LAMMPS (15 Jun 2020) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Mo potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.160 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 3.16 Lattice spacing in x,y,z = 3.16 3.16 3.16 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 (12.64 12.64 12.64) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms create_atoms CPU = 0.000 seconds mass 1 183.84 # choose potential include Mo_Chen_PRM2017.snap # DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) # Generated by Materials Virtual Lab # Definition of SNAP potential. pair_style snap pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 SNAP Element = Mo, Radius 0.5, Weight 1 Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 SNAP keyword rcutfac 4.615858 SNAP keyword twojmax 6 # Setup output 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 = 5.61586 ghost atom cutoff = 5.61586 binsize = 2.80793, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) 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) = 3.271 | 3.271 | 3.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -22.405975 0 -22.3675 2575.7657 10 294.8148 -22.40531 0 -22.3675 2762.0942 20 279.68628 -22.40337 0 -22.3675 3306.7656 30 255.84798 -22.400312 0 -22.3675 4168.2979 40 225.22346 -22.396384 0 -22.367499 5281.9537 50 190.25143 -22.391899 0 -22.367499 6565.6626 60 153.66642 -22.387207 0 -22.367499 7927.3186 70 118.25575 -22.382665 0 -22.367499 9271.9554 80 86.616338 -22.378607 0 -22.367499 10510.959 90 60.935787 -22.375314 0 -22.367498 11568.261 100 42.815823 -22.37299 0 -22.367498 12385.433 Loop time of 0.260783 on 4 procs for 100 steps with 128 atoms Performance: 16.566 ns/day, 1.449 hours/ns, 383.461 timesteps/s 97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23045 | 0.23744 | 0.24455 | 1.2 | 91.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014524 | 0.021267 | 0.027713 | 3.7 | 8.15 Output | 0.00014997 | 0.00040495 | 0.0011623 | 0.0 | 0.16 Modify | 4.2439e-05 | 4.6909e-05 | 5.0068e-05 | 0.0 | 0.02 Other | | 0.00162 | | | 0.62 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 431 ave 431 max 431 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: 1856 ave 1856 max 1856 min Histogram: 4 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: 0:00:00