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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -38.424812 0.0000000) to (19.210622 38.424812 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6370467 4.6370467 3.5673230 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.424812 0.0000000) to (19.210622 38.424812 3.5673230) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6370467 4.6370467 3.5673230 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -38.424812 0.0000000) to (19.210622 38.424812 3.5673230) create_atoms CPU = 0.001 seconds 233 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 28 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 455 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1905.0619 0 -1905.0619 -13106.942 66 0 -1914.5413 0 -1914.5413 7944.9275 Loop time of 3.71725 on 1 procs for 66 steps with 455 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 = -1905.06186875512 -1914.53943633681 -1914.54128643252 Force two-norm initial, final = 7.0698882 0.24281106 Force max component initial, final = 2.6751203 0.089774952 Final line search alpha, max atom move = 0.69009413 0.061953167 Iterations, force evaluations = 66 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7001 | 3.7001 | 3.7001 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.008434 | 0.008434 | 0.008434 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008676 | | | 0.23 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2789.00 ave 2789 max 2789 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: 24386.0 ave 24386 max 24386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24386 Ave neighs/atom = 53.595604 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -1914.5413 0 -1914.5413 7944.9275 5266.5426 83 0 -1915.315 0 -1915.315 5575.7628 5294.5284 Loop time of 0.695676 on 1 procs for 17 steps with 455 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 = -1914.54128643252 -1915.31379206266 -1915.31497685304 Force two-norm initial, final = 123.42347 2.4681516 Force max component initial, final = 87.649561 1.8154622 Final line search alpha, max atom move = 0.00014409600 0.00026160085 Iterations, force evaluations = 17 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68858 | 0.68858 | 0.68858 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014556 | 0.0014556 | 0.0014556 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005642 | | | 0.81 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2849.00 ave 2849 max 2849 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: 26428.0 ave 26428 max 26428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26428 Ave neighs/atom = 58.083516 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1915.315 0 -1915.315 5575.7628 Loop time of 6.686e-06 on 1 procs for 0 steps with 455 atoms 164.5% 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 | | 6.686e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 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: 25668.0 ave 25668 max 25668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25668 Ave neighs/atom = 56.413187 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.587 | 4.587 | 4.587 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 -1915.315 -1915.315 19.42704 76.849623 3.546328 5575.7628 5575.7628 -254.57935 16435.724 546.14349 2.2649765 294.94283 Loop time of 6.906e-06 on 1 procs for 0 steps with 455 atoms 246.2% 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 | | 6.906e-06 | | |100.00 Nlocal: 455.000 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12834.0 ave 12834 max 12834 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25668.0 ave 25668 max 25668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25668 Ave neighs/atom = 56.413187 Neighbor list builds = 0 Dangerous builds = 0 455 -1915.31497685304 eV 2.26497647556238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04