LAMMPS (20 Apr 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta 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) to (12.64 12.64 12.64) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms Time spent = 0.000277281 secs mass 1 183.84 # choose potential include Mo_Chen_PRM2017.snap # DATE: 2017-09-18 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 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 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) = 3.486 | 3.486 | 3.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -22.405975 0 -22.3675 2575.7657 10 294.63153 -22.405286 0 -22.3675 2753.4662 20 278.98535 -22.40328 0 -22.3675 3272.416 30 254.38916 -22.400125 0 -22.3675 4091.8933 40 222.91191 -22.396088 0 -22.367499 5148.5505 50 187.16984 -22.391504 0 -22.367499 6362.2454 60 150.08253 -22.386747 0 -22.367499 7643.2732 70 114.60307 -22.382197 0 -22.367499 8900.2448 80 83.449257 -22.378201 0 -22.367499 10047.619 90 58.862643 -22.375048 0 -22.367498 11012.233 100 42.41931 -22.372939 0 -22.367498 11740.641 Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s 97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63 Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03 Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01 Other | | 0.00481 | | | 0.25 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: 0:00:01