regarding NEB

Dear Lammps users,

I have been trying to run NEB calculations in Lammps to find minimum energy path (MEP). I used 8 processors and got 8 log files, 8 screen files and 8 dump files. However, all the log files and dump files are identical to each other. The NEB command line doesn’t seem to have at all affected the initial input file. If I visualize the dump files, then they are exactly identical to the initial input file. I tried to see if reversing the positions of initial input and final input files would help, but that gave similar outputs again. I have tried altering almost all possible parameters but nothing worked. I would be very grateful if someone could suggest where I have gone wrong.

Here is my Lammps script:

NEB calculation of twin formation

atom_style atomic
dimension 3
units metal
boundary s p p
variable latparam equal 3.18421500000000
variable size equal “v_latparam * 2”
atom_modify map array sort 0 0.0
read_data initialstable.cfg
mass * 24.305
lattice custom 3.184215 a1 1.0 0.0 0.0 a2 0.0 1.732050808 0.0 a3 0.0 0.0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.833333 0.5 basis 0 0.333333 0.5 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

Force fields

pair_style meam
pair_coeff * * library.meam Mg2 Mg2MgS.meam Mg2
neighbor 2.0 bin
variable u uloop 100
reset_timestep 0

timestep 0.005

Group of NEB atoms

region twinembryo block -60 20 25 75 -0.5 29 units box
group nebatoms region twinembryo
group nonneb subtract all nebatoms
fix 1 nonneb setforce 0.0 0.0 0.0
fix 2 nebatoms neb 10
thermo 100
dump 1 all atom 10 tmp.dump.$u
dump_modify 1 scale no

Run NEB

min_style quickmin
neb 0.0 0.1 1000 1000 50 final finalstable.txt

Regards,
Deepesh

Dear Lammps users,

I have been trying to run NEB calculations in Lammps to find minimum
energy path (MEP). I used 8 processors and got 8 log files, 8 screen files
and 8 dump files. However, all the log files and dump files are identical
to each other. The NEB command line doesn't seem to have at all affected
the initial input file. If I visualize the dump files, then they are
exactly identical to the initial input file. I tried to see if reversing
the positions of initial input and final input files would help, but that
gave similar outputs again.

​how can you swap those files around, if they have a very different file
format?
what you describe sounds like your final state, as recognized by LAMMPS, is
identical to the initial state​.

axel.

Hi Axel,

Thank you for your response.
Yes, the initial and final files have different formats but I changed their format to fit in the script. After all, NEB just needs two stable states in the right format.
As you mentioned, the output of the simulation is identical to the file read by the read_data command.

Regards,
Deepesh

Hi Axel,

Thank you for your response.
Yes, the initial and final files have different formats but I changed
their format to fit in the script. After all, NEB just needs two stable
states in the right format.
As you mentioned, the output of the simulation is identical to the file
read by the read_data command.

file the files have meaningful information in the correct format, you
should get at the very least different differences in the result between
the beads while the neb calculation is progressing.

it is very difficult to diagnose such things from remote. please confirm,
that you can reproduce the results in the example/neb folder as described
in the README file in that folder. if those work, then you'll have to debug
your input like everybody else does.

axel.

Hi Axel,
I am very grateful for your suggestion. I was able to get the example working perfectly fine. Apart from some obvious differences, my script is very close to that given in the example and I was able to execute it.

There is one thing which I noticed in the example. The final neb file contains the index and ultimate position of only one atom. So, is it mandatory to have only the data of atoms which have changed their position in the neb file or we can include all the atoms in it ? When I included all the atoms in the neb file (in the example folder), then the visualization of dump files didn’t produce any change. They all looked same and the energy barrier curve didn’t look as smooth as in the earlier case.

Regards,
Deepesh

The neb doc page has a section on output, and discusses dump files,

and 2 python scripts in the tools/python dir which can be used

to massage NEB output in different ways for viz or analysis purposes.

Try them out on the output of examples/neb.

Steve

Dear Lammps users,

Thank you for all of your previous responses.
This is in continuation with my previous query. I have somehow been able to get NEB working and when I visualize the dump files in Ovito, the results look good. But I have not been able to get the energy barrier. The energy of each replica is increasing and it is highest for the last replica. A strange thing is that when I used smaller number of atoms as NEB atoms for the simulation, I got a proper energy barrier.

Actually, in my case I have a twin embryo in the middle of a simulation box. When I considered the entire volume of twin embryo as neb atoms, then I couldn’t get an energy barrier but when I considered only around half of it, then I got a proper energy barrier.

It would really be great if somebody can explain me what could be the issue.

Regards,
Deepesh

There are some new NEB options in the latest

LAMMPS patch. I suggest you try them on your

problem and see if you get better results.

They are part of the fix neb command.

Steve

Thank you Steve.