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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -39.941301 0.0000000) to (8.1529839 39.941301 8.9311464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8917903 5.3255068 5.9540976 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.941301 0.0000000) to (8.1529839 39.941301 8.9311464) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8917903 5.3255068 5.9540976 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.941301 0.0000000) to (8.1529839 39.941301 8.9311464) create_atoms CPU = 0.001 seconds 242 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 2 19 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_331285495617_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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1756.2114 0 -1756.2114 27104.725 87 0 -1844.1292 0 -1844.1292 -6243.5563 Loop time of 0.636646 on 1 procs for 87 steps with 476 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1756.21143834713 -1844.12755593246 -1844.12923597313 Force two-norm initial, final = 185.63990 0.15843574 Force max component initial, final = 65.247006 0.021438356 Final line search alpha, max atom move = 1.0000000 0.021438356 Iterations, force evaluations = 87 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60972 | 0.60972 | 0.60972 | 0.0 | 95.77 Neigh | 0.014993 | 0.014993 | 0.014993 | 0.0 | 2.35 Comm | 0.0069818 | 0.0069818 | 0.0069818 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004956 | | | 0.78 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4792.00 ave 4792 max 4792 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: 105160.0 ave 105160 max 105160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105160 Ave neighs/atom = 220.92437 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -1844.1292 0 -1844.1292 -6243.5563 5816.691 92 0 -1844.1991 0 -1844.1991 2.1383046 5794.1441 Loop time of 0.0296675 on 1 procs for 5 steps with 476 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 = -1844.12923597313 -1844.19843517724 -1844.19905784319 Force two-norm initial, final = 42.569596 0.30849525 Force max component initial, final = 35.601442 0.072268742 Final line search alpha, max atom move = 0.00023741405 1.7157615e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02824 | 0.02824 | 0.02824 | 0.0 | 95.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027721 | 0.00027721 | 0.00027721 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001151 | | | 3.88 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 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: 105616.0 ave 105616 max 105616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105616 Ave neighs/atom = 221.88235 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1844.1991 0 -1844.1991 2.1383046 Loop time of 1.973e-06 on 1 procs for 0 steps with 476 atoms 152.1% 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 | | 1.973e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 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: 105768.0 ave 105768 max 105768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105768 Ave neighs/atom = 222.20168 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.122 | 5.122 | 5.122 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 -1844.1991 -1844.1991 8.15775 79.5889 8.9241404 2.1383046 2.1383046 19.995183 5.9840857 -19.564354 2.3325074 263.22973 Loop time of 2.108e-06 on 1 procs for 0 steps with 476 atoms 237.2% 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 | | 2.108e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52884.0 ave 52884 max 52884 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105768.0 ave 105768 max 105768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105768 Ave neighs/atom = 222.20168 Neighbor list builds = 0 Dangerous builds = 0 476 -1844.19905784319 eV 2.33250740887718 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00