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 = 4.0320820 4.0320820 4.0320820 Created orthogonal box = (0.0000000 -80.842993 0.0000000) to (46.674724 80.842993 6.9837709) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2697390 6.4352632 6.9837709 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -80.842993 0.0000000) to (46.674724 80.842993 6.9837709) create_atoms CPU = 0.011 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2697390 6.4352632 6.9837709 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -80.842993 0.0000000) to (46.674724 80.842993 6.9837709) create_atoms CPU = 0.011 seconds 1609 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 13 43 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 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 3211 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_123629422045_005#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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.623 | 6.623 | 6.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10631.179 0 -10631.179 4104.7521 91 0 -10768.126 0 -10768.126 1220.6948 Loop time of 5.62728 on 1 procs for 91 steps with 3211 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 = -10631.1786916673 -10768.1158329581 -10768.1260737589 Force two-norm initial, final = 54.709007 0.27516768 Force max component initial, final = 7.7913326 0.044474007 Final line search alpha, max atom move = 1.0000000 0.044474007 Iterations, force evaluations = 91 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2801 | 5.2801 | 5.2801 | 0.0 | 93.83 Neigh | 0.25685 | 0.25685 | 0.25685 | 0.0 | 4.56 Comm | 0.039311 | 0.039311 | 0.039311 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05103 | | | 0.91 Nlocal: 3211.00 ave 3211 max 3211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10738.0 ave 10738 max 10738 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: 408938.0 ave 408938 max 408938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 408938 Ave neighs/atom = 127.35534 Neighbor list builds = 5 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 13 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.624 | 6.624 | 6.624 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -10768.126 0 -10768.126 1220.6948 52704.067 95 0 -10768.283 0 -10768.283 -7.3203187 52783.077 Loop time of 0.221085 on 1 procs for 4 steps with 3211 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 = -10768.1260737589 -10768.2816099525 -10768.2830990357 Force two-norm initial, final = 103.50691 1.1160059 Force max component initial, final = 102.25987 1.0453712 Final line search alpha, max atom move = 6.8341748e-05 7.1442498e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21397 | 0.21397 | 0.21397 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013129 | 0.0013129 | 0.0013129 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005797 | | | 2.62 Nlocal: 3211.00 ave 3211 max 3211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10740.0 ave 10740 max 10740 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: 407740.0 ave 407740 max 407740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407740 Ave neighs/atom = 126.98225 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.762 | 6.762 | 6.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10768.283 0 -10768.283 -7.3203187 Loop time of 7.127e-06 on 1 procs for 0 steps with 3211 atoms 196.4% 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: 3211.00 ave 3211 max 3211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10743.0 ave 10743 max 10743 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: 404828.0 ave 404828 max 404828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404828 Ave neighs/atom = 126.07537 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 13 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.558054418218096 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) = 6.762 | 6.762 | 6.762 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 -10768.283 -10768.283 46.646127 162.20395 6.9761802 -7.3203187 -7.3203187 -31.711737 4.1878611 5.5629195 2.5916493 1488.0377 Loop time of 6.235e-06 on 1 procs for 0 steps with 3211 atoms 336.8% 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 | | 6.235e-06 | | |100.00 Nlocal: 3211.00 ave 3211 max 3211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10743.0 ave 10743 max 10743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 202414.0 ave 202414 max 202414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 404828.0 ave 404828 max 404828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404828 Ave neighs/atom = 126.07537 Neighbor list builds = 0 Dangerous builds = 0 3211 -10768.2830990357 eV 2.59164934962494 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06