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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5713293 6.7587367 5.5400000 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) create_atoms CPU = 0.007 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5713293 6.7587367 5.5400000 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) create_atoms CPU = 0.006 seconds 690 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_070797404269_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7675.9722 0 -7675.9722 41301.662 66 0 -7937.0889 0 -7937.0889 6411.1406 Loop time of 6.68788 on 1 procs for 66 steps with 1378 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 = -7675.97223009546 -7937.08157396701 -7937.08886472016 Force two-norm initial, final = 369.40570 0.33190175 Force max component initial, final = 84.742153 0.10422615 Final line search alpha, max atom move = 1.0000000 0.10422615 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6498 | 6.6498 | 6.6498 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018584 | 0.018584 | 0.018584 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01944 | | | 0.29 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5991.00 ave 5991 max 5991 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: 107416.0 ave 107416 max 107416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107416 Ave neighs/atom = 77.950653 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -7937.0889 0 -7937.0889 6411.1406 20679.63 70 0 -7937.3077 0 -7937.3077 78.78231 20751.49 Loop time of 0.318842 on 1 procs for 4 steps with 1378 atoms 94.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7937.08886472016 -7937.30655657337 -7937.30766753039 Force two-norm initial, final = 156.75323 3.2940681 Force max component initial, final = 134.52122 3.1218237 Final line search alpha, max atom move = 0.00011078304 0.00034584511 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31495 | 0.31495 | 0.31495 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080691 | 0.00080691 | 0.00080691 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003088 | | | 0.97 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 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: 106992.0 ave 106992 max 106992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106992 Ave neighs/atom = 77.642961 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7937.3077 0 -7937.3077 78.78231 Loop time of 6.435e-06 on 1 procs for 0 steps with 1378 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 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: 106972.0 ave 106972 max 106972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106972 Ave neighs/atom = 77.628447 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.213 | 5.213 | 5.213 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 -7937.3077 -7937.3077 25.693646 145.7476 5.5414337 78.78231 78.78231 51.391722 241.75021 -56.795002 2.5753873 441.96048 Loop time of 6.806e-06 on 1 procs for 0 steps with 1378 atoms 249.8% 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 | | 6.806e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53486.0 ave 53486 max 53486 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106972.0 ave 106972 max 106972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106972 Ave neighs/atom = 77.628447 Neighbor list builds = 0 Dangerous builds = 0 1378 -7937.30766753039 eV 2.57538732194552 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07