99 lines
3.7 KiB
Plaintext
99 lines
3.7 KiB
Plaintext
LAMMPS (30 Nov 2020)
|
|
# Initialization
|
|
units metal
|
|
boundary p p p
|
|
atom_style charge
|
|
processors * * 1 # domain decomposition over x and y
|
|
|
|
# System and atom definition
|
|
# we use different molecule ids for each layer of hBN
|
|
# so that inter- and intra-layer
|
|
# interactions can be specified separately
|
|
read_data hBN-momolayer-5nm.data
|
|
Reading data file ...
|
|
orthogonal box = (0.0000000 0.0000000 0.0000000) to (46.152980 48.443364 100.00000)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
880 atoms
|
|
read_data CPU = 0.014 seconds
|
|
mass 1 10.8110 # boron mass (g/mole) | membrane
|
|
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
|
|
|
|
######################## Potential defition ########################
|
|
pair_style tersoff shift 0.05
|
|
pair_coeff * * BNC.tersoff B N
|
|
Reading tersoff potential file BNC.tersoff with DATE: 2013-03-21
|
|
####################################################################
|
|
# Neighbor update settings
|
|
neighbor 2.0 bin
|
|
neigh_modify every 1
|
|
neigh_modify delay 0
|
|
neigh_modify check yes
|
|
|
|
#### Simulation settings ####
|
|
timestep 0.001
|
|
#velocity all create 300.0 12345 loop geom
|
|
fix thermostat all nve
|
|
|
|
############# Output ###############
|
|
thermo 100
|
|
thermo_style custom step etotal pe ke temp
|
|
thermo_modify lost warn
|
|
|
|
###### Run molecular dynamics ######
|
|
run 1000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 4.1
|
|
ghost atom cutoff = 4.1
|
|
binsize = 2.05, bins = 23 24 49
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair tersoff, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.670 | 3.670 | 3.670 Mbytes
|
|
Step TotEng PotEng KinEng Temp
|
|
0 -6604.6119 -6604.6119 0 0
|
|
100 -6604.6148 -6604.831 0.21618057 1.9026686
|
|
200 -6604.6142 -6604.812 0.19780992 1.7409831
|
|
300 -6604.6147 -6604.8411 0.22645852 1.9931278
|
|
400 -6604.6143 -6604.7988 0.1844863 1.623718
|
|
500 -6604.6141 -6604.7823 0.16817044 1.4801174
|
|
600 -6604.6145 -6604.8172 0.20269951 1.7840178
|
|
700 -6604.6149 -6604.8489 0.23401257 2.0596132
|
|
800 -6604.6142 -6604.8089 0.19466676 1.7133192
|
|
900 -6604.6146 -6604.8186 0.20395195 1.7950409
|
|
1000 -6604.614 -6604.778 0.1640674 1.4440053
|
|
Loop time of 1.62583 on 1 procs for 1000 steps with 880 atoms
|
|
|
|
Performance: 53.142 ns/day, 0.452 hours/ns, 615.069 timesteps/s
|
|
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 1.5875 | 1.5875 | 1.5875 | 0.0 | 97.64
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.013392 | 0.013392 | 0.013392 | 0.0 | 0.82
|
|
Output | 0.00091558 | 0.00091558 | 0.00091558 | 0.0 | 0.06
|
|
Modify | 0.014704 | 0.014704 | 0.014704 | 0.0 | 0.90
|
|
Other | | 0.009355 | | | 0.58
|
|
|
|
Nlocal: 880.000 ave 880 max 880 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1518.00 ave 1518 max 1518 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 15840.0 ave 15840 max 15840 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 15840
|
|
Ave neighs/atom = 18.000000
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:01
|