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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1928723 3.1928723 2.8601955 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) create_atoms CPU = 0.002 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1928723 3.1928723 2.8601955 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.119266 0.0000000) to (23.059633 46.119266 2.8601955) 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.841 | 4.841 | 4.841 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2152.7599 0 -2152.7599 38032.268 49 0 -2221.8258 0 -2221.8258 7261.5629 Loop time of 8.23167 on 1 procs for 49 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 = -2152.75985413446 -2221.82400131086 -2221.82582551971 Force two-norm initial, final = 86.424996 0.15976810 Force max component initial, final = 21.729291 0.030432692 Final line search alpha, max atom move = 1.0000000 0.030432692 Iterations, force evaluations = 49 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.2172 | 8.2172 | 8.2172 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0073118 | 0.0073118 | 0.0073118 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007131 | | | 0.09 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3304.00 ave 3304 max 3304 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: 30150.0 ave 30150 max 30150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30150 Ave neighs/atom = 57.869482 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.841 | 4.841 | 4.841 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -2221.8258 0 -2221.8258 7261.5629 6083.5976 58 0 -2222.0261 0 -2222.0261 -187.17442 6109.1198 Loop time of 0.973779 on 1 procs for 9 steps with 521 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 = -2221.82582551971 -2222.02567466341 -2222.02612025417 Force two-norm initial, final = 58.681005 1.3251689 Force max component initial, final = 55.310318 0.82151237 Final line search alpha, max atom move = 0.00067216446 0.00055219142 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96989 | 0.96989 | 0.96989 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080652 | 0.00080652 | 0.00080652 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003078 | | | 0.32 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3308.00 ave 3308 max 3308 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: 30106.0 ave 30106 max 30106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30106 Ave neighs/atom = 57.785029 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2222.0261 0 -2222.0261 -187.17442 Loop time of 6.966e-06 on 1 procs for 0 steps with 521 atoms 258.4% 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 | | 6.966e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3312.00 ave 3312 max 3312 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: 30098.0 ave 30098 max 30098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30098 Ave neighs/atom = 57.769674 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.979 | 4.979 | 4.979 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 -2222.0261 -2222.0261 23.008379 93.013425 2.8546113 -187.17442 -187.17442 -163.35131 -183.14293 -215.02903 2.3442667 167.1975 Loop time of 7.247e-06 on 1 procs for 0 steps with 521 atoms 207.0% 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 | | 7.247e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15049.0 ave 15049 max 15049 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30098.0 ave 30098 max 30098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30098 Ave neighs/atom = 57.769674 Neighbor list builds = 0 Dangerous builds = 0 521 -2222.02612025417 eV 2.34426673055632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09