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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -77.484841 0.0000000) to (44.733556 77.484841 7.0147812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6000328 5.9274922 7.0147812 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.484841 0.0000000) to (44.733556 77.484841 7.0147812) create_atoms CPU = 0.009 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6000328 5.9274922 7.0147812 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.484841 0.0000000) to (44.733556 77.484841 7.0147812) create_atoms CPU = 0.009 seconds 1465 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 = 15 52 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2904 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_022920256108_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 = 15 52 3 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) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9686.006 0 -9686.006 1420.2849 46 0 -9712.4414 0 -9712.4414 -2009.0718 Loop time of 7.82773 on 1 procs for 46 steps with 2904 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 = -9686.00603531835 -9712.43320966247 -9712.44141939134 Force two-norm initial, final = 24.280484 0.95428539 Force max component initial, final = 4.8247443 0.43024725 Final line search alpha, max atom move = 0.10876645 0.046796468 Iterations, force evaluations = 46 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7312 | 7.7312 | 7.7312 | 0.0 | 98.77 Neigh | 0.055502 | 0.055502 | 0.055502 | 0.0 | 0.71 Comm | 0.016127 | 0.016127 | 0.016127 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02487 | | | 0.32 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7690.00 ave 7690 max 7690 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: 156040.0 ave 156040 max 156040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156040 Ave neighs/atom = 53.732782 Neighbor list builds = 2 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 = 15 52 3 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -9712.4414 0 -9712.4414 -2009.0718 48628.883 49 0 -9712.5181 0 -9712.5181 -446.50609 48512.149 Loop time of 0.554216 on 1 procs for 3 steps with 2904 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 = -9712.44141939135 -9712.51624744513 -9712.51808778954 Force two-norm initial, final = 79.259703 1.0029784 Force max component initial, final = 68.844752 0.44244295 Final line search alpha, max atom move = 0.00011969932 5.2960122e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54855 | 0.54855 | 0.54855 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010681 | 0.0010681 | 0.0010681 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004594 | | | 0.83 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7692.00 ave 7692 max 7692 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: 156050.0 ave 156050 max 156050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156050 Ave neighs/atom = 53.736226 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 = 15 52 3 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) = 5.403 | 5.403 | 5.403 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9712.5181 0 -9712.5181 -446.50609 Loop time of 6.966e-06 on 1 procs for 0 steps with 2904 atoms 186.6% 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 | | 6.966e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7692.00 ave 7692 max 7692 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: 156062.0 ave 156062 max 156062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156062 Ave neighs/atom = 53.740358 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 = 15 52 3 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) = 5.403 | 5.403 | 5.403 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 -9712.5181 -9712.5181 44.64465 154.96968 7.0118778 -446.50609 -446.50609 1.903757 -1338.1695 -3.2524977 2.5382108 1495.3654 Loop time of 9.753e-06 on 1 procs for 0 steps with 2904 atoms 235.8% 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 | | 9.753e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7692.00 ave 7692 max 7692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78031.0 ave 78031 max 78031 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156062.0 ave 156062 max 156062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156062 Ave neighs/atom = 53.740358 Neighbor list builds = 0 Dangerous builds = 0 2904 -9712.51808778954 eV 2.53821080345275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09