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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -41.846189 0.0000000) to (29.589724 41.846189 5.1123257) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7412898 6.2456999 5.1123257 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.846189 0.0000000) to (29.589724 41.846189 5.1123257) create_atoms CPU = 0.004 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7412898 6.2456999 5.1123257 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.846189 0.0000000) to (29.589724 41.846189 5.1123257) create_atoms CPU = 0.004 seconds 538 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 7 20 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 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_318213562153_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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3595.2154 0 -3595.2154 36709.272 77 0 -3781.0763 0 -3781.0763 5123.8235 Loop time of 3.5154 on 1 procs for 77 steps with 1070 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3595.21541684468 -3781.07273871161 -3781.0763044276 Force two-norm initial, final = 320.97631 0.18492060 Force max component initial, final = 102.44796 0.040040111 Final line search alpha, max atom move = 1.0000000 0.040040111 Iterations, force evaluations = 77 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4365 | 3.4365 | 3.4365 | 0.0 | 97.76 Neigh | 0.032403 | 0.032403 | 0.032403 | 0.0 | 0.92 Comm | 0.02606 | 0.02606 | 0.02606 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02044 | | | 0.58 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827.00 ave 7827 max 7827 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: 223936.0 ave 223936 max 223936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223936 Ave neighs/atom = 209.28598 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3781.0763 0 -3781.0763 5123.8235 12660.339 85 0 -3781.4908 0 -3781.4908 -56.178992 12706.384 Loop time of 0.254376 on 1 procs for 8 steps with 1070 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3781.0763044276 -3781.48869029959 -3781.490755331 Force two-norm initial, final = 114.27971 1.1578353 Force max component initial, final = 113.99185 0.85890169 Final line search alpha, max atom move = 0.00018961358 0.00016285942 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24704 | 0.24704 | 0.24704 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017503 | 0.0017503 | 0.0017503 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005589 | | | 2.20 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7993.00 ave 7993 max 7993 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: 223880.0 ave 223880 max 223880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223880 Ave neighs/atom = 209.23364 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 5.569 | 5.569 | 5.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3781.4908 0 -3781.4908 -56.178992 Loop time of 7.859e-06 on 1 procs for 0 steps with 1070 atoms 165.4% 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 | | 7.859e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7984.00 ave 7984 max 7984 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: 223596.0 ave 223596 max 223596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223596 Ave neighs/atom = 208.96822 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 5.569 | 5.569 | 5.569 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 -3781.4908 -3781.4908 29.510268 84.319451 5.1064729 -56.178992 -56.178992 -108.01003 -85.248894 24.72195 2.3791548 575.54813 Loop time of 7.207e-06 on 1 procs for 0 steps with 1070 atoms 208.1% 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 | | 7.207e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7984.00 ave 7984 max 7984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111798.0 ave 111798 max 111798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223596.0 ave 223596 max 223596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223596 Ave neighs/atom = 208.96822 Neighbor list builds = 0 Dangerous builds = 0 1070 -3781.490755331 eV 2.37915475808188 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04