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It is recommended that the user be somewhat familiar with the use of the code for single configuration (non-NEB) calculations before using NEB.
        H2 + C2H4 &rarr C2H6
Before performing an NEB calculation, you need to have endpoints for
the chain. Before setting up this example, I ran two separate cluster
calculations corresponding to the reactant (
See the
Cluster Tutorial
for details about how to set up molecular calculations.
First, the use of the "frame" option is especially helpful
for molecular calculations.
Second, I use Accelerated Steepest Descent (ASD) for the geometry
relaxation method.
The calculation is allowed to run for 25 steps. This is not
sufficient to converge to a saddle point, but will provide input for
a further calculation, described below.
At the beginning of this section, the user first sets the number of
intermediate images in the NEB chain. I have used
Next, the code requires information about the chain endpoints. The
required input is the energies (in Rydberg!) of the initial
and final chain geometries, einitial, efinal and
coordinates of the final chain endpoint. In this example, I have
included coordinates for the initial state geometry. I have used the
format atom, types, and position, and the coordinates for the
initial image are identical to those in the setup phase. Different
coordinates will override the setup phase coordinates. I chose this
input format for convenience.
The geometries are transferred directly from the lcao.geom output
files of the initial preparatory runs to obtain the converged
endpoints. Notice that the coordinates of the first 3 atoms in the
initial and final geometries meet the same frame
constraints.
Important: The code obtains the atom types from the input in
the setup phase, and this is not overridden here. It is up to
the user to make sure that the setup phase and neb section have
consistent ordering of atom types.
Next comes optional input.
I have used
Also see
NEB Troubleshooting.
Command options
The NEB method is invoked
by including the command option "do neb."
NEB will work with most of the available command options. The "do
relax" is mandatory. The "do cell" is not permitted.
Both chain endpoints and all the intermediate images must have the
same fixed cell. The "do dynamics" is currently not
supported with NEB.
Setup phase data
The input here is the same as a regular, non-NEB run. The atom
position may be superceded by later input in the neb data, atom type
is not. In an NEB run,
you may encounter difficulties with some functions:
Run phase data
Again, the code will accept any of the regular input options. For this
example, I use a few options in the
geometry section.
frame
1 2 3
I have frozen atom 1, (a carbon atom), fixed the direction of the
vector between the atom 1 and 2 (the 2 carbon atoms), and fixed the
plane of atoms 1, 2 and 3. This eliminates translational and
rotational degrees of freedom, and keeps the molecules from "running
away" to avoid the saddle point during the NEB calculation. These
constraints are often not necessary for a bulk
calculation. Important: The initial endpoint calculations were
performed using the same frame constraints.
gmethod
ASD
The is the recommended (and the default) option for NEB relaxation.
The Broyden method, default for single image relaxations, will
often fail for the more complex NEB calculations, and should not
be invoked for an NEB calculation.
neb data
This section begins with the line "neb data" and ends with
the line "end neb data". This section contains chain
coordinates, and allows the user to select
options
to control the NEB run.
images
6
which results in 6 intermediate geometries to be relaxed between the
fixed chain endpoints. A useful NEB chain usually needs at least 3
intermediate images. The maximum number of images is currently limited
to 12 (but could be increased by redimensioning and recompiling).
antikink
which uses a more efficient definition of the path tangent.
This is the recommended setting.
do setup
do iters
do force
do relax
do neb
setup data
title
title2
dimension of system (0=cluster ... 3=bulk)
0
primitive lattice vectors
25.0000000000 0.0000000000 0.0000000000
0.0000000000 30.0000000000 0.0000000000
0.0000000000 0.0000000000 25.0000000000
grid dimensions
90 100 90
atom types
2
atom file
H = h_ps.atm
atom file
C = c.atm
number of atoms in unit cell
8
atom, type, position;
1 C 0.0000000000 0.0000000000 -1.2453000000
2 C 0.0000000000 0.0000000000 1.2489100943
3 H -1.7584758285 0.0000000000 -2.3301860262
4 H 1.7584653078 0.0100205966 -2.3301646065
5 H -1.7585064612 -0.0008441341 2.3338084172
6 H 1.7584894664 0.0097791574 2.3337979751
7 H 0.0003487181 5.6228197807 -0.7233840640
8 H 0.0003518424 5.6189301345 0.7229545354
end setup phase data
run phase input data
convergence criterion
0.000500
geometry relaxation
frame
1 2 3
gsteps
25
gmethod
ASD
end geometry relaxation
end run phase data
neb data
images
6
einitial
-29.6690869400
atom, type, position; H2 molecule plus C2H4
1 C 0.0000000000 0.0000000000 -1.2453000000
2 C 0.0000000000 0.0000000000 1.2489100943
3 H -1.7584758285 0.0000000000 -2.3301860262
4 H 1.7584653078 0.0100205966 -2.3301646065
5 H -1.7585064612 -0.0008441341 2.3338084172
6 H 1.7584894664 0.0097791574 2.3337979751
7 H 0.0003487181 5.6228197807 -0.7233840640
8 H 0.0003518424 5.6189301345 0.7229545354
efinal
-29.8262256994
atom, type, position; C2H6
1 C 0.0000000000 0.0000000000 -1.2453000000
2 C 0.0000000000 0.0000000000 1.6127026368
3 H -1.9325347853 0.0000000000 -2.0125327795
4 H 0.9274168890 -1.7039832670 -1.9973680549
5 H -1.3457830207 -1.3888791220 2.3776347814
6 H 1.8745031884 -0.4702321383 2.3799786218
7 H 1.0056057745 1.6427026553 -2.0259990122
8 H -0.5350756401 1.8581263113 2.3819664428
antikink
end neb data
Return to Top
Using the climb option to get closer to the saddlepoint and
including intermediate image coordinates in the input file
In order to better approach the saddlepoint, use the "climb"
option. It is often advisable to first run the NEB for a few steps
without the climb option, to allow the chain to relax away from any
possible high-energy initial configurations.
Notice that the format
for the coordinates in the neb data section is different this time:
the chain coordinates were transferred directly from the lcao.neb_geom
file output
from the previous run.
do setup
do iters
do force
do relax
do neb
setup data
title
title2
dimension of system (0=cluster ... 3=bulk)
0
primitive lattice vectors
25.0000000000 0.0000000000 0.0000000000
0.0000000000 30.0000000000 0.0000000000
0.0000000000 0.0000000000 25.0000000000
grid dimensions
90 100 90
atom types
2
atom file
H = h_ps.atm
atom file
C = c.atm
number of atoms in unit cell
8
atom, type, position;
1 C 0.0000000000 0.0000000000 -1.2453000000
2 C 0.0000000000 0.0000000000 1.2489100943
3 H -1.7584758285 0.0000000000 -2.3301860262
4 H 1.7584653078 0.0100205966 -2.3301646065
5 H -1.7585064612 -0.0008441341 2.3338084172
6 H 1.7584894664 0.0097791574 2.3337979751
7 H 0.0003487181 5.6228197807 -0.7233840640
8 H 0.0003518424 5.6189301345 0.7229545354
end setup phase data
run phase input data
convergence criterion
0.000500
geometry relaxation
frame
1 2 3
gsteps
50
gmethod
ASD
end geometry relaxation
end run phase data
neb data
images, and number of atoms
6 8
einitial - energy for start-point
-29.66908694
coordinates for start-point
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.2489100943
-1.7584758285 0.0000000000 -2.3301860262
1.7584653078 0.0100205966 -2.3301646065
-1.7585064612 -0.0008441341 2.3338084172
1.7584894664 0.0097791574 2.3337979751
0.0003487181 5.6228197807 -0.7233840640
0.0003518424 5.6189301345 0.7229545354
efinal - energy for end-product
-29.82622570
coordinates for end-product
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.6127026368
-1.9325347853 0.0000000000 -2.0125327795
0.9274168890 -1.7039832670 -1.9973680549
-1.3457830207 -1.3888791220 2.3776347814
1.8745031884 -0.4702321383 2.3799786218
1.0056057745 1.6427026553 -2.0259990122
-0.5350756401 1.8581263113 2.3819664428
antikink
climb
image number in NEB
1
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.2479195030
-1.7682784683 0.0000000000 -2.3154236486
1.7500419238 -0.1247043290 -2.3383997023
-1.7493045783 -0.0109300541 2.3478654821
1.7619199452 -0.0750451854 2.3268306341
0.1890350370 4.8191631072 -0.6616504543
-0.0660714094 4.8901759400 0.7542001906
image number in NEB
2
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.2541414187
-1.7819797665 0.0000000000 -2.2930748462
1.7356773201 -0.2685628527 -2.3430631839
-1.7279616325 -0.1694757922 2.3846761056
1.7653405529 -0.1311556516 2.3339633442
0.2703519792 4.1177421581 -0.6024806639
-0.0208934101 4.0826842503 0.7962020009
image number in NEB
3
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.3180638612
-1.7938737354 0.0000000000 -2.2704139519
1.7002459021 -0.4502238630 -2.3286795024
-1.7053842796 -0.3467362060 2.4710612762
1.7840583963 -0.1906836189 2.3977228119
0.2594739311 3.4283310041 -0.7017886632
-0.0033894971 3.3388665739 0.8930933197
image number in NEB
4
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.5444241806
-1.7907946750 0.0000000000 -2.2695930873
1.6742300910 -0.5409416714 -2.3270244692
-1.7285814109 -0.4690410031 2.5205993441
1.8118215409 -0.2315843468 2.4462524518
0.2813849417 3.0236504843 -1.0905114021
-0.0573080325 2.8605801098 1.2868029533
image number in NEB
5
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.5869071781
-1.8088017879 0.0000000000 -2.2450191195
1.6305034787 -0.6796305224 -2.3191696089
-1.7125118531 -0.5948140327 2.5549212425
1.8259490870 -0.3255847865 2.4736259746
0.3494746795 2.4863018167 -1.3937245145
-0.1060411804 2.3304575331 1.6256081269
image number in NEB
6
coordinates for this image
0.0000000000 0.0000000000 -1.2453000000
0.0000000000 0.0000000000 1.6105030358
-1.8847231299 0.0000000000 -2.1180612900
1.3877240462 -1.1601595177 -2.2467239353
-1.5674330749 -0.9943891796 2.5274907833
1.8215855438 -0.5150435933 2.4533053967
0.5550633906 1.9941659708 -1.6992747907
-0.2522113539 2.0254380432 2.0768958092
end neb data
Return to Top
Calculations using periodic boundary conditions
When using NEB in a periodic calculation, avoid running chains across
the periodic boundaries, as the results can be unpredictable.
Additional issues
Return to Top
or Input Manual
or User Guides
or SeqQuest Home
Send questions and comments to:
Peter Schultz
at
paschul@sandia.gov
or
Renee Van Ginhoven
at
rmvangi@sandia.gov
Last updated:
April 3, 2006