Animation for pullout of CNT

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1

Dear Lammps users,

Simulations are done for pulout of CNT from a stationary diamond matrix by applying discrete displacements. For that I made a loop to carry out displacements step by step. Although I am able to pullout the CNT from the matrix, I am not able to visualise it. Dump file generated is giving only the final coordinates of the CNT and matrix. Whereas I want to animate the whole thing. Can anyone help me out with this? Input file is given below -

units real
dimension 3
boundary p p s

atom_style atomic

neighbor 2.0 bin
neigh_modify delay 5

create geometry

lattice diamond 3.57
region diamondBox block 0 34 0 34 0 34 units box

create_box 1 diamondBox
create_atoms 1 region diamondBox

group matrix region diamondBox

mass * 12.0107

velocity all create 300.0 4928459 dist gaussian

LJ potentials

pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5

region 1 cylinder z 17 17 3 0 34 units box
group cnt region 1

delete_atoms region 1 compress no

read_data data.CNT add merge shift 17 17 0
group CNT region 1

displace_atoms CNT move 0 0 9.33 units box

minimize 1.0e-4 1.0e-6 100 1000
min_style cg

velocity matrix scale 300.0 dist gaussian

fix

fix 1 matrix nvt temp 500 500 100
run 500

variable z equal 9.33

label my_loop

displace_atoms CNT move 0 0 0.05

variable z equal $z+0.05

#dump 2 all image 250 image.*.cfg type type zoom 1.6 adiam 1.5

if “$z <= 34” then “jump in.new my_loop”
print “Out of loop”

fix 2 all nvt temp 500 500 10
run 50

timestep 0.003
thermo 500

dump 1 all atom 500 dump.new

run 5000

print “WORKING”

Thanking you in advanceand regards!
Prasoon Singh

2

Dear Lammps users,

Simulations are done for pulout of CNT from a stationary diamond matrix by applying discrete displacements. For that I made a loop to carry out displacements step by step. Although I am able to pullout the CNT from the matrix, I am not able to visualise it. Dump file generated is giving only the final coordinates of the CNT and matrix. Whereas I want to animate the whole thing. Can anyone help me out with this? Input file is given below -

why not use fix move?
the problem in your input is that you re-initialize the dump in every loop iteration and thus truncate any existing file.

axel.

3

Where are u asking me to use the fix move command? If you are telling to use it instead of displace atoms, it is displacing the other atoms excluding CNT also. Also I have to provide discrete displacements, would that be possible by using this? please explain it to me. It would be very grateful of you.
Thanks a lot!

4

Where are u asking me to use the fix move command?

i want to know why you cannot use fix move, which is - in my personal opinion - the right tool for this kind of process.

If you are telling to use it instead of displace atoms, it is displacing the other atoms excluding CNT also.

that is nonsense. if fix move moves the wrong atoms, you are not using it correctly.

Also I have to provide discrete displacements, would that be possible by using this?

why discrete displacements? that seems unphysical to me. atoms just don’t “jump”. in fact, i would not move the entire CNT, but only a fraction that is well outside the matrix it is embedded in and then also move it with a physically meaningful speed (most of the time, people move way too fast, since physical speeds usually make the simulations last too long for them).

please explain it to me. It would be very grateful of you.

the onus of explaining is on you.

axel.