lammps/examples/mliap/log.04Dec20.mliap.pytorch.Ta06A.g++.1

LAMMPS (10 Feb 2021)
  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 = 3.3160000 3.3160000 3.3160000
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 (13.264000 13.264000 13.264000)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 128 atoms
  create_atoms CPU = 0.000 seconds

mass 1 180.88

# choose potential

include Ta06A.pytorch.mliap
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)

# Definition of SNAP potential Ta_Cand06A
# Assumes 1 LAMMPS atom type

variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 73

# Specify hybrid with SNAP, ZBL

pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
pair_style hybrid/overlay zbl 4 4.8 mliap model mliappy Ta06A.mliap.pytorch.model.pt descriptor sna Ta06A.mliap.descriptor
Loading python model complete.
Reading potential file Ta06A.mliap.descriptor with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637 
SNAP keyword twojmax 6 
SNAP keyword nelems 1 
SNAP keyword elems Ta 
SNAP keyword radelems 0.5 
SNAP keyword welems 1 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword bzeroflag 0 
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
pair_coeff * * mliap 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 = 5.8
  ghost atom cutoff = 5.8
  binsize = 2.9, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair zbl, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (2) 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) = 18.15 | 18.15 | 18.15 Mbytes
Step Temp E_pair c_energy TotEng Press v_press 
       0          300    -11.85157    -11.85157   -11.813095    2717.1661   -2717.1661 
      10    296.01467   -11.851059   -11.851059   -11.813095    2697.4796   -2697.4796 
      20    284.53666   -11.849587   -11.849587   -11.813095    2289.1527   -2289.1527 
      30    266.51577   -11.847275   -11.847275   -11.813095    1851.7131   -1851.7131 
      40    243.05007   -11.844266   -11.844266   -11.813095     1570.684    -1570.684 
      50    215.51032   -11.840734   -11.840734   -11.813094    1468.1899   -1468.1899 
      60    185.48331   -11.836883   -11.836883   -11.813094    1524.8757   -1524.8757 
      70     154.6736   -11.832931   -11.832931   -11.813094    1698.3351   -1698.3351 
      80    124.79303   -11.829099   -11.829099   -11.813094    1947.0715   -1947.0715 
      90    97.448054   -11.825592   -11.825592   -11.813094    2231.9563   -2231.9563 
     100    74.035418   -11.822589   -11.822589   -11.813094    2515.8526   -2515.8526 
Loop time of 2.0472 on 1 procs for 100 steps with 128 atoms

Performance: 2.110 ns/day, 11.373 hours/ns, 48.847 timesteps/s
100.2% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.0443     | 2.0443     | 2.0443     |   0.0 | 99.86
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.001157   | 0.001157   | 0.001157   |   0.0 |  0.06
Output  | 0.00080857 | 0.00080857 | 0.00080857 |   0.0 |  0.04
Modify  | 0.00053188 | 0.00053188 | 0.00053188 |   0.0 |  0.03
Other   |            | 0.0004304  |            |       |  0.02

Nlocal:        128.000 ave         128 max         128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        727.000 ave         727 max         727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        3712.00 ave        3712 max        3712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      7424.00 ave        7424 max        7424 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7424
Ave neighs/atom = 58.000000
Neighbor list builds = 0
Dangerous builds = 0

Total wall time: 0:00:03