each of which has a potential energy gradient -parallel to the MEP itself. The configuration of highest energy along -a MEP corresponds to a saddle point. The replica states will also be -roughly equally spaced along the MEP due to the inter-replica nudging -force added by the "fix neb"_fix_neb.html command. +3N-dimensional spin states, each of which has a potential energy +gradient parallel to the MEP itself. +The configuration of highest energy along a MEP corresponds to a saddle +point. The replica states will also be roughly equally spaced along +the MEP due to the inter-replica nudging force added by the +"fix neb"_fix_neb.html command. -In the second stage of NEB, the replica with the highest energy is +In the second stage of GNEB, 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 +that drives its spin coordinates to the top or saddle point of the barrier, via the barrier-climbing calculation described in -"(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange +"(Bessarab)"_#Bessarab. As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced. -When both stages are complete, if the NEB calculation was successful, +When both stages are complete, if the GNEB calculation was successful, the configurations of the replicas should be along (close to) the MEP -and the replica with the highest energy should be an atomic +and the replica with the highest energy should be a spin configuration at (close to) the saddle point of the transition. The potential energies for the set of replicas represents the energy profile of the transition along the MEP. +################################################################### + :line A few other settings in your input script are required or advised to