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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -74.678300 0.0000000) to (37.339150 74.678300 4.0499994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106935 5.7106935 4.0499994 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678300 0.0000000) to (37.339150 74.678300 4.0499994) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106935 5.7106935 4.0499994 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678300 0.0000000) to (37.339150 74.678300 4.0499994) create_atoms CPU = 0.002 seconds 682 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_117656786760_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.508 | 5.508 | 5.508 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4522.0123 0 -4522.0123 5307.2 71 0 -4570.8355 0 -4570.8355 2949.8206 Loop time of 3.85348 on 1 procs for 71 steps with 1362 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4522.01234644337 -4570.83168576785 -4570.83545406402 Force two-norm initial, final = 28.050652 0.13823718 Force max component initial, final = 4.3256121 0.010493924 Final line search alpha, max atom move = 1.0000000 0.010493924 Iterations, force evaluations = 71 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7643 | 3.7643 | 3.7643 | 0.0 | 97.69 Neigh | 0.033682 | 0.033682 | 0.033682 | 0.0 | 0.87 Comm | 0.033082 | 0.033082 | 0.033082 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02241 | | | 0.58 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10438.0 ave 10438 max 10438 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: 237152.0 ave 237152 max 237152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237152 Ave neighs/atom = 174.12041 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4570.8355 0 -4570.8355 2949.8206 22586.233 76 0 -4570.9976 0 -4570.9976 -180.79834 22675.362 Loop time of 0.205761 on 1 procs for 5 steps with 1362 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 = -4570.83545406402 -4570.99316146316 -4570.99761558949 Force two-norm initial, final = 81.758006 4.5351503 Force max component initial, final = 73.154054 3.2704668 Final line search alpha, max atom move = 0.00012167852 0.00039794556 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19955 | 0.19955 | 0.19955 | 0.0 | 96.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014994 | 0.0014994 | 0.0014994 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004709 | | | 2.29 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9793.00 ave 9793 max 9793 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: 237604.0 ave 237604 max 237604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237604 Ave neighs/atom = 174.45228 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.638 | 5.638 | 5.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4570.9976 0 -4570.9976 -180.79834 Loop time of 7.027e-06 on 1 procs for 0 steps with 1362 atoms 156.5% 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 | | 7.027e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9778.00 ave 9778 max 9778 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: 237216.0 ave 237216 max 237216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237216 Ave neighs/atom = 174.16740 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.638 | 5.638 | 5.638 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 -4570.9976 -4570.9976 37.330211 150.08696 4.0471641 -180.79834 -180.79834 -176.0811 -135.39381 -230.9201 2.5582179 197.8891 Loop time of 7.216e-06 on 1 procs for 0 steps with 1362 atoms 277.2% 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 | | 7.216e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9778.00 ave 9778 max 9778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118608.0 ave 118608 max 118608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237216.0 ave 237216 max 237216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237216 Ave neighs/atom = 174.16740 Neighbor list builds = 0 Dangerous builds = 0 1362 -4487.59729152095 eV 2.55821791911363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04