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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -63.263182 0.0000000) to (31.631591 63.263182 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7040574 5.7040574 4.0500102 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -63.263182 0.0000000) to (31.631591 63.263182 4.0500102) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7040574 5.7040574 4.0500102 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -63.263182 0.0000000) to (31.631591 63.263182 4.0500102) create_atoms CPU = 0.002 seconds 490 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 34 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3180.8104 0 -3180.8104 26435.376 91 0 -3310.0007 0 -3310.0007 3323.5307 Loop time of 2.18708 on 1 procs for 91 steps with 978 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 = -3180.81037526321 -3309.99797986698 -3310.00067778233 Force two-norm initial, final = 166.25597 0.12593581 Force max component initial, final = 33.117394 0.028512675 Final line search alpha, max atom move = 1.0000000 0.028512675 Iterations, force evaluations = 91 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0912 | 2.0912 | 2.0912 | 0.0 | 95.62 Neigh | 0.047364 | 0.047364 | 0.047364 | 0.0 | 2.17 Comm | 0.026741 | 0.026741 | 0.026741 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02176 | | | 0.99 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7122.00 ave 7122 max 7122 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: 115784.0 ave 115784 max 115784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115784 Ave neighs/atom = 118.38855 Neighbor list builds = 3 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 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 91 0 -3310.0007 0 -3310.0007 3323.5307 16209.073 96 0 -3310.1361 0 -3310.1361 -121.81882 16280.647 Loop time of 0.0931067 on 1 procs for 5 steps with 978 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3310.00067778233 -3310.13548505342 -3310.13614868763 Force two-norm initial, final = 67.028104 2.5276977 Force max component initial, final = 56.011014 1.9985809 Final line search alpha, max atom move = 0.00042797049 0.00085533363 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088648 | 0.088648 | 0.088648 | 0.0 | 95.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010265 | 0.0010265 | 0.0010265 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003433 | | | 3.69 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7092.00 ave 7092 max 7092 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: 119196.0 ave 119196 max 119196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119196 Ave neighs/atom = 121.87730 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.137 | 5.137 | 5.137 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3310.1361 0 -3310.1361 -121.81882 Loop time of 6.244e-06 on 1 procs for 0 steps with 978 atoms 208.2% 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 | | 6.244e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7102.00 ave 7102 max 7102 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: 113536.0 ave 113536 max 113536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113536 Ave neighs/atom = 116.08998 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 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 -3310.1361 -3310.1361 31.585162 127.02021 4.0580341 -121.81882 -121.81882 -196.39142 -151.25856 -17.806495 2.5887221 196.74176 Loop time of 8.36e-06 on 1 procs for 0 steps with 978 atoms 215.3% 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 | | 8.36e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7102.00 ave 7102 max 7102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56768.0 ave 56768 max 56768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113536.0 ave 113536 max 113536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113536 Ave neighs/atom = 116.08998 Neighbor list builds = 0 Dangerous builds = 0 978 -3310.13614868763 eV 2.58872212458266 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02