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 -47.5248 0) to (33.6029 47.5248 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.30572 5.41914 4.45081 Created 458 atoms create_atoms CPU = 0.000337124 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.30572 5.41914 4.45081 Created 458 atoms create_atoms CPU = 0.000212908 secs 458 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 = 11 31 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 8 atoms, new total = 908 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 = 11 31 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) = 4.55 | 4.55 | 4.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6064.9517 0 -6064.9517 29566.721 23 0 -6153.0949 0 -6153.0949 -3942.2051 Loop time of 0.0447819 on 1 procs for 23 steps with 908 atoms 89.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6064.95173747 -6153.09204796 -6153.09488413 Force two-norm initial, final = 188.417 0.206262 Force max component initial, final = 56.39 0.0377064 Final line search alpha, max atom move = 1 0.0377064 Iterations, force evaluations = 23 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043167 | 0.043167 | 0.043167 | 0.0 | 96.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083876 | 0.00083876 | 0.00083876 | 0.0 | 1.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007763 | | | 1.73 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3995 ave 3995 max 3995 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: 52780 ave 52780 max 52780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52780 Ave neighs/atom = 58.1278 Neighbor list builds = 0 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.55 | 4.55 | 4.55 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -6153.0949 0 -6153.0949 -3942.2051 14215.647 26 0 -6153.1378 0 -6153.1378 -156.40477 14196.691 Loop time of 0.00674391 on 1 procs for 3 steps with 908 atoms 148.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6153.09488413 -6153.13780617 -6153.13783408 Force two-norm initial, final = 61.2562 0.267454 Force max component initial, final = 58.4729 0.0642392 Final line search alpha, max atom move = 0.00070235 4.51184e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0062802 | 0.0062802 | 0.0062802 | 0.0 | 93.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011182 | 0.00011182 | 0.00011182 | 0.0 | 1.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003519 | | | 5.22 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4006 ave 4006 max 4006 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: 52992 ave 52992 max 52992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52992 Ave neighs/atom = 58.3612 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 = 11 31 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) = 4.688 | 4.688 | 4.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6153.1378 0 -6153.1378 -156.40477 Loop time of 9.53674e-07 on 1 procs for 0 steps with 908 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: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4006 ave 4006 max 4006 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: 53000 ave 53000 max 53000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53000 Ave neighs/atom = 58.37 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) = 4.688 | 4.688 | 4.688 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 -6153.1378 -6153.1378 33.551706 95.049649 4.4516603 -156.40477 -156.40477 -7.2387099 -461.46689 -0.50871314 2.4274559 576.21648 Loop time of 9.53674e-07 on 1 procs for 0 steps with 908 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: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4006 ave 4006 max 4006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26500 ave 26500 max 26500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53000 ave 53000 max 53000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53000 Ave neighs/atom = 58.37 Neighbor list builds = 0 Dangerous builds = 0 908 -6153.13783407652 eV 2.4274558842119 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