LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.1472 3.1472 3.1472 Created orthogonal box = (0 -41.2783 0) to (29.1859 41.2783 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.42994 5.27938 4.45081 Created 346 atoms create_atoms CPU = 0.000253916 secs 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.42994 5.27938 4.45081 Created 346 atoms create_atoms CPU = 0.000152111 secs 346 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 27 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 688 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4523.6734 0 -4523.6734 71383.298 42 0 -4666.3259 0 -4666.3259 3561.0976 Loop time of 0.0778749 on 1 procs for 42 steps with 688 atoms 102.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4523.673357 -4666.32172065 -4666.32592685 Force two-norm initial, final = 241.97 0.256521 Force max component initial, final = 60.4837 0.0309082 Final line search alpha, max atom move = 1 0.0309082 Iterations, force evaluations = 42 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073976 | 0.073976 | 0.073976 | 0.0 | 94.99 Neigh | 0.001174 | 0.001174 | 0.001174 | 0.0 | 1.51 Comm | 0.0015924 | 0.0015924 | 0.0015924 | 0.0 | 2.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001132 | | | 1.45 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3852 ave 3852 max 3852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40516 ave 40516 max 40516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40516 Ave neighs/atom = 58.8895 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -4666.3259 0 -4666.3259 3561.0976 10724.192 44 0 -4666.3421 0 -4666.3421 1124.6796 10733.041 Loop time of 0.00639987 on 1 procs for 2 steps with 688 atoms 156.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4666.32592685 -4666.33945133 -4666.34206223 Force two-norm initial, final = 32.0003 0.277648 Force max component initial, final = 31.2697 0.0357169 Final line search alpha, max atom move = 0.000103496 3.69656e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.005919 | 0.005919 | 0.005919 | 0.0 | 92.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012898 | 0.00012898 | 0.00012898 | 0.0 | 2.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003519 | | | 5.50 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3824 ave 3824 max 3824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40496 ave 40496 max 40496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40496 Ave neighs/atom = 58.8605 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4666.3421 0 -4666.3421 1124.6796 Loop time of 9.53674e-07 on 1 procs for 0 steps with 688 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3836 ave 3836 max 3836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40480 ave 40480 max 40480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40480 Ave neighs/atom = 58.8372 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.645 | 4.645 | 4.645 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4666.3421 -4666.3421 29.17822 82.556576 4.4556629 1124.6796 1124.6796 -1.8338027 3380.4578 -4.5852631 2.4362577 383.49309 Loop time of 9.53674e-07 on 1 procs for 0 steps with 688 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 688 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3836 ave 3836 max 3836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20240 ave 20240 max 20240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40480 ave 40480 max 40480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40480 Ave neighs/atom = 58.8372 Neighbor list builds = 0 Dangerous builds = 0 688 -4666.34206222626 eV 2.43625774057052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42