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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -43.226950 0.0000000) to (52.941985 43.226950 8.9488288) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0505126 5.5577507 5.9658858 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -43.226950 0.0000000) to (52.941985 43.226950 8.9488288) create_atoms CPU = 0.003 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0505126 5.5577507 5.9658858 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -43.226950 0.0000000) to (52.941985 43.226950 8.9488288) create_atoms CPU = 0.003 seconds 1688 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 20 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 7.890 | 7.890 | 7.890 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9528.9466 0 -9528.9466 56034.497 94 0 -10909.71 0 -10909.71 -2023.1264 Loop time of 3.75234 on 1 procs for 94 steps with 3352 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9528.94655541901 -10909.6992411821 -10909.7097979634 Force two-norm initial, final = 955.35451 0.41196473 Force max component initial, final = 83.282986 0.026437610 Final line search alpha, max atom move = 1.0000000 0.026437610 Iterations, force evaluations = 94 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5245 | 3.5245 | 3.5245 | 0.0 | 93.93 Neigh | 0.17833 | 0.17833 | 0.17833 | 0.0 | 4.75 Comm | 0.02104 | 0.02104 | 0.02104 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02847 | | | 0.76 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12694.0 ave 12694 max 12694 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: 751578.0 ave 751578 max 751578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 751578 Ave neighs/atom = 224.21778 Neighbor list builds = 4 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.887 | 7.887 | 7.887 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -10909.71 0 -10909.71 -2023.1264 40959.156 98 0 -10910.132 0 -10910.132 -138.90539 40898.757 Loop time of 0.141416 on 1 procs for 4 steps with 3352 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 = -10909.7097979635 -10910.1215084104 -10910.1319836623 Force two-norm initial, final = 208.96178 7.1453536 Force max component initial, final = 190.46002 6.4812391 Final line search alpha, max atom move = 3.6986755e-05 0.00023972000 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13708 | 0.13708 | 0.13708 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059405 | 0.00059405 | 0.00059405 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003738 | | | 2.64 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12428.0 ave 12428 max 12428 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: 750172.0 ave 750172 max 750172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 750172 Ave neighs/atom = 223.79833 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 8.025 | 8.025 | 8.025 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10910.132 0 -10910.132 -138.90539 Loop time of 2.628e-06 on 1 procs for 0 steps with 3352 atoms 152.2% 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 | | 2.628e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12429.0 ave 12429 max 12429 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: 750380.0 ave 750380 max 750380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 750380 Ave neighs/atom = 223.86038 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 8.025 | 8.025 | 8.025 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 -10910.132 -10910.132 52.767431 86.665136 8.9433398 -138.90539 -138.90539 -83.983938 -78.990533 -253.74169 2.3710334 2354.6526 Loop time of 2.598e-06 on 1 procs for 0 steps with 3352 atoms 307.9% 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 | | 2.598e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12429.0 ave 12429 max 12429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 375190.0 ave 375190 max 375190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 750380.0 ave 750380 max 750380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 750380 Ave neighs/atom = 223.86038 Neighbor list builds = 0 Dangerous builds = 0 3352 -10910.1319836623 eV 2.3710334145387 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04