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minor changes to NEB doc pages and examples

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This commit is contained in:
Steve Plimpton
2017-06-20 08:19:23 -06:00
parent 326a8a1289
commit d2610d9e7c
17 changed files with 57 additions and 62 deletions
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48
doc/src/fix_neb.txt
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@ -14,10 +14,10 @@ fix ID group-ID neb Kspring keyword value :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
neb = style name of this fix command :l
Kspring = parallel spring constant (force/distance units or force units, see nudge keyword) :l
Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l
zero or more keyword/value pairs may be appended :l
keyword = {nudge} or {perp} or {ends} :l
{nudge} value = {neigh} or {ideal}
keyword = {parallel} or {perp} or {end} :l
{parallel} value = {neigh} or {ideal}
{neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
{ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units)
{perp} value = {Kspring2}
@ -59,22 +59,22 @@ interatomic force Fi = -Grad(V) for each replica I is altered. For
all intermediate replicas (i.e. for 1 < I < N, except the climbing
replica) the force vector becomes:
Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fspring_perp :pre
Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre
T' is the unit "tangent" vector for replica I and is a function of Ri,
Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
roughly in the direction of (Ri+i - Ri-1); see the
"(Henkelman1)"_#Henkelman1 paper for details. Ri gives the atomic
"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic
coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
neighbor replicas. The term (Grad(V) dot T') is used to remove the
component of the gradient parallel to the path which would tend to
distribute the replica unevenly along the path. Fnudge_parallel is an
artificial nudging force which is applied only in the tangent
direction and which maintains the equal spacing between replicas (see
below for more information). Fspring_perp is an optional artificial
spring which is applied only perpendicular to the tangent and which
prevent the paths from forming acute kinks (see below for more
information).
below for more information). Fnudge_perp is an optional artificial
spring which is applied in a direction perpendicular to the tangent
direction and which prevent the paths from forming acute kinks (see
below for more information).
In the second stage of the NEB calculation, the interatomic force Fi
for the climbing replica (the replica of highest energy after the
@ -86,7 +86,7 @@ and the relaxation procedure is continued to a new converged MEP.
:line
The keyword {nudge} specifies how the parallel nudging force is
The keyword {parallel} specifies how the parallel nudging force is
computed. With a value of {neigh}, the parallel nudging force is
computed as in "(Henkelman1)"_#Henkelman1 by connecting each
intermediate replica with the previous and the next image:
@ -113,15 +113,16 @@ keeping the replicas equally spaced.
:line
The keyword {perp} adds a spring force perpendicular to the path in
order to prevent the path from becoming too kinky. It
can significantly improve the convergence of the NEB calculation when
the resolution is poor. I.e. when too few replicas are used; see
The keyword {perp} specifies if and how a perpendicual nudging force
is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too kinky. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
"(Maras)"_#Maras1 for details.
The perpendicular spring force is given by
Fspring_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
where {Kspring2} is the specified value. F(Ri-1 Ri R+1) is a smooth
scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when
@ -133,11 +134,11 @@ force is added.
:line
By default, no nudging forces act on the first and last replicas during
the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word {end}, additional forces
can be applied to the first or last replica, to enable them to relax
toward a MEP while constraining their energy.
By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word {end}, additional
forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy.
The interatomic force Fi for the specified replica becomes:
@ -177,9 +178,10 @@ only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
After converging a NEB calculation using an {estyle} of {last/efirst/middle},
you should check that all intermediate replicas have a larger energy than the
first replica. If this is not the case, the path is probably not a MEP.
After converging a NEB calculation using an {estyle} of
{last/efirst/middle}, you should check that all intermediate replicas
have a larger energy than the first replica. If this is not the case,
the path is probably not a MEP.
Finally, note that if the last replica converges toward a local
minimum which has a larger energy than the energy of the first