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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.418113 0.0000000) to (37.418113 37.418113 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -37.418113 0.0000000) to (37.418113 37.418113 3.5200000) create_atoms CPU = 0.002 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9670062 4.9670062 3.5200000 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -37.418113 0.0000000) to (37.418113 37.418113 3.5200000) create_atoms CPU = 0.002 seconds 453 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 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 904 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.400 | 5.400 | 5.400 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3938.9999 0 -3938.9999 13277.736 51 0 -4011.7088 0 -4011.7088 4240.3385 Loop time of 2.99871 on 1 procs for 51 steps with 904 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 = -3938.9998832054 -4011.70555110504 -4011.70875829366 Force two-norm initial, final = 35.294358 0.17685744 Force max component initial, final = 4.6039769 0.016675712 Final line search alpha, max atom move = 1.0000000 0.016675712 Iterations, force evaluations = 51 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9403 | 2.9403 | 2.9403 | 0.0 | 98.05 Neigh | 0.028392 | 0.028392 | 0.028392 | 0.0 | 0.95 Comm | 0.018169 | 0.018169 | 0.018169 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01181 | | | 0.39 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8718.00 ave 8718 max 8718 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: 223064.0 ave 223064 max 223064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223064 Ave neighs/atom = 246.75221 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 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.393 | 5.393 | 5.393 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -4011.7088 0 -4011.7088 4240.3385 9856.8108 55 0 -4011.8279 0 -4011.8279 -328.03225 9881.8419 Loop time of 0.19949 on 1 procs for 4 steps with 904 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 = -4011.70875829369 -4011.82549027903 -4011.827902157 Force two-norm initial, final = 67.470660 4.1542972 Force max component initial, final = 56.123960 3.8403983 Final line search alpha, max atom move = 0.00019719161 0.00075729430 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1954 | 0.1954 | 0.1954 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001003 | 0.001003 | 0.001003 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003086 | | | 1.55 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8072.00 ave 8072 max 8072 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: 223490.0 ave 223490 max 223490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223490 Ave neighs/atom = 247.22345 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 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.531 | 5.531 | 5.531 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4011.8279 0 -4011.8279 -328.03225 Loop time of 5.913e-06 on 1 procs for 0 steps with 904 atoms 186.0% 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 | | 5.913e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8072.00 ave 8072 max 8072 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: 223316.0 ave 223316 max 223316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223316 Ave neighs/atom = 247.03097 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 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.531 | 5.531 | 5.531 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 -4011.8279 -4011.8279 37.33496 75.020536 3.5281094 -328.03225 -328.03225 -186.86511 -624.19029 -173.04136 2.2295861 134.34262 Loop time of 6.665e-06 on 1 procs for 0 steps with 904 atoms 240.1% 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 | | 6.665e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8072.00 ave 8072 max 8072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111658.0 ave 111658 max 111658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223316.0 ave 223316 max 223316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223316 Ave neighs/atom = 247.03097 Neighbor list builds = 0 Dangerous builds = 0 904 -4011.827902157 eV 2.22958611214216 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04