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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -40.703337 0.0000000) to (28.781606 40.703337 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5844907 6.0751250 4.9727041 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -40.703337 0.0000000) to (28.781606 40.703337 4.9727041) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5844907 6.0751250 4.9727041 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.703337 0.0000000) to (28.781606 40.703337 4.9727041) create_atoms CPU = 0.001 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 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 8.9 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4696.7469 0 -4696.7469 116082.11 68 0 -5206.1042 0 -5206.1042 760.74928 Loop time of 2.11777 on 1 procs for 68 steps with 1070 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4696.74686043653 -5206.09989720025 -5206.10421797978 Force two-norm initial, final = 977.79436 0.22747839 Force max component initial, final = 313.35601 0.037663524 Final line search alpha, max atom move = 1.0000000 0.037663524 Iterations, force evaluations = 68 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0639 | 2.0639 | 2.0639 | 0.0 | 97.45 Neigh | 0.032969 | 0.032969 | 0.032969 | 0.0 | 1.56 Comm | 0.011907 | 0.011907 | 0.011907 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009042 | | | 0.43 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8452.00 ave 8452 max 8452 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: 277176.0 ave 277176 max 277176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 277176 Ave neighs/atom = 259.04299 Neighbor list builds = 2 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -5206.1042 0 -5206.1042 760.74928 11651.119 73 0 -5206.38 0 -5206.38 -20.21128 11655.657 Loop time of 0.119839 on 1 procs for 5 steps with 1070 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 = -5206.10421797978 -5206.37621431162 -5206.38001920372 Force two-norm initial, final = 93.244904 1.3739233 Force max component initial, final = 73.116908 1.0200921 Final line search alpha, max atom move = 0.00012070609 0.00012313134 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11708 | 0.11708 | 0.11708 | 0.0 | 97.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049421 | 0.00049421 | 0.00049421 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002261 | | | 1.89 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8398.00 ave 8398 max 8398 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: 276116.0 ave 276116 max 276116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 276116 Ave neighs/atom = 258.05234 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.589 | 5.589 | 5.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5206.38 0 -5206.38 -20.21128 Loop time of 2.19e-06 on 1 procs for 0 steps with 1070 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 | | 2.19e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8443.00 ave 8443 max 8443 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: 275208.0 ave 275208 max 275208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275208 Ave neighs/atom = 257.20374 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.589 | 5.589 | 5.589 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 -5206.38 -5206.38 28.658497 81.746537 4.9752393 -20.21128 -20.21128 -33.628981 -140.80639 113.80153 2.3005774 528.2362 Loop time of 2.814e-06 on 1 procs for 0 steps with 1070 atoms 248.8% 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 | | 2.814e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8443.00 ave 8443 max 8443 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 137604.0 ave 137604 max 137604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275208.0 ave 275208 max 275208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275208 Ave neighs/atom = 257.20374 Neighbor list builds = 0 Dangerous builds = 0 1070 -5206.38001920372 eV 2.30057740822019 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02