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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222039) create_atoms CPU = 0.004 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355200 4.9780317 5.7481359 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.692444 0.0000000) to (42.677732 69.692444 8.6222039) create_atoms CPU = 0.003 seconds 2357 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 13 41 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 4692 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20573.251 0 -20573.251 6272.0031 99 0 -20824.546 0 -20824.546 5053.6101 Loop time of 4.72771 on 1 procs for 99 steps with 4692 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20573.2512509951 -20824.5268303051 -20824.5458588189 Force two-norm initial, final = 81.963122 0.48694256 Force max component initial, final = 10.199663 0.12590076 Final line search alpha, max atom move = 1.0000000 0.12590076 Iterations, force evaluations = 99 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5677 | 4.5677 | 4.5677 | 0.0 | 96.62 Neigh | 0.083513 | 0.083513 | 0.083513 | 0.0 | 1.77 Comm | 0.029504 | 0.029504 | 0.029504 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04697 | | | 0.99 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12839.0 ave 12839 max 12839 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: 622642.0 ave 622642 max 622642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622642 Ave neighs/atom = 132.70290 Neighbor list builds = 2 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 13 41 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -20824.546 0 -20824.546 5053.6101 51290.308 104 0 -20825.087 0 -20825.087 -23.059061 51436.561 Loop time of 0.208342 on 1 procs for 5 steps with 4692 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 = -20824.5458588192 -20825.0850566095 -20825.0869947428 Force two-norm initial, final = 334.86802 4.4486333 Force max component initial, final = 308.85242 3.3698654 Final line search alpha, max atom move = 4.2471126e-05 0.00014312198 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20128 | 0.20128 | 0.20128 | 0.0 | 96.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089134 | 0.00089134 | 0.00089134 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006173 | | | 2.96 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817.0 ave 12817 max 12817 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: 622480.0 ave 622480 max 622480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622480 Ave neighs/atom = 132.66837 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 10.92 | 10.92 | 10.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20825.087 0 -20825.087 -23.059061 Loop time of 2.259e-06 on 1 procs for 0 steps with 4692 atoms 177.1% 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 | | 2.259e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817.0 ave 12817 max 12817 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: 622332.0 ave 622332 max 622332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622332 Ave neighs/atom = 132.63683 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 13 41 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 10.92 | 10.92 | 10.92 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 -20825.087 -20825.087 42.662082 139.91385 8.6172597 -23.059061 -23.059061 -104.92807 -42.052491 77.80338 2.2128927 1758.7415 Loop time of 2.916e-06 on 1 procs for 0 steps with 4692 atoms 240.1% 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 | | 2.916e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817.0 ave 12817 max 12817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 311166.0 ave 311166 max 311166 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 622332.0 ave 622332 max 622332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622332 Ave neighs/atom = 132.63683 Neighbor list builds = 0 Dangerous builds = 0 4692 -20825.0869947428 eV 2.21289272105156 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05