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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -42.772370 0.0000000) to (52.385241 42.772370 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9868847 5.4993048 5.9031479 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.772370 0.0000000) to (52.385241 42.772370 8.8547219) create_atoms CPU = 0.011 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9868847 5.4993048 5.9031479 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.772370 0.0000000) to (52.385241 42.772370 8.8547219) create_atoms CPU = 0.007 seconds 1687 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 3349 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.551 | 6.551 | 6.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11155.715 0 -11155.715 56788.252 117 0 -11810.16 0 -11810.16 1337.961 Loop time of 10.2559 on 1 procs for 117 steps with 3349 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 = -11155.7154067921 -11810.1484678789 -11810.1599402406 Force two-norm initial, final = 548.80457 0.37418243 Force max component initial, final = 50.766552 0.11032819 Final line search alpha, max atom move = 0.38950586 0.042973475 Iterations, force evaluations = 117 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.5839 | 9.5839 | 9.5839 | 0.0 | 93.45 Neigh | 0.5419 | 0.5419 | 0.5419 | 0.0 | 5.28 Comm | 0.056237 | 0.056237 | 0.056237 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07387 | | | 0.72 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10645.0 ave 10645 max 10645 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: 478792.0 ave 478792 max 478792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478792 Ave neighs/atom = 142.96566 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.554 | 6.554 | 6.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -11810.16 0 -11810.16 1337.961 39680.505 121 0 -11810.333 0 -11810.333 -2.0933225 39718.475 Loop time of 0.326244 on 1 procs for 4 steps with 3349 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 = -11810.1599402406 -11810.3331678073 -11810.3334019596 Force two-norm initial, final = 110.59412 0.64038731 Force max component initial, final = 109.36104 0.32107171 Final line search alpha, max atom move = 0.00019253073 6.1816170e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31775 | 0.31775 | 0.31775 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016255 | 0.0016255 | 0.0016255 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006864 | | | 2.10 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10636.0 ave 10636 max 10636 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: 478730.0 ave 478730 max 478730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478730 Ave neighs/atom = 142.94715 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.692 | 6.692 | 6.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11810.333 0 -11810.333 -2.0933225 Loop time of 6.164e-06 on 1 procs for 0 steps with 3349 atoms 227.1% 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 | | 6.164e-06 | | |100.00 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 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: 478140.0 ave 478140 max 478140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478140 Ave neighs/atom = 142.77098 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.692 | 6.692 | 6.692 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 -11810.333 -11810.333 52.35307 85.802592 8.8419898 -2.0933225 -2.0933225 11.656362 -5.0034594 -12.93287 2.3107186 1840.034 Loop time of 6.846e-06 on 1 procs for 0 steps with 3349 atoms 277.5% 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 | | 6.846e-06 | | |100.00 Nlocal: 3349.00 ave 3349 max 3349 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239070.0 ave 239070 max 239070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478140.0 ave 478140 max 478140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478140 Ave neighs/atom = 142.77098 Neighbor list builds = 0 Dangerous builds = 0 3349 -11810.3501469596 eV 2.31071861635098 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11