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 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) create_atoms CPU = 0.002 seconds 692 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2186617 6.0462295 5.0973115 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.274126 0.0000000) to (33.425307 47.274126 5.0973115) create_atoms CPU = 0.002 seconds 692 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 = 12 32 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 24 atoms, new total = 1360 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 = 12 32 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5736.3954 0 -5736.3954 -5072.685 605 0 -5797.5114 0 -5797.5114 -28209.067 Loop time of 54.0418 on 1 procs for 605 steps with 1360 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 = -5736.39538032932 -5797.50561482953 -5797.51136890388 Force two-norm initial, final = 10.791432 0.21852785 Force max component initial, final = 2.0558172 0.032436655 Final line search alpha, max atom move = 1.0000000 0.032436655 Iterations, force evaluations = 605 1086 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.662 | 53.662 | 53.662 | 0.0 | 99.30 Neigh | 0.20874 | 0.20874 | 0.20874 | 0.0 | 0.39 Comm | 0.086189 | 0.086189 | 0.086189 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08456 | | | 0.16 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5593.00 ave 5593 max 5593 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: 88688.0 ave 88688 max 88688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88688 Ave neighs/atom = 65.211765 Neighbor list builds = 26 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 = 12 32 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 : 605 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.667 | 4.667 | 4.667 Mbytes Step Temp E_pair E_mol TotEng Press Volume 605 0 -5797.5114 0 -5797.5114 -28209.067 16109.055 633 0 -5807.3908 0 -5807.3908 4800.6148 15768.615 Loop time of 1.45476 on 1 procs for 28 steps with 1360 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 = -5797.51136890386 -5807.39057899964 -5807.39082071855 Force two-norm initial, final = 734.41763 4.2565560 Force max component initial, final = 729.46750 3.1302781 Final line search alpha, max atom move = 0.0049325628 0.015440293 Iterations, force evaluations = 28 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4435 | 1.4435 | 1.4435 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015953 | 0.0015953 | 0.0015953 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009696 | | | 0.67 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5598.00 ave 5598 max 5598 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: 88626.0 ave 88626 max 88626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88626 Ave neighs/atom = 65.166176 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 = 12 32 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) = 4.806 | 4.806 | 4.806 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5807.3908 0 -5807.3908 4800.6148 Loop time of 2.56e-06 on 1 procs for 0 steps with 1360 atoms 156.2% 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 | | 2.56e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5700.00 ave 5700 max 5700 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: 89032.0 ave 89032 max 89032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89032 Ave neighs/atom = 65.464706 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 = 12 32 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) = 4.806 | 4.806 | 4.806 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 -5807.3908 -5807.3908 33.61729 94.548252 4.9610928 4800.6148 4800.6148 -274.61246 14986.011 -309.55363 2.3044523 2290.4308 Loop time of 3.093e-06 on 1 procs for 0 steps with 1360 atoms 258.6% 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 | | 3.093e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5700.00 ave 5700 max 5700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 44516.0 ave 44516 max 44516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 89032.0 ave 89032 max 89032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89032 Ave neighs/atom = 65.464706 Neighbor list builds = 0 Dangerous builds = 0 1360 -5807.39082071855 eV 2.30445231052709 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:55