Question Regarding Deposition of Nickel Atoms on a CNT Substrate

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1

Hi,

I am trying to use a do-loop to deposit clusters of nickel atoms onto a CNT substrate (which is read from an outside file). I am running into a group limit of 32 groups, and was wondering if there was a way to overcome this.

If I created random atoms one-by-one, could I assign them velocities without assigning them to a group?

Would the fix_deposit command help overcome this limit?

My code is shown below:

##—————INITIALIZATION——————————-
units metal
dimension 3
boundary p p p
atom_style atomic
variable latparam equal 3.52

----------------------- ATOM DEFINITION ----------------------------

read_data input.atoms

region CNT block 0 40 0 40 0 50
group CNT region CNT
##—————SETTINGS———————————

pair_style hybrid airebo 3.0 eam/alloy morse 3.0
pair_coeff * * airebo CH.airebo C NULL
pair_coeff * * eam/alloy Ni99.eam.alloy NULL Ni
pair_coeff 1 2 morse 0.234 1.975 2.27 3.0

mass 1 12.0111
mass 2 58.6934

minimize 1.0e-10 1.0e-10 10000 10000

dump 65 all xyz 100 dump.xyz

reset_timestep 0
timestep 0.001
velocity all create 300 12345 mom yes rot no

fix 1 all nvt temp 300 300 100 drag 1

fix 2 CNT momentum 10 linear 1 1 1
fix 3 CNT momentum 10 angular
thermo 20
thermo_style custom step temp
run 20
unfix 1

----------------------- NCs DEPOSITION ----------------------------

reset_timestep 0
fix 1 all npt temp 300 300 1 z 0 0 100 drag 1

variable max equal 45
variable i loop {max} variable pos equal 45 variable p loop {pos}

label loop1

print “Cluster i=$i”

region {i} sphere 0 15 {p} 1.76 units box
lattice fcc {latparam} orient x 1 1 0 orient y -1 1 0 orient z 0 0 1 create_atoms 2 region {i}
group {i} region {i}
velocity ${i} set 0 -0.8 0
run 1000

next p

next i

jump TestDo.txt loop1

Thanks,

Alex

2

Hi,

I am trying to use a do-loop to deposit clusters of nickel atoms onto a
CNT substrate (which is read from an outside file). I am running into a
group limit of 32 groups, and was wondering if there was a way to overcome
this.

​i don't see any reason why you need to define a *new* group ​with every
iteration of your loop.
just use the same group and then delete it after you are done. then you
will use *only one* group.

If I created random atoms one-by-one, could I assign them velocities

without assigning them to a group?

​no.​

Would the fix_deposit command help overcome this limit?

​possibly, by defining one or more clusters via a molecule command then
then deposit them via the mol and/or molfrac option.

axel.

3

Axel,

Thank you for the help. The only reason to use more than one group is to see how the clusters react in proximity to each other when forming a layer on the nanotube. I’ll see what I can do to modify my process.

Best,

Alex

4

Axel,

Thank you for the help. The only reason to use more than one group is to see
how the clusters react in proximity to each other when forming a layer on
the nanotube. I'll see what I can do to modify my process.

no need for using groups to do that. just assign molecule ids. just as
easy to keep track of and no problem with the limit of groups.

axel.