127 lines
4.7 KiB
Groff
127 lines
4.7 KiB
Groff
LAMMPS (21 Nov 2023 - Development - e94d89ee3c-modified)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Demonstrate MLIAP/PyTorch interface to linear SNAP potential
|
|
|
|
# Initialize simulation
|
|
|
|
variable nsteps index 100
|
|
variable nrep equal 4
|
|
variable a equal 3.316
|
|
units metal
|
|
|
|
# generate the box and atom positions using a BCC 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 bcc $a
|
|
lattice bcc 3.316
|
|
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
|
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 0 0) to (13.264 13.264 13.264)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 128 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
|
create_atoms CPU = 0.000 seconds
|
|
|
|
mass 1 180.88
|
|
|
|
# choose potential
|
|
|
|
pair_style mliap model mliappy Ta_ACE.mliap.pytorch.model.pt descriptor ace linear_ACE_ccs.yace
|
|
Loading python model complete.
|
|
pair_coeff * * Ta
|
|
|
|
# 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 = 10.62
|
|
ghost atom cutoff = 10.62
|
|
binsize = 5.3099999, bins = 3 3 3
|
|
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) = 58.24 | 58.24 | 58.24 Mbytes
|
|
Step Temp E_pair c_energy TotEng Press v_press
|
|
0 300 -10.649822 -10.649822 -10.611347 -149369.7 149369.7
|
|
10 301.54363 -10.65002 -10.65002 -10.611347 -149189.04 149189.04
|
|
20 310.2497 -10.651137 -10.651137 -10.611347 -148663.85 148663.85
|
|
30 325.56462 -10.653101 -10.653101 -10.611347 -147792.6 147792.6
|
|
40 346.54011 -10.655791 -10.655791 -10.611347 -146568.54 146568.54
|
|
50 371.896 -10.659043 -10.659043 -10.611348 -144972.13 144972.13
|
|
60 400.11547 -10.662663 -10.662663 -10.611348 -143011.4 143011.4
|
|
70 429.4367 -10.666423 -10.666423 -10.611348 -140773.79 140773.79
|
|
80 457.62121 -10.685721 -10.685721 -10.627031 -137496.07 137496.07
|
|
90 481.87191 -10.697719 -10.697719 -10.635919 -133888.57 133888.57
|
|
100 500.38073 -10.708101 -10.708101 -10.643927 -130768.99 130768.99
|
|
Loop time of 24.6242 on 4 procs for 100 steps with 128 atoms
|
|
|
|
Performance: 0.175 ns/day, 136.801 hours/ns, 4.061 timesteps/s, 519.813 atom-step/s
|
|
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 23.421 | 24.105 | 24.588 | 8.7 | 97.89
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.032393 | 0.51582 | 1.1996 | 59.7 | 2.09
|
|
Output | 0.0020103 | 0.0020589 | 0.0021633 | 0.1 | 0.01
|
|
Modify | 0.00021557 | 0.00023585 | 0.00025912 | 0.0 | 0.00
|
|
Other | | 0.001166 | | | 0.00
|
|
|
|
Nlocal: 32 ave 32 max 32 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1499 ave 1499 max 1499 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 9024 ave 9024 max 9024 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 36096
|
|
Ave neighs/atom = 282
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:26
|