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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -50.574035 0.0000000) to (13.763508 50.574035 9.0103308) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8986461 5.6189285 6.0068872 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -50.574035 0.0000000) to (13.763508 50.574035 9.0103308) create_atoms CPU = 0.003 seconds 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8986461 5.6189285 6.0068872 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -50.574035 0.0000000) to (13.763508 50.574035 9.0103308) create_atoms CPU = 0.002 seconds 507 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 33 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 999 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4171.3766 0 -4171.3766 5895.875 72 0 -4205.2103 0 -4205.2103 -10680.232 Loop time of 0.931961 on 1 procs for 72 steps with 999 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 = -4171.3765833665 -4205.20679925573 -4205.21029693727 Force two-norm initial, final = 39.608786 0.19930719 Force max component initial, final = 9.1050384 0.049165051 Final line search alpha, max atom move = 1.0000000 0.049165051 Iterations, force evaluations = 72 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88912 | 0.88912 | 0.88912 | 0.0 | 95.40 Neigh | 0.013824 | 0.013824 | 0.013824 | 0.0 | 1.48 Comm | 0.01313 | 0.01313 | 0.01313 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01589 | | | 1.70 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4017.00 ave 4017 max 4017 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: 77830.0 ave 77830 max 77830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77830 Ave neighs/atom = 77.907908 Neighbor list builds = 1 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -4205.2103 0 -4205.2103 -10680.232 12543.752 76 0 -4205.3631 0 -4205.3631 -4835.9215 12474.563 Loop time of 0.04297 on 1 procs for 4 steps with 999 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4205.21029693727 -4205.35921172059 -4205.36311144173 Force two-norm initial, final = 75.444893 2.8006443 Force max component initial, final = 63.191566 2.7481726 Final line search alpha, max atom move = 8.9688743e-05 0.00024648015 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040348 | 0.040348 | 0.040348 | 0.0 | 93.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050327 | 0.00050327 | 0.00050327 | 0.0 | 1.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002119 | | | 4.93 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3943.00 ave 3943 max 3943 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: 77790.0 ave 77790 max 77790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77790 Ave neighs/atom = 77.867868 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.708 | 4.708 | 4.708 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4205.3631 0 -4205.3631 -4835.9215 Loop time of 6.284e-06 on 1 procs for 0 steps with 999 atoms 159.1% 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 | | 6.284e-06 | | |100.00 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3943.00 ave 3943 max 3943 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: 77828.0 ave 77828 max 77828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77828 Ave neighs/atom = 77.905906 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 5 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.708 | 4.708 | 4.708 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 -4205.3631 -4205.3631 13.738129 101.14807 8.9771845 -4835.9215 -4835.9215 352.31204 -14799.906 -60.170999 2.3275741 484.65896 Loop time of 6.905e-06 on 1 procs for 0 steps with 999 atoms 231.7% 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 | | 6.905e-06 | | |100.00 Nlocal: 999.000 ave 999 max 999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3943.00 ave 3943 max 3943 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38914.0 ave 38914 max 38914 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77828.0 ave 77828 max 77828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77828 Ave neighs/atom = 77.905906 Neighbor list builds = 0 Dangerous builds = 0 999 -4205.36301154173 eV 2.32757414318101 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01