BN sheet not expanding, but boundary lines are expanding.(tensile test)

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1

Dear all,
I’m simulating boron nitride system with 5nm*5nm (960 atoms ) prepared with VMD. I had an error with preparation of lammps data file from vmd tk console. I got wrong boundary conditions. I changed it manually. But when applied strain to x direction (0.001 ), the sheet is not expanding but boundaries are expanding.
here is my input script

echo both
units metal
atom_style full

boundary p p p
newton on

dimension 3
read_data bn.layer

pair_style tersoff
pair_coeff * * BNC.tersoff B N

neighbor 0.2 bin
neigh_modify every 20 delay 100 check no

timestep 0.0005
fix 1 all npt temp 300.0 300.0 0.05 y 0 0 0.05
thermo 200
compute 1 all stress/atom NULL
compute 2 all pe/atom pair bond
compute 3 all reduce sum c_1[1] c_1[2] c_1[3]
thermo_style custom step temp pe ke etotal press lx ly lz pxx pyy pzz c_3[1] c_3[2] c_3[3]

run 60000
unfix 1

fix 1 all nvt temp 300 300 0.05
fix 2 all ave/atom 1 1000 1000 c_1[1] c_1[2] c_1[3] c_2 fx fy fz
fix 3 all ave/time 1 1000 1000 c_thermo_press[2] file stress.all
dump 1 all custom 1000 dump.new.* id type x y z vx vy vz c_1[1] c_1[2] c_1[3] c_2 f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7]
dump 2 all xyz 1000 dump.graphene.*.xyz

variable tmp equal “lx”
variable L0 equal {tmp} print "Initial Length, L0: {L0}"
variable srate equal 1.0e9
variable srate1 equal “v_srate/1.0e12”
fix 4 all deform 1 x erate ${srate1} units box remap x
variable strain equal “(lx-v_L0)/v_L0”
variable p0 equal “v_strain”
variable p1 equal “-(pxx33)/10000"
variable p2 equal "-(pyy33)/10000”

fix 5 all print 1000 "{p0} {p1} ${p2} " file strain.txt screen no
thermo_style custom step temp v_strain v_p1 v_p2 press
run 600000
echo both

data file :

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.4 on Wed Jul 02 15:35:43 IST 2014
960 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
2 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
-5 55 xlo xhi
-5 55 ylo yhi
-5.000000 5.000000 zlo zhi

Pair Coeffs

2

But when applied strain to x direction (0.001 ), the sheet is not expanding but boundaries are expanding.​

How do you know this? Looking at values in a dump file (are they scaled or unscaled). Performing
a viz?

If you are expanding the box too fast, the atoms may not have time to respond.

Steve

3

Dear all,
           I'm simulating boron nitride system with 5nm*5nm (960 atoms )
prepared with VMD. I had an error with preparation of lammps data file from
vmd tk console. I got wrong boundary conditions. I changed it manually. But
when applied strain to x direction (0.001 ), the sheet is not expanding but
boundaries are expanding.
here is my input script

without looking into details, some parts of your input make no sense,
e.g. neighbor list skin and update settings, computing per atom bond
energy for a system with no explicit bonded interactions, ignoring
lost atoms.

better you build a small test case and add to the input piece by piece
and check each step if it works correctly.

4

I’ve seen it using dump files in ovito software, boundary lines were expanding and sheet remains same.

5

Axel,
I have used tersoff potential which doesn’t need any explicit bonds, hence I’ve not created any bonds, angles, etc in my data file. I used compute per-atom values just to visualize it through dump files.

I changed neighbour skin setiings as well,

neighbor 2.0 bin
neigh_modify delay 1
but didn’t get any elongation in sheet.
Steve,
I have checked my simulation with different strain rates from 0.00001 to 0.01, but nothing worked.
only box boundary lines are expanding and sheet remains same.

using command “fix 4 all deform 1 x erate 0.00001 units box remap x”

I’ve attached my input and data files for reference.
I kindly request you to give me the insight of causes for only boundary line elongations.

bn.layer (52.8 KB)

in.boron (1.29 KB)