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 = 4.07372 4.07372 4.07372 Created orthogonal box = (0 -42.7296 0) to (52.3279 42.7296 9.97853) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.65991 6.21462 6.65235 Created 1324 atoms create_atoms CPU = 0.000699043 secs 1324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.65991 6.21462 6.65235 Created 1324 atoms create_atoms CPU = 0.000514984 secs 1324 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 19 3 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 46 atoms, new total = 2602 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 6.913 | 6.913 | 6.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7923.7268 0 -7923.7268 450.01232 33 0 -7954.2495 0 -7954.2495 -3595.4287 Loop time of 0.77118 on 1 procs for 33 steps with 2602 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7923.72676482 -7954.24372449 -7954.24949746 Force two-norm initial, final = 27.0988 0.179116 Force max component initial, final = 5.9076 0.0181676 Final line search alpha, max atom move = 1 0.0181676 Iterations, force evaluations = 33 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73672 | 0.73672 | 0.73672 | 0.0 | 95.53 Neigh | 0.027827 | 0.027827 | 0.027827 | 0.0 | 3.61 Comm | 0.0033436 | 0.0033436 | 0.0033436 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003288 | | | 0.43 Nlocal: 2602 ave 2602 max 2602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900 ave 9900 max 9900 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: 514024 ave 514024 max 514024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514024 Ave neighs/atom = 197.55 Neighbor list builds = 2 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.914 | 6.914 | 6.914 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -7954.2495 0 -7954.2495 -3595.4287 44622.949 37 0 -7954.4474 0 -7954.4474 -1214.572 44402.801 Loop time of 0.0719709 on 1 procs for 4 steps with 2602 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7954.24949746 -7954.44646578 -7954.44744422 Force two-norm initial, final = 109.895 0.212341 Force max component initial, final = 86.1332 0.0230076 Final line search alpha, max atom move = 0.000236142 5.43306e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.070522 | 0.070522 | 0.070522 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032139 | 0.00032139 | 0.00032139 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001127 | | | 1.57 Nlocal: 2602 ave 2602 max 2602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9899 ave 9899 max 9899 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: 514020 ave 514020 max 514020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514020 Ave neighs/atom = 197.548 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 12 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 7.052 | 7.052 | 7.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7954.4474 0 -7954.4474 -1214.572 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2602 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 | | 1.907e-06 | | |100.00 Nlocal: 2602 ave 2602 max 2602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9903 ave 9903 max 9903 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: 514350 ave 514350 max 514350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514350 Ave neighs/atom = 197.675 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) = 7.052 | 7.052 | 7.052 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 -7954.4474 -7954.4474 52.235802 85.45918 9.9468 -1214.572 -1214.572 -0.13534784 -3644.3885 0.8077694 2.5934031 2136.7811 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2602 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 | | 2.146e-06 | | |100.00 Nlocal: 2602 ave 2602 max 2602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9903 ave 9903 max 9903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 257175 ave 257175 max 257175 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 514350 ave 514350 max 514350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 514350 Ave neighs/atom = 197.675 Neighbor list builds = 0 Dangerous builds = 0 2602 -8326.78171125503 eV 2.59340310142911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01