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 = 4.12887 4.12887 4.12887 Created orthogonal box = (0 -44.0884 0) to (31.1723 44.0884 5.83911) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.10947 6.96068 5.83911 Created 458 atoms create_atoms CPU = 0.000445127 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.10947 6.96068 5.83911 Created 458 atoms create_atoms CPU = 0.000286102 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 20 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3327.2016 0 -3327.2016 -1687.2038 63 0 -3349.8759 0 -3349.8759 -6114.4972 Loop time of 0.669448 on 1 procs for 63 steps with 904 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3327.20163169 -3349.87330398 -3349.87591824 Force two-norm initial, final = 25.9648 0.124995 Force max component initial, final = 7.87902 0.0219075 Final line search alpha, max atom move = 1 0.0219075 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6535 | 0.6535 | 0.6535 | 0.0 | 97.62 Neigh | 0.0085502 | 0.0085502 | 0.0085502 | 0.0 | 1.28 Comm | 0.0045896 | 0.0045896 | 0.0045896 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00281 | | | 0.42 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6446 ave 6446 max 6446 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: 161092 ave 161092 max 161092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161092 Ave neighs/atom = 178.199 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.999 | 4.999 | 4.999 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -3349.8759 0 -3349.8759 -6114.4972 16049.799 67 0 -3350.0066 0 -3350.0066 -1239.6215 15971.766 Loop time of 0.0484428 on 1 procs for 4 steps with 904 atoms 103.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3349.87591824 -3350.00659917 -3350.00661965 Force two-norm initial, final = 75.701 0.15375 Force max component initial, final = 54.2807 0.0626893 Final line search alpha, max atom move = 0.00319126 0.000200058 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047334 | 0.047334 | 0.047334 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002861 | 0.0002861 | 0.0002861 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008223 | | | 1.70 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432 ave 6432 max 6432 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: 160700 ave 160700 max 160700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160700 Ave neighs/atom = 177.765 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3350.0066 0 -3350.0066 -1239.6215 Loop time of 1.19209e-06 on 1 procs for 0 steps with 904 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 | | 1.192e-06 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432 ave 6432 max 6432 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: 162612 ave 162612 max 162612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162612 Ave neighs/atom = 179.881 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) = 5.137 | 5.137 | 5.137 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 -3350.0066 -3350.0066 31.092877 88.176825 5.8255586 -1239.6215 -1239.6215 6.2725362 -3725.0077 -0.1295316 2.7602016 1036.9524 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6432 ave 6432 max 6432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81306 ave 81306 max 81306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162612 ave 162612 max 162612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162612 Ave neighs/atom = 179.881 Neighbor list builds = 0 Dangerous builds = 0 904 -3350.00661964526 eV 2.7602016077747 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00