Energy fluctuations while sliding motion

Hello,

I am using Lammps 14May 2016 version. My system is I have 3 layers. The top layer moves to the right and the bottom layer moves to the left. The middle layer is stationary.There are bonds, angles, dihedrals between the atoms and also non bonded lj potential. The middle layer has same type of atoms and the atoms in the top and bottom layers are different. The top layer has 5 chains and the bottom layer also has 5 chains.

I have specified the bonded and non-bonded potentials between each of them.

My question is while running the simulation, the energy is rising exceptionally high and then dropping. Such changes in energy and force are abrupt. The visualized trajectory looks to me to cause the movement I intend. But one chain is coming out of the plane. Can someone please look at my input file and provide a feedback? Thank you so much.

I am also attaching the log file and the data file below.

Input file

dimension 3
boundary p p p

units real
atom_style full
newton on

read_data data.hybrid

neighbor 2.0 nsq
neigh_modify every 10 delay 10 check yes

group upper type 2 3 4 5 6
group lower type 8 9 7 10 11
group middle type 1
group nfcs union upper lower

group point1_rightmove id 521
group point2_leftmove id 641

dump 1 all custom 500 Hybrid.lammpstrj id type x y z

###SPECIFYING THE POTENTIAL

##NON BONDED POTENTIALS

pair_style hybrid lj/cut 15.0 lj96/cut 5.0
pair_modify shift yes

##BETWEEN GRAPHENE ATOMS
pair_coeff 1 1 lj/cut 0.15358321 3.4

##BETWEEN BEADS IN A SINGLE CHAIN
pair_coeff 2 2 lj/cut 9.02 4.42
pair_coeff 3 3 lj/cut 9.02 4.42
pair_coeff 4 4 lj/cut 9.02 4.42
pair_coeff 5 5 lj/cut 9.02 4.42
pair_coeff 6 6 lj/cut 9.02 4.42
pair_coeff 7 7 lj/cut 9.02 4.42
pair_coeff 8 8 lj/cut 9.02 4.42
pair_coeff 9 9 lj/cut 9.02 4.42
pair_coeff 10 10 lj/cut 9.02 4.42
pair_coeff 11 11 lj/cut 9.02 4.42

##BETWEEN GRAPHENE AND BEADS
pair_coeff 1 2 lj/cut 1.177 3.91
pair_coeff 1 3 lj/cut 1.177 3.91
pair_coeff 1 4 lj/cut 1.177 3.91
pair_coeff 1 5 lj/cut 1.177 3.91
pair_coeff 1 6 lj/cut 1.177 3.91
pair_coeff 1 7 lj/cut 1.177 3.91
pair_coeff 1 8 lj/cut 1.177 3.91
pair_coeff 1 9 lj/cut 1.177 3.91
pair_coeff 1 10 lj/cut 1.177 3.91
pair_coeff 1 11 lj/cut 1.177 3.91

##BETWEEN BEADS OF DIFFERENT CHAINS (INTRA)

pair_coeff 2 3 lj96/cut 16.705 3.64
pair_coeff 2 4 lj96/cut 16.705 3.64
pair_coeff 2 5 lj96/cut 16.705 3.64
pair_coeff 2 6 lj96/cut 16.705 3.64
pair_coeff 2 7 lj96/cut 16.705 3.64
pair_coeff 3 4 lj96/cut 16.705 3.64
pair_coeff 3 5 lj96/cut 16.705 3.64
pair_coeff 3 6 lj96/cut 16.705 3.64
pair_coeff 3 7 lj96/cut 16.705 3.64
pair_coeff 4 5 lj96/cut 16.705 3.64
pair_coeff 4 6 lj96/cut 16.705 3.64
pair_coeff 4 7 lj96/cut 16.705 3.64
pair_coeff 5 6 lj96/cut 16.705 3.64
pair_coeff 5 7 lj96/cut 16.705 3.64
pair_coeff 6 7 lj96/cut 16.705 3.64
pair_coeff 6 8 lj96/cut 16.705 3.64
pair_coeff 6 9 lj96/cut 16.705 3.64
pair_coeff 6 10 lj96/cut 16.705 3.64
pair_coeff 6 11 lj96/cut 16.705 3.64
pair_coeff 7 8 lj96/cut 16.705 3.64
pair_coeff 7 9 lj96/cut 16.705 3.64
pair_coeff 7 10 lj96/cut 16.705 3.64
pair_coeff 7 11 lj96/cut 16.705 3.64
pair_coeff 8 9 lj96/cut 16.705 3.64
pair_coeff 8 10 lj96/cut 16.705 3.64
pair_coeff 8 11 lj96/cut 16.705 3.64
pair_coeff 9 10 lj96/cut 16.705 3.64
pair_coeff 9 11 lj96/cut 16.705 3.64
pair_coeff 10 11 lj96/cut 16.705 3.64

##BONDED POTENTIALS

bond_style harmonic
bond_coeff 1 547.225 5.68
bond_coeff 2 90.283 5.6393

angle_style hybrid harmonic cosine/squared
angle_coeff 1 cosine/squared 1074.965 120.0
angle_coeff 2 harmonic 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1

special_bonds lj/coul 1.0 1.0 1.0

thermo_style custom step cpu temp press vol pe ke ebond eangle edihed etotal
thermo 500
thermo_modify flush yes
timestep 0.25

fix 22 middle setforce 0.0 0.0 0.0
fix 11 middle store/force
fix 55 upper store/force
fix 66 lower store/force
fix 77 nfcs store/force

displace_atoms all random 0.01 0.01 0.01 443322

min_style cg
min_modify line quadratic
minimize 1.0e-20 1.0e-15 10000 1000000

fix 3 all nvt temp 300.0 300.0 10
run 10000
unfix 3

write_restart equil.restart1

fix 4 middle nve
reset_timestep 0
dump 11 middle custom 500 force_disp_middle.myforce id x f_11[1]
dump 55 upper custom 500 force_disp_upper.myforce id x f_55[1]
dump 66 lower custom 500 force_disp_lower.myforce id x f_66[1]
dump 77 nfcs custom 500 force_disp_nfc.myforce id x f_77[1]

dump 3 point1_rightmove custom 500 point1_rightmove.lammpstrj id type x y z
dump 4 point2_leftmove custom 500 point2_leftmove.lammpstrj id type x y z

fix 8 upper move linear 0.005 0.0 0.0 units box
fix 9 lower move linear -0.005 0.0 0.0 units box
run 210000
write_restart equil.restart2

LOg file

LAMMPS (14 May 2016)
dimension 3
boundary p p p

units real
atom_style full
newton on

read_data data.hybrid
orthogonal box = (-5.5 -15.5 -10.5) to (225.5 120.5 10.5)
1 by 1 by 1 MPI processor grid
reading atoms …
760 atoms
scanning bonds …
2 = max bonds/atom
scanning angles …
3 = max angles/atom
scanning dihedrals …
1 = max dihedrals/atom
reading bonds …
903 bonds
reading angles …
1354 angles
reading dihedrals …
370 dihedrals
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
18 = max # of 1-4 neighbors
18 = max # of special neighbors

neighbor 2.0 nsq
neigh_modify every 10 delay 10 check yes

group upper type 2 3 4 5 6
200 atoms in group upper
group lower type 8 9 7 10 11
200 atoms in group lower
group middle type 1
360 atoms in group middle
group nfcs union upper lower
400 atoms in group nfcs

group point1_rightmove id 521
1 atoms in group point1_rightmove
group point2_leftmove id 641
1 atoms in group point2_leftmove

dump 1 all custom 500 Hybrid.lammpstrj id type x y z

###SPECIFYING THE POTENTIAL

##NON BONDED POTENTIALS

pair_style hybrid lj/cut 15.0 lj96/cut 5.0
pair_modify shift yes

##BETWEEN GRAPHENE ATOMS
pair_coeff 1 1 lj/cut 0.15358321 3.4

##BETWEEN BEADS IN A SINGLE CHAIN
pair_coeff 2 2 lj/cut 9.02 4.42
pair_coeff 3 3 lj/cut 9.02 4.42
pair_coeff 4 4 lj/cut 9.02 4.42
pair_coeff 5 5 lj/cut 9.02 4.42
pair_coeff 6 6 lj/cut 9.02 4.42
pair_coeff 7 7 lj/cut 9.02 4.42
pair_coeff 8 8 lj/cut 9.02 4.42
pair_coeff 9 9 lj/cut 9.02 4.42
pair_coeff 10 10 lj/cut 9.02 4.42
pair_coeff 11 11 lj/cut 9.02 4.42

##BETWEEN GRAPHENE AND BEADS
pair_coeff 1 2 lj/cut 1.177 3.91
pair_coeff 1 3 lj/cut 1.177 3.91
pair_coeff 1 4 lj/cut 1.177 3.91
pair_coeff 1 5 lj/cut 1.177 3.91
pair_coeff 1 6 lj/cut 1.177 3.91
pair_coeff 1 7 lj/cut 1.177 3.91
pair_coeff 1 8 lj/cut 1.177 3.91
pair_coeff 1 9 lj/cut 1.177 3.91
pair_coeff 1 10 lj/cut 1.177 3.91
pair_coeff 1 11 lj/cut 1.177 3.91

##BETWEEN BEADS OF DIFFERENT CHAINS (INTRA)

pair_coeff 2 3 lj96/cut 16.705 3.64
pair_coeff 2 4 lj96/cut 16.705 3.64
pair_coeff 2 5 lj96/cut 16.705 3.64
pair_coeff 2 6 lj96/cut 16.705 3.64
pair_coeff 2 7 lj96/cut 16.705 3.64
pair_coeff 3 4 lj96/cut 16.705 3.64
pair_coeff 3 5 lj96/cut 16.705 3.64
pair_coeff 3 6 lj96/cut 16.705 3.64
pair_coeff 3 7 lj96/cut 16.705 3.64
pair_coeff 4 5 lj96/cut 16.705 3.64
pair_coeff 4 6 lj96/cut 16.705 3.64
pair_coeff 4 7 lj96/cut 16.705 3.64
pair_coeff 5 6 lj96/cut 16.705 3.64
pair_coeff 5 7 lj96/cut 16.705 3.64
pair_coeff 6 7 lj96/cut 16.705 3.64
pair_coeff 6 8 lj96/cut 16.705 3.64
pair_coeff 6 9 lj96/cut 16.705 3.64
pair_coeff 6 10 lj96/cut 16.705 3.64
pair_coeff 6 11 lj96/cut 16.705 3.64
pair_coeff 7 8 lj96/cut 16.705 3.64
pair_coeff 7 9 lj96/cut 16.705 3.64
pair_coeff 7 10 lj96/cut 16.705 3.64
pair_coeff 7 11 lj96/cut 16.705 3.64
pair_coeff 8 9 lj96/cut 16.705 3.64
pair_coeff 8 10 lj96/cut 16.705 3.64
pair_coeff 8 11 lj96/cut 16.705 3.64
pair_coeff 9 10 lj96/cut 16.705 3.64
pair_coeff 9 11 lj96/cut 16.705 3.64
pair_coeff 10 11 lj96/cut 16.705 3.64

##BONDED POTENTIALS

bond_style harmonic
bond_coeff 1 547.225 5.68
bond_coeff 2 90.283 5.6393

angle_style hybrid harmonic cosine/squared
angle_coeff 1 cosine/squared 1074.965 120.0
angle_coeff 2 harmonic 366068.3768 163.272

dihedral_style harmonic
dihedral_coeff 1 37442.11445 1 1

special_bonds lj/coul 1.0 1.0 1.0
3 = max # of 1-2 neighbors
3 = max # of special neighbors

thermo_style custom step cpu temp press vol pe ke ebond eangle edihed etotal
thermo 500
thermo_modify flush yes
timestep 0.25

fix 22 middle setforce 0.0 0.0 0.0
fix 11 middle store/force
fix 55 upper store/force
fix 66 lower store/force
fix 77 nfcs store/force

displace_atoms all random 0.01 0.01 0.01 443322

min_style cg
min_modify line quadratic
minimize 1.0e-20 1.0e-15 10000 1000000
WARNING: Resetting reneighboring criteria during minimization (…/min.cpp:168)
Neighbor list info …
3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
WARNING: Bond/angle/dihedral extent > half of periodic box length (…/domain.cpp:895)
Memory usage per processor = 10.3318 Mbytes
Step CPU Temp Press Volume PotEng KinEng E_bond E_angle E_dihed TotEng
0 0 0 -466.88522 659736 17274451 0 21.797129 11596813 5680600.8 17274451
500 0.60127807 0 -416.79051 659736 -3892.7037 0 38.879416 4.3321039 0.1961581 -3892.7037
1000 1.243576 0 -363.2002 659736 -4039.1832 0 26.756189 4.1439492 0.0090811175 -4039.1832
1500 1.8032801 0 -183.70568 659736 -4068.4475 0 31.818727 4.1421654 0.0066521225 -4068.4475
2000 2.3934591 0 598.3461 659736 -4339.7851 0 228.26613 4.6085051 0.31706081 -4339.7851
2500 3.1568441 0 520.07398 659736 -4463.6434 0 201.4229 4.1656894 0.067278221 -4463.6434
3000 3.869936 0 483.0964 659736 -4522.4152 0 183.96094 4.1544575 0.035893124 -4522.4152
3500 4.4386921 0 146.83893 659736 -4592.1766 0 78.852201 4.15704 0.025029278 -4592.1766
4000 5.017473 0 -659.56381 659736 -4752.2553 0 57.02124 6.8841059 0.66438563 -4752.2553
4500 5.6792731 0 -583.1942 659736 -4831.81 0 42.697662 6.4862422 0.28959159 -4831.81
5000 6.240016 0 -151.82483 659736 -4917.3984 0 32.652412 4.8401137 0.074603086 -4917.3984
5500 6.825774 0 33.205103 659736 -4928.906 0 55.054087 5.7179307 0.097572822 -4928.906
6000 7.4047031 0 147.08445 659736 -4950.2618 0 80.012278 4.5096039 0.13985291 -4950.2618
6500 7.986623 0 121.8298 659736 -4957.6129 0 73.703948 4.3095582 0.18745186 -4957.6129
7000 8.6333671 0 104.71444 659736 -4960.6129 0 69.831151 4.2750928 0.13937029 -4960.6129
7500 9.238673 0 89.253409 659736 -4963.0988 0 66.471732 4.2591331 0.11693637 -4963.0988
8000 9.953588 0 76.862932 659736 -4964.9386 0 63.864557 4.2529833 0.11001699 -4964.9386
8500 10.78947 0 62.471019 659736 -4966.8749 0 60.93527 4.2518838 0.11116483 -4966.8749
9000 11.619031 0 48.422074 659736 -4968.5605 0 58.190729 4.2558307 0.11811791 -4968.5605
9500 12.453743 0 26.872579 659736 -4970.8893 0 54.219001 4.2730776 0.132317 -4970.8893
10000 13.228545 0 -14.407621 659736 -4975.5341 0 47.421246 4.2783767 0.13985681 -4975.5341
WARNING: Bond/angle/dihedral extent > half of periodic box length (…/domain.cpp:895)
Loop time of 13.2286 on 1 procs for 10000 steps with 760 atoms

99.9% CPU use with 1 MPI tasks x no OpenMP threads

Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
17274450.8391 -4975.52162238 -4975.53413942
Force two-norm initial, final = 1.3927e+08 54.7056
Force max component initial, final = 3.27886e+07 9.75764
Final line search alpha, max atom move = 0.000727028 0.00709408
Iterations, force evaluations = 10000 21061

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

If you’re driving a system by moving the layers, you can easily

induce bad dynamics if you move to fast or drive it with

too much force. You should first verify that your dynamics

are good and stable with no relative motion. Then ramp

the motion up slowly, one simulation at a time and observe

if you can come to equilibrium (temp, velocity profiles, etc).

Steve