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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -57.628625 0.0000000) to (40.747102 57.628625 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0816571 5.5904952 4.9780508 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.628625 0.0000000) to (40.747102 57.628625 4.9780508) create_atoms CPU = 0.008 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0816571 5.5904952 4.9780508 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.628625 0.0000000) to (40.747102 57.628625 4.9780508) create_atoms CPU = 0.007 seconds 1079 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2128 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.472 | 6.472 | 6.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9384.2924 0 -9384.2924 2981.6098 112 0 -9443.7854 0 -9443.7854 -8349.1245 Loop time of 10.7127 on 1 procs for 112 steps with 2128 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 = -9384.29240545614 -9443.77678011819 -9443.7854021799 Force two-norm initial, final = 32.486051 0.30541626 Force max component initial, final = 5.7797574 0.020069066 Final line search alpha, max atom move = 1.0000000 0.020069066 Iterations, force evaluations = 112 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.405 | 10.405 | 10.405 | 0.0 | 97.12 Neigh | 0.19786 | 0.19786 | 0.19786 | 0.0 | 1.85 Comm | 0.060911 | 0.060911 | 0.060911 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04934 | | | 0.46 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12585.0 ave 12585 max 12585 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: 478774.0 ave 478774 max 478774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478774 Ave neighs/atom = 224.98778 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.477 | 6.477 | 6.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -9443.7854 0 -9443.7854 -8349.1245 23378.913 115 0 -9443.8639 0 -9443.8639 -5054.6398 23335.147 Loop time of 0.300669 on 1 procs for 3 steps with 2128 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 = -9443.7854021799 -9443.86284977842 -9443.86386663169 Force two-norm initial, final = 89.317538 0.32540875 Force max component initial, final = 85.342484 0.045209714 Final line search alpha, max atom move = 0.00010038187 4.5382354e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29402 | 0.29402 | 0.29402 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015602 | 0.0015602 | 0.0015602 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005084 | | | 1.69 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 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: 477868.0 ave 477868 max 477868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 477868 Ave neighs/atom = 224.56203 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.615 | 6.615 | 6.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9443.8639 0 -9443.8639 -5054.6398 Loop time of 6.335e-06 on 1 procs for 0 steps with 2128 atoms 173.6% 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 | | 6.335e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 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: 478008.0 ave 478008 max 478008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478008 Ave neighs/atom = 224.62782 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.615 | 6.615 | 6.615 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 -9443.8639 -9443.8639 40.744834 115.25725 4.9690085 -5054.6398 -5054.6398 -3.1038977 -15158.828 -1.9877774 2.3376333 858.27523 Loop time of 7.097e-06 on 1 procs for 0 steps with 2128 atoms 267.7% 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 | | 7.097e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12560.0 ave 12560 max 12560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239004.0 ave 239004 max 239004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478008.0 ave 478008 max 478008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478008 Ave neighs/atom = 224.62782 Neighbor list builds = 0 Dangerous builds = 0 2128 -9385.85160370348 eV 2.33763329164475 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12