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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -84.424279 0.0000000) to (48.742380 84.424279 7.2931469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5474839 6.7203406 7.2931469 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -84.424279 0.0000000) to (48.742380 84.424279 7.2931469) create_atoms CPU = 0.010 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5474839 6.7203406 7.2931469 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -84.424279 0.0000000) to (48.742380 84.424279 7.2931469) create_atoms CPU = 0.010 seconds 1609 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 11 38 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3216 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_878712978062_003#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 = 11 38 2 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) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11669.134 0 -11669.134 23077.775 41 0 -11975.799 0 -11975.799 1453.9609 Loop time of 5.94841 on 1 procs for 41 steps with 3216 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 = -11669.1336132903 -11975.7887657802 -11975.7992276436 Force two-norm initial, final = 682.30947 0.19507077 Force max component initial, final = 277.73964 0.070127152 Final line search alpha, max atom move = 1.0000000 0.070127152 Iterations, force evaluations = 41 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.744 | 5.744 | 5.744 | 0.0 | 96.56 Neigh | 0.15299 | 0.15299 | 0.15299 | 0.0 | 2.57 Comm | 0.024485 | 0.024485 | 0.024485 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02691 | | | 0.45 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14078.0 ave 14078 max 14078 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: 558834.0 ave 558834 max 558834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558834 Ave neighs/atom = 173.76679 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 38 2 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.94 | 10.94 | 10.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -11975.799 0 -11975.799 1453.9609 60023.186 45 0 -11975.929 0 -11975.929 55.329451 60233.685 Loop time of 0.584648 on 1 procs for 4 steps with 3216 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11975.7992276436 -11975.9282208818 -11975.9294892835 Force two-norm initial, final = 97.059597 3.6821163 Force max component initial, final = 72.912276 2.6796986 Final line search alpha, max atom move = 0.00030306412 0.00081212049 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5759 | 0.5759 | 0.5759 | 0.0 | 98.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020459 | 0.0020459 | 0.0020459 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006699 | | | 1.15 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13855.0 ave 13855 max 13855 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: 558644.0 ave 558644 max 558644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558644 Ave neighs/atom = 173.70771 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 = 11 38 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) = 10.45 | 10.45 | 10.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11975.929 0 -11975.929 55.329451 Loop time of 6.355e-06 on 1 procs for 0 steps with 3216 atoms 204.6% 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 | | 6.355e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13490.0 ave 13490 max 13490 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: 558018.0 ave 558018 max 558018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558018 Ave neighs/atom = 173.51306 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 = 11 38 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) = 10.45 | 10.45 | 10.45 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 -11975.929 -11975.929 48.735179 169.41562 7.2953044 55.329451 55.329451 50.322859 71.517607 44.147886 2.7015205 1990.6999 Loop time of 7.107e-06 on 1 procs for 0 steps with 3216 atoms 365.8% 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 | | 7.107e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13490.0 ave 13490 max 13490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279009.0 ave 279009 max 279009 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 558018.0 ave 558018 max 558018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 558018 Ave neighs/atom = 173.51306 Neighbor list builds = 0 Dangerous builds = 0 3216 -11975.9294892835 eV 2.70152045955178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08