Hello everyone,
I have built a single layer graphene sheet in Materials studio and converted in LAMMPS file. My goal is to test uniaxial tensile strength of graphene. At first I used fix deform command to stretch the simulation box in x-direction. But the graphene continued to stretch untill when the box length is equal to the twice the initial box length and the strength is around 200 GPa. I stopped the simulation after that and the sheet still did not fracture. But from the literature we know that fracture stress of graphene is around 120 GPa and strain is 0.18-0.27. So, my simulation setup is clearly wrong.
So, now I am trying to set one layer of atoms in the graphene sheet fixed. I used region command in LAMMPS to fix the atoms but LAMMPS showed me an error saying I have to use create_box command first. But I am reading the data file from read_data command. I need an advice about how to fix a portion of atoms when I am creating the box from read_data command. I am using CVFF potential, not tersoff or AIREBO potential.
I greatly appreciate your help.
LAMMPS input file:
echo screen
log debug_grapsingle.log
units real
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style cvff
pair_style lj/cut/coul/long 9.0 10.0 # cutoff1 = 2.5*sigma
kspace_style ewald 1e-4
neighbor 5.0 bin
#neigh_modify delay 0 every 1 one 10000 check yes
neigh_modify delay 0 every 1 check yes
boundary p p p
read_data data.grapsingle
pair_coeff * * 0.1479999981 3.6170487995 # value1 = epsilon, value2 = sigma
#pair_coeff * * CH.airebo C
pair_modify mix arithmetic tail no
group graphene type 1
compute tmpall graphene temp
compute mobile_temp graphene temp
velocity graphene create 298.0 12345 temp mobile_temp dist gaussian mom yes rot no
#velocity graphene set 1000000 0.0 0.0 temp mobile_temp units box
#------------------energy minimization-----------------------------xxx
#------------------NVE + Temp/rescale------------------------------xxx
minimize 1.0e-4 1.0e-6 100 1000
min_style cg
min_modify dmax 0.1
fix 2 all nve
fix 3 all temp/rescale 1 298.0 298.0 1.0 0.5
fix 4 all langevin 298.0 298.0 100.0 2341456
timestep 1
thermo 100
#thermo_style custom step temp pe etotal press vol density evdwl ecoul elong epair ebond eangle edihed eimp emol # epair = evdwl+ecoul+elong;
thermo_style custom step temp pe etotal press vol density
thermo_modify lost error flush yes # emol = ebond+eangle+edihed+eimp;
run 500 # 500 ps
dump 1 all xyz 1 grap.xyz
#dump_modify 1 element C H O
write_data data.grapsingle_nve pair ij # Data after NVE+Langevin
unfix 2
unfix 3
unfix 4
#---------------------------NPT------------------------------------xxx
reset_timestep 0
fix 7 all npt temp 298.0 298.0 100.0 iso 1.01325 1.01325 1000.0 pchain 1 # Pressure unit in (atm)
timestep 1
thermo 100
#thermo_style custom step temp pe etotal press vol density evdwl ecoul elong epair ebond eangle edihed eimp emol # epair = evdwl+ecoul+elong;
thermo_style custom step temp pe etotal press vol density
thermo_modify lost error flush yes # emol = ebond+eangle+edihed+eimp;
run 500 # 1000 ps
dump 2 all xyz 1 grap.xyz
write_data data.grapsingle_npt pair ij # Data after NVE+temp/rescaling+Langevin+NPT
unfix 7
#---------------------------MD simulation------------------------------------xxx
reset_timestep 0
compute peratom graphene stress/atom mobile_temp
compute p graphene reduce sum c_peratom[1] c_peratom[2] c_peratom[3] c_peratom[4] c_peratom[5] c_peratom[6]
variable tmp equal “lx”
variable l0 equal {tmp}
print "initial length, l0: {l0}"
variable erate equal “1e9”
variable erate1 equal “v_erate/1e15” # engineering strain rate in fs
variable strain equal “(lx-v_l0)/v_l0”
variable p1 equal “v_strain”
variable p2 equal “-pxx”
variable p3 equal “-pyy”
variable p4 equal “-pzz”
variable stress equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) # per-atom stress is negative of total pressure p
per-atom stress is sum of diagonal components in stress tensor
fix 8 all nvt temp 298.0 298.0 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
fix print all print 100 “${p1} {p2} {p3} {p4}” file wgw.defo.txt screen no
timestep 1
thermo 100
#thermo_style custom step temp pe etotal vol press v_strain v_stress lx ly lz
thermo_style custom step temp vol press v_strain v_stress lx emol
dump 3 all xyz 5000 grap.xyz
dump 4 all image 25000 dump.*.jpg type type
run 5000
write_data data.grapsingle_md pair ij
unfix 8
unfix 9