LAMMPS (19 Mar 2020) # Demonstrate SNAP Ta 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 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms create_atoms CPU = 0.000254 secs mass 1 180.88 # choose potential include Ta06A.snap # DATE: 2014-09-05 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} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05 SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword bzeroflag 0 SNAP keyword quadraticflag 0 # 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 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 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) = 6.591 | 6.591 | 6.591 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 300 -11.85157 -11.85157 -11.813095 2717.1661 -2717.1661 10 295.96579 -11.851053 -11.851053 -11.813095 2696.1559 -2696.1559 20 284.32535 -11.84956 -11.84956 -11.813095 2301.3713 -2301.3713 30 266.04602 -11.847215 -11.847215 -11.813095 1832.1745 -1832.1745 40 242.2862 -11.844168 -11.844168 -11.813095 1492.6765 -1492.6765 50 214.48968 -11.840603 -11.840603 -11.813094 1312.8908 -1312.8908 60 184.32523 -11.836734 -11.836734 -11.813094 1284.582 -1284.582 70 153.58055 -11.832791 -11.832791 -11.813094 1374.4457 -1374.4457 80 124.04276 -11.829003 -11.829003 -11.813094 1537.703 -1537.703 90 97.37622 -11.825582 -11.825582 -11.813094 1734.9662 -1734.9662 100 75.007873 -11.822714 -11.822714 -11.813094 1930.8005 -1930.8005 Loop time of 0.995328 on 1 procs for 100 steps with 128 atoms Performance: 4.340 ns/day, 5.530 hours/ns, 100.469 timesteps/s 99.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99426 | 0.99426 | 0.99426 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000305 | 0.000305 | 0.000305 | 0.0 | 0.03 Output | 0.000413 | 0.000413 | 0.000413 | 0.0 | 0.04 Modify | 0.000159 | 0.000159 | 0.000159 | 0.0 | 0.02 Other | | 0.000191 | | | 0.02 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 727 ave 727 max 727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3712 ave 3712 max 3712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7424 ave 7424 max 7424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7424 Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:01