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 = 4.2107185 4.2107185 4.2107185 Created orthogonal box = (0.0000000 -49.821894 0.0000000) to (61.019109 49.821894 10.314112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9736124 6.4056720 6.8760746 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -49.821894 0.0000000) to (61.019109 49.821894 10.314112) create_atoms CPU = 0.008 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9736124 6.4056720 6.8760746 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -49.821894 0.0000000) to (61.019109 49.821894 10.314112) create_atoms CPU = 0.010 seconds 1690 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 = 9 ghost atom cutoff = 9 binsize = 4.5, 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_137572817842_000#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.969 | 6.969 | 6.969 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17408.668 0 -17408.668 -186409.68 14 0 -67706.14 0 -67706.14 -101060.22 Loop time of 7.86006 on 1 procs for 14 steps with 3356 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -17408.6681706441 -67706.1404975116 -67706.1404975116 Force two-norm initial, final = 7530.0950 16396.523 Force max component initial, final = 1718.8974 10471.728 Final line search alpha, max atom move = 1.6290468e-17 1.7058936e-13 Iterations, force evaluations = 14 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7991 | 7.7991 | 7.7991 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032669 | 0.032669 | 0.032669 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02833 | | | 0.36 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10723.0 ave 10723 max 10723 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: 586552.0 ave 586552 max 586552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586552 Ave neighs/atom = 174.77712 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 14 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.969 | 6.969 | 6.969 Mbytes Step Temp E_pair E_mol TotEng Press Volume 14 0 -67706.14 0 -67706.14 -101060.22 62711.606 1014 0 -316710.04 0 -316710.04 -66548678 17431.31 Loop time of 119.929 on 1 procs for 1000 steps with 3356 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -67706.1404975116 -314097.229929637 -316710.036464569 Force two-norm initial, final = 17982.442 2392544.5 Force max component initial, final = 10471.728 2161903.4 Final line search alpha, max atom move = 4.6206891e-10 0.00099894836 Iterations, force evaluations = 1000 1000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 106.67 | 106.67 | 106.67 | 0.0 | 88.94 Neigh | 11.31 | 11.31 | 11.31 | 0.0 | 9.43 Comm | 0.42708 | 0.42708 | 0.42708 | 0.0 | 0.36 Output | 0.00012165 | 0.00012165 | 0.00012165 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 1.525 | | | 1.27 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19721.0 ave 19721 max 19721 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: 1.93387e+06 ave 1.93387e+06 max 1.93387e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1933868 Ave neighs/atom = 576.24195 Neighbor list builds = 86 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 21 6 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 16.36 | 16.36 | 16.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -316710.04 0 -316710.04 -66548678 Loop time of 6.194e-06 on 1 procs for 0 steps with 3356 atoms 193.7% 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 | | 6.194e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19926.0 ave 19926 max 19926 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: 1.97603e+06 ave 1.97603e+06 max 1.97603e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1976026 Ave neighs/atom = 588.80393 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 21 6 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 16.36 | 16.36 | 16.36 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 -316710.04 -316710.04 90.949298 25.891658 7.4023705 -66548678 -66548678 -1.3910196e+08 -51632867 -8911206.6 0.0053440668 3600.2236 Loop time of 7.127e-06 on 1 procs for 0 steps with 3356 atoms 280.6% 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 | | 7.127e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19926.0 ave 19926 max 19926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 988013.0 ave 988013 max 988013 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.97603e+06 ave 1.97603e+06 max 1.97603e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1976026 Ave neighs/atom = 588.80393 Neighbor list builds = 0 Dangerous builds = 0 3356 -316387.695416489 eV 0.00534406678335679 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:10