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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -50.925282 0.0000000) to (25.462641 50.925282 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3090624 4.3090624 3.1582519 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -50.925282 0.0000000) to (25.462641 50.925282 3.1582519) create_atoms CPU = 0.002 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3090624 4.3090624 3.1582519 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -50.925282 0.0000000) to (25.462641 50.925282 3.1582519) create_atoms CPU = 0.001 seconds 261 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3087.0988 0 -3087.0988 92541.052 96 0 -3305.8044 0 -3305.8044 19448.843 Loop time of 1.65358 on 1 procs for 96 steps with 521 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 = -3087.09879607426 -3305.80136055907 -3305.80444225625 Force two-norm initial, final = 405.93770 0.31247524 Force max component initial, final = 149.18985 0.049641646 Final line search alpha, max atom move = 0.93825854 0.046576699 Iterations, force evaluations = 96 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6005 | 1.6005 | 1.6005 | 0.0 | 96.79 Neigh | 0.012843 | 0.012843 | 0.012843 | 0.0 | 0.78 Comm | 0.024097 | 0.024097 | 0.024097 | 0.0 | 1.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01616 | | | 0.98 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6057.00 ave 6057 max 6057 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: 86488.0 ave 86488 max 86488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86488 Ave neighs/atom = 166.00384 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -3305.8044 0 -3305.8044 19448.843 8190.5613 160 0 -3314.2395 0 -3314.2395 419.55367 8239.9392 Loop time of 0.700335 on 1 procs for 64 steps with 521 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 = -3305.80444225625 -3314.23766658418 -3314.23949617428 Force two-norm initial, final = 269.25222 6.1684777 Force max component initial, final = 232.08289 3.6999872 Final line search alpha, max atom move = 0.00013050447 0.00048286487 Iterations, force evaluations = 64 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62955 | 0.62955 | 0.62955 | 0.0 | 89.89 Neigh | 0.032064 | 0.032064 | 0.032064 | 0.0 | 4.58 Comm | 0.0096039 | 0.0096039 | 0.0096039 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02912 | | | 4.16 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5937.00 ave 5937 max 5937 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: 84992.0 ave 84992 max 84992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84992 Ave neighs/atom = 163.13244 Neighbor list builds = 3 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3314.2395 0 -3314.2395 419.55367 Loop time of 6.023e-06 on 1 procs for 0 steps with 521 atoms 182.6% 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 | | 6.023e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5931.00 ave 5931 max 5931 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: 84890.0 ave 84890 max 84890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84890 Ave neighs/atom = 162.93666 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.646 | 4.646 | 4.646 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 -3314.2395 -3314.2395 26.111834 105.01284 3.0049983 419.55367 419.55367 737.76918 484.31815 36.573681 2.6358584 381.99541 Loop time of 6.465e-06 on 1 procs for 0 steps with 521 atoms 278.4% 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 | | 6.465e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5931.00 ave 5931 max 5931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42445.0 ave 42445 max 42445 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84890.0 ave 84890 max 84890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84890 Ave neighs/atom = 162.93666 Neighbor list builds = 0 Dangerous builds = 0 521 -3314.23949617428 eV 2.63585843111164 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02