LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -57.975723 0.0000000) to (47.333781 57.975723 9.5955616) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8356716 5.5589403 6.3970410 Created 1755 atoms create_atoms CPU = 0.001 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8356716 5.5589403 6.3970410 Created 1755 atoms create_atoms CPU = 0.001 seconds 1755 atoms in group lower Displacing atoms ... 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 36 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 46 atoms, new total = 3464 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.705 | 5.705 | 5.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19751.23 0 -19751.23 5793.9139 105 0 -19904.095 0 -19904.095 -10232.467 Loop time of 4.84105 on 1 procs for 105 steps with 3464 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19751.2303289672 -19904.0779746957 -19904.0948947588 Force two-norm initial, final = 133.89608 0.55635860 Force max component initial, final = 16.891602 0.093877136 Final line search alpha, max atom move = 1.0000000 0.093877136 Iterations, force evaluations = 105 189 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8176 | 4.8176 | 4.8176 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010097 | 0.010097 | 0.010097 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01338 | | | 0.28 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8400.00 ave 8400 max 8400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266900.0 ave 266900 max 266900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266900 Ave neighs/atom = 77.049654 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 105 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.705 | 5.705 | 5.705 Mbytes Step Temp E_pair E_mol TotEng Press Volume 105 0 -19904.095 0 -19904.095 -10232.467 52664.476 109 0 -19904.929 0 -19904.929 -1362.5052 52401.256 Loop time of 0.185855 on 1 procs for 4 steps with 3464 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19904.0948947586 -19904.9255950693 -19904.9287328745 Force two-norm initial, final = 466.64086 0.77396504 Force max component initial, final = 340.99366 0.12174967 Final line search alpha, max atom move = 7.3192359e-05 8.9111452e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18383 | 0.18383 | 0.18383 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003478 | 0.0003478 | 0.0003478 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001674 | | | 0.90 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8082.00 ave 8082 max 8082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267624.0 ave 267624 max 267624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267624 Ave neighs/atom = 77.258661 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.841 | 5.841 | 5.841 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19904.929 0 -19904.929 -1362.5052 Loop time of 2.30002e-06 on 1 procs for 0 steps with 3464 atoms 130.4% 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 | | 2.3e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267672.0 ave 267672 max 267672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267672 Ave neighs/atom = 77.272517 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) = 5.841 | 5.841 | 5.841 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 -19904.929 -19904.929 47.193257 115.95145 9.5760317 -1362.5052 -1362.5052 -1.9585417 -4083.5713 -1.9856612 2.4743021 2183.9243 Loop time of 2.20002e-06 on 1 procs for 0 steps with 3464 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8162.00 ave 8162 max 8162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133836.0 ave 133836 max 133836 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267672.0 ave 267672 max 267672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267672 Ave neighs/atom = 77.272517 Neighbor list builds = 0 Dangerous builds = 0 3464 -19904.9287328745 eV 2.47430213377944 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05