regarding pull-out of CNT from polymer

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1

dear all
i am trying to perform pull-out of CNT from polymer matrix. After equilibration, when i am trying to pull-out CNT from polymer matrix, while keeping polymer atoms fixed or keeping polymer atoms fixed in the region near boundary and use NVT integrator for all.

  1. Keeping periodic boundary condition in x and y direction and z as shrink wrapped.
    2 Scale the boundary in z direction and keeping periodic boundary condition in x,y and z
    ==>> pull-out by using following Command
    Fix smd
    or
    velocity CNT set
    or
    fix setforce

this warning comes :bond/angle/dihedral extent half of periodic box length

and the value of the energies in simulation become very large.

while reading from previous threads, i found that there is problem in equilibration of polymer, bad dynamics, improper structure and force-fields.
But after equilibration my pressure is also varying under the range of -500 to 500.

please help out in eliminating this warning!
Thank you

2

dear all
i am trying to perform pull-out of CNT from polymer matrix. After
equilibration, when i am trying to pull-out CNT from polymer matrix, while
keeping polymer atoms fixed or keeping polymer atoms fixed in the region
near boundary and use NVT integrator for all.
1. Keeping periodic boundary condition in x and y direction and z as shrink
wrapped.
2 Scale the boundary in z direction and keeping periodic boundary condition
in x,y and z
==>> pull-out by using following Command
Fix smd
or
velocity CNT set
or
fix setforce

this warning comes :bond/angle/dihedral extent half of periodic box length
and the value of the energies in simulation become very large.

while reading from previous threads, i found that there is problem in
equilibration of polymer, bad dynamics, improper structure and force-fields.
But after equilibration my pressure is also varying under the range of -500
to 500.

this is all too vague and unspecific to give any specific advice.

axel.

3

Thanks Axel for the reply
this is my input script for pull out after equilibration

Initials of the Data file (created by using moltemplate)

1740 atoms
1717 bonds
3328 angles
4620 dihedrals

4 atom types
7 bond types
15 angle types
37 dihedral types

-10.0 27.0 xlo xhi
-10.0 27.0 ylo yhi
-1.7 14.24 zlo zhi

Masses

1 12.011 #CT “Alkane CH3-” 6 partial charge=-0.18
2 12.011 #CT “Alkane -CH2-” 6 partial charge=-0.12
3 1.008 #HC “Alkane H-C” 1 partial charge=0.06
4 12.010700

Pair Coeffs # lj/cut

1 0.066 3.5
2 0.066 3.5
3 0.03 2.5
4 0.07 3.55

Bond Coeffs # harmonic

1 469 1.4
2 268 1.529
3 268 1.529
4 268 1.529
5 268 1.529
6 340 1.09
7 340 1.09

Angle Coeffs # harmonic

1 85 120
2 58.35 112.7
3 58.35 112.7
4 58.35 112.7
5 58.35 112.7
6 58.35 112.7
7 58.35 112.7
8 58.35 112.7
9 58.35 112.7
10 33 107.8
11 33 107.8
12 37.5 110.7
13 37.5 110.7
14 37.5 110.7
15 37.5 110.7

Dihedral Coeffs # opls

1 0 2.65 0 0
2 1.711 -0.5 0.663 0
3 1.711 -0.5 0.663 0
4 1.711 -0.5 0.663 0
5 1.711 -0.5 0.663 0
6 1.711 -0.5 0.663 0
7 1.711 -0.5 0.663 0
8 1.711 -0.5 0.663 0
9 1.711 -0.5 0.663 0
10 1.3 -0.05 0.2 0
11 1.3 -0.05 0.2 0
12 1.3 -0.05 0.2 0
13 1.3 -0.05 0.2 0
14 1.3 -0.05 0.2 0
15 1.3 -0.05 0.2 0
16 1.3 -0.05 0.2 0
17 1.3 -0.05 0.2 0
18 1.3 -0.05 0.2 0
19 1.3 -0.05 0.2 0
20 1.3 -0.05 0.2 0
21 1.3 -0.05 0.2 0
22 1.3 -0.05 0.2 0
23 1.3 -0.05 0.2 0
24 1.3 -0.05 0.2 0
25 1.3 -0.05 0.2 0
26 0 0 0.3 0
27 0 0 0.3 0
28 0 0 0.3 0
29 0 0 0.3 0
30 0 0 0.3 0
31 0 0 0.3 0
32 0 0 0.3 0
33 0 0 0.3 0
34 0 0 0.3 0
35 0 0 0.3 0
36 0 0 0.3 0
37 0 0 0.3 0

########### script ############
echo screen

----------------- Init Section -----------------

include “D:\ch2-ch3-05-10cnt\system.in.init”

----------------- Atom Definition Section -----------------

read_restart “D:\ch2-ch3-05-10cnt\equi4.restart”

----------------- Settings Section -----------------

include “D:\ch2-ch3-05-10cnt\system.in.settings”

group cnt type 4
group pp type 1 2 3
velocity all create 100.0 154578 dist gaussian mom no rot no

neighbor 3.0 bin
neigh_modify one 25000 page 250000

############## Boundary #############################
#change_box all x scale 1.5 y scale 1.5 z scale 2.0 units box
#change_box all z final -3.5 25.5 boundary p p p remap units box
change_box all boundary p p s #remap units box

################ Group ###############################
region lower block INF 2.4 INF INF INF INF units box
region upper block 16 INF INF INF INF INF units box

group upper region upper
group lower region lower
fix him lower setforce 0.0 0.0 0.0
fix hipp upper setforce 0.0 0.0 0.0

################## for fixing whole polymer ###############
#fix 2 pp setforce 0.0 0.0 0.0
#velocity pp set 0 0 0 #units box

#################### compute ################
compute ape all pe/atom
compute comp all reduce sum c_ape
compute pent cnt reduce sum c_ape
compute pepp pp reduce sum c_ape

#compute cntf cnt property/atom fx fy fz

reset_timestep 0
timestep 0.001
thermo 1000
fix fxnvt all nvt temp 100.0 100.0 1.0

fix pull cnt smd cvel 100.0 -0.080 tether NULL NULL -100.0 1.0

thermo_style custom step temp pe density etotal emol press lx ly f_pull[3] lz c_pent c_pepp c_comp

dump dumpeq1 all custom 3000 pull.lammpstrj id mol type x y z ix iy iz
log pull1.txt
run 1000000

unfix fxnvt
undump dumpeq1
unfix pull

write_restart pull1.restart
write_data pull1.data

issue is that when i perform pull-out test
this warning comes :bond/angle/dihedral extent half of periodic box length
and the value of the energies in simulation become very large.

1- Is there any problem in my pullout script?

2- if there is any problem in equilibration of structure then how to control polymer chain (contains 20 monomer) so that they will not move out of simulation box.

4

Thanks Axel for the reply
this is my input script for pull out after equilibration

this has even less useful information than your previous e-mails.
how can you expect that somebody would understand what you are doing
from some chunks of numbers and input file fragments??
ask yourself, what can *you* read from it?

the only thing that stands out for me is that a system with < 2000
atoms seem rather small for what you describe that you are doing.

sorry, but i have no superhuman abilities...

    axel.

5

S reddy wrote:

the issue is that when i perform pull-out test

this warning comes :bond/angle/dihedral extent half of periodic box length
and the value of the energies in simulation become very large.

It looks like you have already tried reducing the timestep to no avail.

The standard advice in situations like this is to simplify the system as much as possible until the problem(s) goes away. For example, do you still have stability problems when you do NOT attempt to pull out the nanotube? Is your system of polymers stable? If you get rid of the nanotube entirely (…or turn off the interactions between the nanotube and the polymers), does the problem go away?

Keep commenting out lines from your input script until your problem goes away.
You can also try setting coeffs in your “system.in.settings” file to 0.

Eventually the problem will go away. Knowing what you changed to make it happen will point you in the direction of the solution. Sorry I can’t be more concrete than this. This hard work needs to be done by you.

Andrew

P.S. One other remote possibility is that your system is too small. If it is not too difficult, what happens if you make the system twice as large in the x,y, and z directions (for example)? I realize this is probably not the issue, but given the error message you are getting, it’s worth trying if everything else fails.