135 lines
4.6 KiB
Groff
135 lines
4.6 KiB
Groff
LAMMPS (10 Feb 2021)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Demonstrate MLIAP interface to SNAP nn Cu potential
|
|
|
|
# Initialize simulation
|
|
|
|
variable nsteps index 100
|
|
variable nrep equal 4
|
|
variable a equal 3.621262
|
|
units metal
|
|
|
|
# generate the box and atom positions using a FCC lattice
|
|
|
|
variable nx equal ${nrep}
|
|
variable nx equal 4
|
|
variable ny equal ${nrep}
|
|
variable ny equal 4
|
|
variable nz equal ${nrep}
|
|
variable nz equal 4
|
|
|
|
boundary p p p
|
|
|
|
lattice fcc $a
|
|
lattice fcc 3.621262
|
|
Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
|
|
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
|
region box block 0 4 0 ${ny} 0 ${nz}
|
|
region box block 0 4 0 4 0 ${nz}
|
|
region box block 0 4 0 4 0 4
|
|
create_box 1 box
|
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 256 atoms
|
|
create_atoms CPU = 0.000 seconds
|
|
|
|
mass 1 63.546
|
|
|
|
# choose potential
|
|
|
|
pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
|
|
Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
|
|
Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
|
|
SNAP keyword rcutfac 5.0
|
|
SNAP keyword twojmax 6
|
|
SNAP keyword nelems 1
|
|
SNAP keyword elems Cu
|
|
SNAP keyword radelems 0.5
|
|
SNAP keyword welems 1.0
|
|
SNAP keyword rfac0 0.99363
|
|
SNAP keyword rmin0 0
|
|
SNAP keyword bzeroflag 0
|
|
SNAP keyword switchflag 1
|
|
pair_coeff * * Cu
|
|
|
|
# Setup output
|
|
|
|
compute eatom all pe/atom
|
|
compute energy all reduce sum c_eatom
|
|
|
|
compute satom all stress/atom NULL
|
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
|
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
|
|
|
thermo_style custom step temp epair c_energy etotal press v_press
|
|
thermo 10
|
|
thermo_modify norm yes
|
|
|
|
# Set up NVE run
|
|
|
|
timestep 0.5e-3
|
|
neighbor 1.0 bin
|
|
neigh_modify once no every 1 delay 0 check yes
|
|
|
|
# Run MD
|
|
|
|
velocity all create 300.0 4928459 loop geom
|
|
fix 1 all nve
|
|
run ${nsteps}
|
|
run 100
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 6
|
|
ghost atom cutoff = 6
|
|
binsize = 3, bins = 5 5 5
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair mliap, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes
|
|
Step Temp E_pair c_energy TotEng Press v_press
|
|
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
|
|
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
|
|
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
|
|
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
|
|
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
|
|
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
|
|
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
|
|
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
|
|
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
|
|
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
|
|
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
|
|
Loop time of 3.22769 on 4 procs for 100 steps with 256 atoms
|
|
|
|
Performance: 1.338 ns/day, 17.932 hours/ns, 30.982 timesteps/s
|
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 3.19 | 3.2037 | 3.2196 | 0.7 | 99.26
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.0061415 | 0.022081 | 0.035855 | 8.9 | 0.68
|
|
Output | 0.00093221 | 0.00094824 | 0.00098861 | 0.0 | 0.03
|
|
Modify | 0.0002173 | 0.00022773 | 0.00024477 | 0.0 | 0.01
|
|
Other | | 0.0006805 | | | 0.02
|
|
|
|
Nlocal: 64.0000 ave 64 max 64 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 843.000 ave 843 max 843 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 4992.00 ave 4992 max 4992 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 19968
|
|
Ave neighs/atom = 78.000000
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:03
|