NEB

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1

Dear LAMMPS users,

I am trying to find MEP for twinning in Cu using LAMMPS (11 Aug 2017).
I created a simulation cell which has the boundary p p f. Bottom half of the cell is un-twinned structure and top half is the twined structure.
First i ran it with 8 replicas. I visualized it in ovito and centro-symmetry parameter in the final step in all replicas showed reasonable behavior. However, when I ran it with 30 replicas, in two replicas the centro-symmetry parameter is very high in the boundaries of the simulation cell even in the un-twinned part of the simulation cell. I can’t understand why it happens.

I would appreciate if I can have your comments.

Thanks,

Leila

2

Dear LAMMPS users,

I am trying to find MEP for twinning in Cu using LAMMPS (11 Aug 2017).
I created a simulation cell which has the boundary p p f. Bottom half of
the cell is un-twinned structure and top half is the twined structure.
First i ran it with 8 replicas. I visualized it in ovito and
centro-symmetry parameter in the final step in all replicas showed
reasonable behavior. However, when I ran it with 30 replicas, in two
replicas the centro-symmetry parameter is very high in the boundaries of
the simulation cell even in the un-twinned part of the simulation cell. I
can't understand why it happens.
I would appreciate if I can have your comments.

​i don't think that anybody will be able to make any serious suggestions
without seeing your specific input.
the NEB implementation in LAMMPS has a selection of options to tweak/adjust
its behavior...

you may also want to try out the latest patch version of LAMMPS, in case
there is a bug in the version that you are using that has been fixes since.

axel.​

3

Dear Axel,

Many thanks for your comments.

About options to adjust the behavior in NEB: So far I tried adding a perpendicular spring force and changing minimization method, which helped me getting more reasonable answers. I believe that the perfect crystal (first replica) and twined structure (last replica) don’t need additional forces so i didn’t use end.

Unfortunately, latest version of patches didn’t help. I still have problem with centro-symmetry parameter in some replicas.

The following is my input script. I’d appreciate if I can have your comments.

Regards,

Leila

---------- Initialize Simulation ---------------------

clear
units metal
dimension 3
boundary p p f
atom_style atomic
atom_modify map array sort 0 0.0
variable u uloop 30

#----------- Create Box ----------------
region box prism 0.000000000000 39.620960716835 -0.000000000000 37.633348035685 -111.723599073640 111.723599073640 1.278095506995 0.000000000000 -0.000000000000 units box
create_box 1 box
read_dump s3Twin_0.dump 0 x y z box yes add yes

---------- Define Interatomic Potential ---------------------

pair_style eam/alloy
pair_coeff * * Cu01.eam.alloy Cu

neighbor 2.0 bin
neigh_modify delay 1 check yes

---------- Define Settings ---------------------

compute eng all pe/atom
compute eatoms all reduce sum c_eng
compute csym all centro/atom fcc

#saving atomic coordinates
dump 1 all custom 100 si_xyz_bulk.out id type x y z

thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms
min_style cg
minimize 1e-25 1e-25 1000 10000

reset_timestep 0
timestep 0.03

Group of NEB atoms

region twinembryo prism 0.000000000000 39.620960716835 -0.000000000000 37.633348035685 -5 111.723599073640 1.278095506995 0.000000000000 -0.000000000000 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 perp 1
#fix 3 all enforce2d

thermo 100

dump 2 all custom 100 dump.allatoms.$u id type x y z c_eng c_csym

run NEB for 100000 steps or to force tolerance

min_style fire

neb 1e-6 1e-6 100000 100000 100 final MyFile.txt.7

4

Dear Axel,

Many thanks for your comments.
About options to adjust the behavior in NEB: So far I tried adding a
perpendicular spring force and changing minimization method, which helped
me getting more reasonable answers. I believe that the perfect crystal
(first replica) and twined structure (last replica) don't need additional
forces so i didn't use* end. *
Unfortunately, latest version of patches didn't help. I still have problem
with centro-symmetry parameter in some replicas.
The following is my input script. I'd appreciate if I can have your
comments.

​my practical experience ​with NEB in LAMMPS is very limited. i mostly know
about it and have been helping to integrate recent improvements to the code
base, which doesn't require much knowledge outside of running provided
tests inputs. i am copying emile maras, who contributed those changes.
perhaps, he has some suggestions.

axel.

5

Dear Leila,

I would first try to include all atoms in the NEB which should be more rigorous. I would also try using a smaller timestep.

Also can you provide the output of your calculations when you add the verbose keyword in the neb command?
It would help find out what goes wrong.

Regards,

Emile