Hello everyone,
I am simulating Aluminum atoms on graphene monolayer and I am using Lammps 14May-2016 version.
I ran two cases. In the first case there was a monolayer of graphene (type 2 of 1008 atoms) and a monolayer of Aluminum atoms (type 1 with 292 atoms). The Al layer was placed at a distance of 3 Angstorm in the z-direction from the plane of graphene. This case was running and I was able to see the output when I heated up the whole system to 2200K.
Then I changed the data file to model another system. In this case, I kept the graphene layer of the same size and the number of Al atoms to be same. However, I divided the Al atoms into 2 layers. One layer was at a distance of 3Angstorm from graphene in z-direction and another was at a distance of 5 Angstorm from graphene in z-direction. EVen though I used the same input script, this case was producing nan output just after minimization. I visualized the trajectory and saw that I could not see the Al atoms right after the first frame although there were no “lost atoms” error. I understand this is bad dynamics but could not get where I got wrong. Can someone please help me?
I am attaching the data file here.
Thank you so much for your help.
INPUT SCRIPT
echo screen
dimension 3
boundary p p s
atom_style atomic
units metal
newton on
read_data data.AlonGNR
dump 4 all custom 1 releasedall_equilibrate_heatingandcooling.lammpstrj id type x y z
dump 1 all custom 1 releasedall_equilibrate_till_minimize.lammpstrj id type x y z
##SPECIFYING SEPARATE GROUPS
group aluminum type 1
group graphene type 2
fix 5 graphene setforce 0.0 0.0 0.0
#POTENTIAL FIX (C-C interactions in Graphene mapped by Tersoff)
pair_style hybrid eam/alloy tersoff lj/cut 15.0
pair_coeff * * eam/alloy Al99.eam.alloy Al NULL
pair_coeff * * tersoff SiC.tersoff NULL C
pair_coeff 1 2 lj/cut 0.0079 3.9495
timestep 0.0001
thermo 100
thermo_style custom step temp press vol pe ke etotal
neighbor 3.0 bin
neigh_modify delay 0 every 1 check yes
min_style cg
min_modify line quadratic
minimize 1.0e-20 1.0e-15 10000 1000000
undump 1
thermo 500
thermo_style custom step temp press vol pe ke etotal
dump 2 all custom 5000 releasedall_equilibrate_heatingtill2200K.lammpstrj id type x y z
velocity aluminum create 300.0 4928459 dist gaussian units box
##HEATING STARTS
fix 1 graphene rigid/nvt single temp 300.0 2200.0 50
fix 2 aluminum nvt temp 300.0 2200.0 50
run 50000
#run 19000000
unfix 1
unfix 2
undump 2
write_restart equil.restart1
LOG FILE
LAMMPS (14 May 2016)
echo screen
orthogonal box = (-10.5 -10.5 -5.5) to (70.5 70.5 50.5)
1 by 1 by 1 MPI processor grid
reading atoms …
1299 atoms
291 atoms in group aluminum
1008 atoms in group graphene
Reading potential file SiC.tersoff with DATE: 2011-04-26
Neighbor list info …
5 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9 -> bins = 9 9 1
Memory usage per processor = 5.89809 Mbytes
Step Temp Press Volume PotEng KinEng TotEng
0 0 nan 32878.483 -nan 0 -nan
1 0 nan 32878.483 -nan 0 -nan
Loop time of 8.46811 on 1 procs for 1 steps with 1299 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-nan -nan -nan
Force two-norm initial, final = nan nan
Force max component initial, final = 25.7686 25.7686
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1 1068
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
data.AlonGNR (49.9 KB)