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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2299022 4.3171259 4.6763329 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) create_atoms CPU = 0.003 seconds 529 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2299022 4.3171259 4.6763329 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) create_atoms CPU = 0.002 seconds 529 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1050 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4331.9713 0 -4331.9713 36512.363 86 0 -4481.3698 0 -4481.3698 -703.73421 Loop time of 8.52145 on 1 procs for 86 steps with 1050 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 = -4331.97131383565 -4481.36806021765 -4481.36980897246 Force two-norm initial, final = 184.03193 0.31826050 Force max component initial, final = 31.582185 0.090198868 Final line search alpha, max atom move = 1.0000000 0.090198868 Iterations, force evaluations = 86 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.4528 | 8.4528 | 8.4528 | 0.0 | 99.19 Neigh | 0.035356 | 0.035356 | 0.035356 | 0.0 | 0.41 Comm | 0.013758 | 0.013758 | 0.013758 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01958 | | | 0.23 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3659.00 ave 3659 max 3659 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: 61068.0 ave 61068 max 61068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61068 Ave neighs/atom = 58.160000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -4481.3698 0 -4481.3698 -703.73421 12400.232 88 0 -4481.396 0 -4481.396 2459.6835 12377.424 Loop time of 0.280952 on 1 procs for 2 steps with 1050 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 = -4481.36980897246 -4481.39590729838 -4481.39599526442 Force two-norm initial, final = 40.001984 0.31855761 Force max component initial, final = 29.483349 0.092138837 Final line search alpha, max atom move = 0.00087971036 8.1055489e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27887 | 0.27887 | 0.27887 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039347 | 0.00039347 | 0.00039347 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001688 | | | 0.60 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3679.00 ave 3679 max 3679 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: 60998.0 ave 60998 max 60998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60998 Ave neighs/atom = 58.093333 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4481.396 0 -4481.396 2459.6835 Loop time of 6.314e-06 on 1 procs for 0 steps with 1050 atoms 190.1% 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 | | 6.314e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3679.00 ave 3679 max 3679 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: 61002.0 ave 61002 max 61002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61002 Ave neighs/atom = 58.097143 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.686 | 4.686 | 4.686 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 -4481.396 -4481.396 23.240387 75.987143 7.0088509 2459.6835 2459.6835 4.9530809 7380.3237 -6.2264439 2.2689973 823.86078 Loop time of 6.736e-06 on 1 procs for 0 steps with 1050 atoms 296.9% 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 | | 6.736e-06 | | |100.00 Nlocal: 1050.00 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3679.00 ave 3679 max 3679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30501.0 ave 30501 max 30501 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61002.0 ave 61002 max 61002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61002 Ave neighs/atom = 58.097143 Neighbor list builds = 0 Dangerous builds = 0 1050 -4481.39599526442 eV 2.2689973441093 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09