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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -63.753676 0.0000000) to (22.539084 63.753676 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0470713 5.4420865 4.9780508 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.753676 0.0000000) to (22.539084 63.753676 4.9780508) create_atoms CPU = 0.006 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0470713 5.4420865 4.9780508 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.753676 0.0000000) to (22.539084 63.753676 4.9780508) create_atoms CPU = 0.005 seconds 658 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5766.6059 0 -5766.6059 1532.4244 33 0 -5790.4752 0 -5790.4752 -6632.9728 Loop time of 1.91531 on 1 procs for 33 steps with 1304 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 = -5766.60590759439 -5790.4694354912 -5790.47517136956 Force two-norm initial, final = 20.748535 0.25666667 Force max component initial, final = 4.7004160 0.025986604 Final line search alpha, max atom move = 1.0000000 0.025986604 Iterations, force evaluations = 33 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8524 | 1.8524 | 1.8524 | 0.0 | 96.72 Neigh | 0.038559 | 0.038559 | 0.038559 | 0.0 | 2.01 Comm | 0.014298 | 0.014298 | 0.014298 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01002 | | | 0.52 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10342.0 ave 10342 max 10342 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: 292708.0 ave 292708 max 292708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292708 Ave neighs/atom = 224.46933 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -5790.4752 0 -5790.4752 -6632.9728 14306.415 35 0 -5790.5185 0 -5790.5185 -2952.635 14276.653 Loop time of 0.126721 on 1 procs for 2 steps with 1304 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 = -5790.47517136956 -5790.51382988723 -5790.51848625088 Force two-norm initial, final = 54.087958 4.2736253 Force max component initial, final = 48.710818 4.2514243 Final line search alpha, max atom move = 6.0242219e-05 0.00025611523 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12331 | 0.12331 | 0.12331 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094582 | 0.00094582 | 0.00094582 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002464 | | | 1.94 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 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: 292720.0 ave 292720 max 292720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292720 Ave neighs/atom = 224.47853 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5790.5185 0 -5790.5185 -2952.635 Loop time of 6.195e-06 on 1 procs for 0 steps with 1304 atoms 177.6% 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 | | 6.195e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 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: 292812.0 ave 292812 max 292812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292812 Ave neighs/atom = 224.54908 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.687 | 5.687 | 5.687 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 -5790.5185 -5790.5185 22.527255 127.50735 4.9703034 -2952.635 -2952.635 476.85948 -9295.8792 -38.885409 2.3135408 414.8121 Loop time of 7.488e-06 on 1 procs for 0 steps with 1304 atoms 0.0% 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 | | 7.488e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10333.0 ave 10333 max 10333 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146406.0 ave 146406 max 146406 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292812.0 ave 292812 max 292812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292812 Ave neighs/atom = 224.54908 Neighbor list builds = 0 Dangerous builds = 0 1304 -5754.9696183663 eV 2.31354080880999 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03