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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -47.958563 0.0000000) to (29.368502 47.958563 8.8549365) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397276 5.4498367 5.9032910 Created 1043 atoms using lattice units in orthogonal box = (0.0000000 -47.958563 0.0000000) to (29.368502 47.958563 8.8549365) create_atoms CPU = 0.002 seconds 1043 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397276 5.4498367 5.9032910 Created 1067 atoms using lattice units in orthogonal box = (0.0000000 -47.958563 0.0000000) to (29.368502 47.958563 8.8549365) create_atoms CPU = 0.001 seconds 1067 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 28 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2110 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_028979335952_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.546 | 5.546 | 5.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7074.9306 0 -7074.9306 42538.018 128 0 -7448.8691 0 -7448.8691 1884.8975 Loop time of 21.8318 on 1 procs for 128 steps with 2110 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 = -7074.93062349933 -7448.86191548178 -7448.8690824668 Force two-norm initial, final = 301.07684 0.26396397 Force max component initial, final = 56.730801 0.043014165 Final line search alpha, max atom move = 1.0000000 0.043014165 Iterations, force evaluations = 128 194 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.665 | 21.665 | 21.665 | 0.0 | 99.23 Neigh | 0.12831 | 0.12831 | 0.12831 | 0.0 | 0.59 Comm | 0.016157 | 0.016157 | 0.016157 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0228 | | | 0.10 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7114.00 ave 7114 max 7114 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: 280162.0 ave 280162 max 280162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280162 Ave neighs/atom = 132.77820 Neighbor list builds = 7 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.546 | 5.546 | 5.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -7448.8691 0 -7448.8691 1884.8975 24943.845 133 0 -7449.0763 0 -7449.0763 148.01023 24973.614 Loop time of 0.743655 on 1 procs for 5 steps with 2110 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7448.86908246679 -7449.07558002167 -7449.07630042503 Force two-norm initial, final = 94.383917 4.3576344 Force max component initial, final = 93.279979 3.6614561 Final line search alpha, max atom move = 0.00022306581 0.00081674569 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74092 | 0.74092 | 0.74092 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040831 | 0.00040831 | 0.00040831 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002322 | | | 0.31 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 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: 280070.0 ave 280070 max 280070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280070 Ave neighs/atom = 132.73460 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.684 | 5.684 | 5.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7449.0763 0 -7449.0763 148.01023 Loop time of 2.291e-06 on 1 procs for 0 steps with 2110 atoms 130.9% 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 | | 2.291e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 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: 279990.0 ave 279990 max 279990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279990 Ave neighs/atom = 132.69668 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.684 | 5.684 | 5.684 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 -7449.0763 -7449.0763 29.306907 96.312311 8.847684 148.01023 148.01023 83.587508 235.86769 124.5755 2.3720023 542.33428 Loop time of 2.185e-06 on 1 procs for 0 steps with 2110 atoms 183.1% 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 | | 2.185e-06 | | |100.00 Nlocal: 2110.00 ave 2110 max 2110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7126.00 ave 7126 max 7126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139995.0 ave 139995 max 139995 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 279990.0 ave 279990 max 279990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279990 Ave neighs/atom = 132.69668 Neighbor list builds = 0 Dangerous builds = 0 2110 -7449.07630042503 eV 2.37200230943762 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23