LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -39.792222 0.0000000) to (13.262848 39.792222 3.6784521) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1010953 5.1010953 3.6784521 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.792222 0.0000000) to (13.262848 39.792222 3.6784521) create_atoms CPU = 0.002 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1010953 5.1010953 3.6784521 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -39.792222 0.0000000) to (13.262848 39.792222 3.6784521) create_atoms CPU = 0.001 seconds 158 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 26 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 312 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_024705128470_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1291.4208 0 -1291.4208 23277.945 35 0 -1312.164 0 -1312.164 70.775816 Loop time of 0.17374 on 1 procs for 35 steps with 312 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 = -1291.42080855175 -1312.16275231723 -1312.16404038448 Force two-norm initial, final = 32.923009 0.12686408 Force max component initial, final = 10.760490 0.028584750 Final line search alpha, max atom move = 1.0000000 0.028584750 Iterations, force evaluations = 35 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16478 | 0.16478 | 0.16478 | 0.0 | 94.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046846 | 0.0046846 | 0.0046846 | 0.0 | 2.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004277 | | | 2.46 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2820.00 ave 2820 max 2820 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: 24364.0 ave 24364 max 24364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24364 Ave neighs/atom = 78.089744 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1312.164 0 -1312.164 70.775816 3882.6665 48 0 -1312.3359 0 -1312.3359 -3561.0986 3893.7018 Loop time of 0.0460212 on 1 procs for 13 steps with 312 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 = -1312.16404038448 -1312.33502240295 -1312.33594561971 Force two-norm initial, final = 20.369774 0.45308442 Force max component initial, final = 16.165960 0.095552841 Final line search alpha, max atom move = 0.00085154324 8.1367376e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040961 | 0.040961 | 0.040961 | 0.0 | 89.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001244 | 0.001244 | 0.001244 | 0.0 | 2.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003816 | | | 8.29 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2820.00 ave 2820 max 2820 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: 24220.0 ave 24220 max 24220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24220 Ave neighs/atom = 77.628205 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1312.3359 0 -1312.3359 -3561.0986 Loop time of 6.034e-06 on 1 procs for 0 steps with 312 atoms 198.9% 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 | | 6.034e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2830.00 ave 2830 max 2830 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: 24212.0 ave 24212 max 24212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24212 Ave neighs/atom = 77.602564 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.566 | 4.566 | 4.566 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 -1312.3359 -1312.3359 13.13103 79.584444 3.7259388 -3561.0986 -3561.0986 29.812347 -10673.736 -39.372096 2.3124601 153.20898 Loop time of 6.826e-06 on 1 procs for 0 steps with 312 atoms 263.7% 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 | | 6.826e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2830.00 ave 2830 max 2830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12106.0 ave 12106 max 12106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24212.0 ave 24212 max 24212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24212 Ave neighs/atom = 77.602564 Neighbor list builds = 0 Dangerous builds = 0 312 -1312.33591441971 eV 2.31246012023194 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00