LAMMPS (15 Jun 2020) # Demonstrate MLIAP interface to quadratic SNAP potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.1803 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 3.1803 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 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 0.0 0.0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms create_atoms CPU = 0.000 seconds displace_atoms all random 0.01 0.01 0.01 12345 mass 1 183.84 # choose potential include W.quadratic.mliap # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 # Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor pair_style hybrid/overlay zbl 4 ${zblcutouter} mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor pair_style hybrid/overlay zbl 4 4.8 mliap model quadratic W.quadratic.mliap.model descriptor sna W.quadratic.mliap.descriptor SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 6 SNAP keyword nelems 1 SNAP keyword elems W SNAP keyword radelems 0.5 SNAP keyword welems 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword bzeroflag 1 pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 74 ${zblz} pair_coeff 1 1 zbl 74 74 pair_coeff * * mliap W # 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 no # 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 no 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) = 6.031 | 6.032 | 6.033 Mbytes Step Temp E_pair c_energy TotEng Press v_press 0 300 -1.1602728 -1.1602728 -1.1217977 600047.3 -600047.3 10 288.46387 -1.1587932 -1.1587932 -1.1217976 600359.75 -600359.75 20 268.69718 -1.1562579 -1.1562579 -1.1217974 600870.22 -600870.22 30 243.19855 -1.1529874 -1.1529874 -1.1217971 601511.5 -601511.5 40 215.13122 -1.1493875 -1.1493875 -1.1217969 602202.36 -602202.36 50 187.82673 -1.1458855 -1.1458855 -1.1217966 602860.26 -602860.26 60 164.26822 -1.1428639 -1.1428639 -1.1217965 603413.25 -603413.25 70 146.65179 -1.1406045 -1.1406045 -1.1217964 603809.35 -603809.35 80 136.10769 -1.1392522 -1.1392522 -1.1217964 604022.32 -604022.32 90 132.62756 -1.138806 -1.138806 -1.1217964 604053.33 -604053.33 100 135.19841 -1.1391358 -1.1391358 -1.1217966 603928.48 -603928.48 Loop time of 0.520935 on 4 procs for 100 steps with 128 atoms Performance: 8.293 ns/day, 2.894 hours/ns, 191.963 timesteps/s 99.7% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4001 | 0.44784 | 0.49877 | 6.8 | 85.97 Neigh | 0.00728 | 0.0080255 | 0.008793 | 0.8 | 1.54 Comm | 0.012664 | 0.064342 | 0.11287 | 18.2 | 12.35 Output | 0.000511 | 0.00053725 | 0.000613 | 0.0 | 0.10 Modify | 7.3e-05 | 7.925e-05 | 8.3e-05 | 0.0 | 0.02 Other | | 0.0001087 | | | 0.02 Nlocal: 32 ave 35 max 29 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 431 ave 434 max 428 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 928 ave 1019 max 837 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 1856 ave 2030 max 1682 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 7424 Ave neighs/atom = 58 Neighbor list builds = 100 Dangerous builds not checked Total wall time: 0:00:00