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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -60.995816 0.0000000) to (24.900000 60.995816 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9760000 5.2859988 5.7504086 Created 1203 atoms create_atoms CPU = 0.001 seconds 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9760000 5.2859988 5.7504086 Created 1203 atoms create_atoms CPU = 0.001 seconds 1203 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 = 8 38 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 22 atoms, new total = 2384 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 = 8 38 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) = 5.628 | 5.628 | 5.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10542.67 0 -10542.67 3704.9603 25 0 -10575.278 0 -10575.278 -6888.1064 Loop time of 2.16444 on 1 procs for 25 steps with 2384 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 = -10542.6699505405 -10575.2689098245 -10575.2776943491 Force two-norm initial, final = 41.630228 0.30290248 Force max component initial, final = 7.1909349 0.034792082 Final line search alpha, max atom move = 1.0000000 0.034792082 Iterations, force evaluations = 25 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1521 | 2.1521 | 2.1521 | 0.0 | 99.43 Neigh | 0.0081854 | 0.0081854 | 0.0081854 | 0.0 | 0.38 Comm | 0.0020545 | 0.0020545 | 0.0020545 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002128 | | | 0.10 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7995.00 ave 7995 max 7995 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: 207838.0 ave 207838 max 207838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207838 Ave neighs/atom = 87.180369 Neighbor list builds = 1 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.628 | 5.628 | 5.628 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -10575.278 0 -10575.278 -6888.1064 26201.09 28 0 -10575.419 0 -10575.419 -2018.0931 26132.025 Loop time of 0.313345 on 1 procs for 3 steps with 2384 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 = -10575.2776943491 -10575.4172443544 -10575.418913034 Force two-norm initial, final = 137.58679 0.30719342 Force max component initial, final = 118.98252 0.036189977 Final line search alpha, max atom move = 9.3955391e-05 3.4002435e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31191 | 0.31191 | 0.31191 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003203 | 0.0003203 | 0.0003203 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001113 | | | 0.36 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7984.00 ave 7984 max 7984 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: 208638.0 ave 208638 max 208638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208638 Ave neighs/atom = 87.515940 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 = 8 38 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) = 5.765 | 5.765 | 5.765 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10575.419 0 -10575.419 -2018.0931 Loop time of 2.2e-06 on 1 procs for 0 steps with 2384 atoms 136.4% 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 | | 2.2e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7989.00 ave 7989 max 7989 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: 208724.0 ave 208724 max 208724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208724 Ave neighs/atom = 87.552013 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) = 5.765 | 5.765 | 5.765 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 -10575.419 -10575.419 24.883992 121.99163 8.6084104 -2018.0931 -2018.0931 -1.4515327 -6052.483 -0.34476344 2.3098837 653.61091 Loop time of 2.3e-06 on 1 procs for 0 steps with 2384 atoms 217.4% 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: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7989.00 ave 7989 max 7989 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104362.0 ave 104362 max 104362 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208724.0 ave 208724 max 208724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208724 Ave neighs/atom = 87.552013 Neighbor list builds = 0 Dangerous builds = 0 2384 -10575.418913034 eV 2.3098836990341 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02