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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -50.976719 0.0000000) to (25.486557 50.976719 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0778492 4.0778492 3.6043435 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -50.976719 0.0000000) to (25.486557 50.976719 3.6043435) create_atoms CPU = 0.001 seconds 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0778492 4.0778492 3.6043435 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -50.976719 0.0000000) to (25.486557 50.976719 3.6043435) create_atoms CPU = 0.000 seconds 402 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 ghost atom cutoff = 6 binsize = 3, 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 796 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_492310898779_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3348.9035 0 -3348.9035 7075.6825 23 0 -3370.6499 0 -3370.6499 -4420.1419 Loop time of 0.952298 on 1 procs for 23 steps with 796 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 = -3348.9034982398 -3370.64731801926 -3370.64988209392 Force two-norm initial, final = 26.182962 0.13894203 Force max component initial, final = 7.3701799 0.029940544 Final line search alpha, max atom move = 1.0000000 0.029940544 Iterations, force evaluations = 23 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94784 | 0.94784 | 0.94784 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021171 | 0.0021171 | 0.0021171 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002342 | | | 0.25 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5078.00 ave 5078 max 5078 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: 61760.0 ave 61760 max 61760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61760 Ave neighs/atom = 77.587940 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 ghost atom cutoff = 6 binsize = 3, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -3370.6499 0 -3370.6499 -4420.1419 9365.6781 36 0 -3370.9026 0 -3370.9026 -2038.8045 9351.0666 Loop time of 0.38541 on 1 procs for 13 steps with 796 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 = -3370.64988209393 -3370.90081787544 -3370.90256141319 Force two-norm initial, final = 33.479543 1.3115248 Force max component initial, final = 32.826169 0.88289564 Final line search alpha, max atom move = 0.00059086196 0.00052166945 Iterations, force evaluations = 13 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38211 | 0.38211 | 0.38211 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055429 | 0.00055429 | 0.00055429 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002743 | | | 0.71 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 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: 61608.0 ave 61608 max 61608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61608 Ave neighs/atom = 77.396985 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 ghost atom cutoff = 6 binsize = 3, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3370.9026 0 -3370.9026 -2038.8045 Loop time of 2.341e-06 on 1 procs for 0 steps with 796 atoms 170.9% 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 | | 2.341e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 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: 61720.0 ave 61720 max 61720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61720 Ave neighs/atom = 77.537688 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 ghost atom cutoff = 6 binsize = 3, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.683 | 4.683 | 4.683 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 -3370.9026 -3370.9026 25.156188 101.95344 3.6459814 -2038.8045 -2038.8045 128.08625 -6397.5193 153.01952 2.2891172 208.5192 Loop time of 2.26e-06 on 1 procs for 0 steps with 796 atoms 132.7% 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 | | 2.26e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30860.0 ave 30860 max 30860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61720.0 ave 61720 max 61720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61720 Ave neighs/atom = 77.537688 Neighbor list builds = 0 Dangerous builds = 0 796 -3370.90256141319 eV 2.28911717917328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01