forked from lijiext/lammps
106 lines
4.9 KiB
Groff
106 lines
4.9 KiB
Groff
LAMMPS (28 Mar 2023 - Development)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
#Carbon SNAP example: 216 atom diamond unit cell simulated NVT at ~1,000GPa and 5,000K
|
|
|
|
units metal
|
|
atom_style atomic
|
|
boundary p p p
|
|
|
|
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
|
|
# Crystal orientation and MD box creation #
|
|
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
|
|
lattice diamond 2.845
|
|
Lattice spacing in x,y,z = 2.845 2.845 2.845
|
|
region Bbox block 0 3 0 3 0 3
|
|
create_box 1 Bbox
|
|
Created orthogonal box = (0 0 0) to (8.535 8.535 8.535)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 region Bbox basis 1 1
|
|
Created 216 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (8.535 8.535 8.535)
|
|
create_atoms CPU = 0.000 seconds
|
|
|
|
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
|
|
# Interatomic potential parameters #
|
|
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
|
|
# Specify hybrid with SNAP, ZBL, and long-range C_SNAP_2021.10.15.quadratic.ulomb
|
|
|
|
pair_style hybrid/overlay zbl 0.1 0.2 snap
|
|
pair_coeff 1 1 zbl 10 10
|
|
pair_coeff * * snap C_SNAP_2021.10.15.quadratic.snapcoeff C_SNAP_2021.10.15.quadratic.snapparam C
|
|
SNAP Element = C, Radius 0.5, Weight 1
|
|
SNAP keyword rcutfac 2.7
|
|
SNAP keyword twojmax 8
|
|
SNAP keyword rfac0 0.99363
|
|
SNAP keyword rmin0 0.0
|
|
SNAP keyword bzeroflag 0
|
|
SNAP keyword quadraticflag 1
|
|
|
|
mass * 12.01
|
|
velocity all create 8000.0 3412461 loop geom
|
|
|
|
fix NVE all nve
|
|
fix NVT all langevin 5000.0 5000.0 0.1 3216548
|
|
thermo 50
|
|
thermo_style custom step temp ke pe etotal press pxx pyy pzz
|
|
run 500
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 4.7
|
|
ghost atom cutoff = 4.7
|
|
binsize = 2.35, bins = 4 4 4
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair zbl, perpetual, half/full trim from (2)
|
|
attributes: half, newton on, cut 2.2
|
|
pair build: halffull/newton/trim
|
|
stencil: none
|
|
bin: none
|
|
(2) pair snap, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.681 | 4.681 Mbytes
|
|
Step Temp KinEng PotEng TotEng Press Pxx Pyy Pzz
|
|
0 8000 222.32745 -846.66062 -624.33318 10234249 10210805 10267435 10224506
|
|
50 4382.3571 121.78978 -715.70492 -593.91513 10262157 10278549 10181545 10326376
|
|
100 4546.1549 126.34188 -713.11818 -586.77631 10261694 10257647 10333666 10193770
|
|
150 5109.4576 141.99658 -708.87952 -566.88294 10268132 10248182 10248240 10307974
|
|
200 4764.2181 132.40206 -712.16881 -579.76675 10329903 10238991 10379394 10371323
|
|
250 4989.5099 138.66313 -710.39748 -571.73435 10282678 10321057 10274124 10252854
|
|
300 4853.3102 134.87801 -699.98167 -565.10366 10343314 10204138 10430172 10395634
|
|
350 4788.1153 133.06618 -705.14381 -572.07763 10325571 10312657 10267999 10396058
|
|
400 5055.7813 140.50487 -707.38537 -566.8805 10323176 10357258 10310733 10301536
|
|
450 5182.3198 144.02149 -695.11614 -551.09465 10345564 10358486 10346325 10331881
|
|
500 5311.077 147.59977 -691.32767 -543.7279 10308823 10242668 10214102 10469700
|
|
Loop time of 11.5932 on 4 procs for 500 steps with 216 atoms
|
|
|
|
Performance: 3.726 ns/day, 6.441 hours/ns, 43.129 timesteps/s, 9.316 katom-step/s
|
|
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 10.241 | 10.446 | 10.695 | 5.0 | 90.11
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.87613 | 1.1187 | 1.3179 | 14.9 | 9.65
|
|
Output | 0.0002656 | 0.0010016 | 0.0015521 | 1.5 | 0.01
|
|
Modify | 0.0019493 | 0.0020668 | 0.0021577 | 0.2 | 0.02
|
|
Other | | 0.02508 | | | 0.22
|
|
|
|
Nlocal: 54 ave 54 max 54 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1082 ave 1082 max 1082 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 432 ave 432 max 432 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 8532 ave 8532 max 8532 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 34128
|
|
Ave neighs/atom = 158
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:11
|