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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -38.013960 0.0000000) to (26.877412 38.013960 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1299360 6.0016421 5.0346005 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.013960 0.0000000) to (26.877412 38.013960 5.0346005) create_atoms CPU = 0.004 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1299360 6.0016421 5.0346005 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.013960 0.0000000) to (26.877412 38.013960 5.0346005) create_atoms CPU = 0.003 seconds 458 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3905.3595 0 -3905.3595 6828.164 83 0 -3962.0057 0 -3962.0057 2213.7979 Loop time of 2.64209 on 1 procs for 83 steps with 904 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3905.35954040395 -3962.00212048157 -3962.00567201873 Force two-norm initial, final = 47.380715 0.26741154 Force max component initial, final = 9.0674153 0.045780680 Final line search alpha, max atom move = 1.0000000 0.045780680 Iterations, force evaluations = 83 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5802 | 2.5802 | 2.5802 | 0.0 | 97.66 Neigh | 0.021369 | 0.021369 | 0.021369 | 0.0 | 0.81 Comm | 0.022025 | 0.022025 | 0.022025 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01849 | | | 0.70 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6380.00 ave 6380 max 6380 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: 157848.0 ave 157848 max 157848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157848 Ave neighs/atom = 174.61062 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -3962.0057 0 -3962.0057 2213.7979 10287.872 89 0 -3962.2096 0 -3962.2096 -995.08423 10303.965 Loop time of 0.137847 on 1 procs for 6 steps with 904 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3962.00567201873 -3962.20938946936 -3962.20956879085 Force two-norm initial, final = 70.305680 1.2411827 Force max component initial, final = 67.598458 1.0277167 Final line search alpha, max atom move = 0.00049532625 0.00050905507 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13345 | 0.13345 | 0.13345 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003387 | | | 2.46 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6380.00 ave 6380 max 6380 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: 157464.0 ave 157464 max 157464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157464 Ave neighs/atom = 174.18584 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3962.2096 0 -3962.2096 -995.08423 Loop time of 6.735e-06 on 1 procs for 0 steps with 904 atoms 178.2% 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 | | 6.735e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6344.00 ave 6344 max 6344 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: 157364.0 ave 157364 max 157364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157364 Ave neighs/atom = 174.07522 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.133 | 5.133 | 5.133 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 -3962.2096 -3962.2096 27.012529 76.02792 5.0172533 -995.08423 -995.08423 -73.120186 -2752.8821 -159.25036 2.3851639 772.40704 Loop time of 7.016e-06 on 1 procs for 0 steps with 904 atoms 313.6% 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 | | 7.016e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6344.00 ave 6344 max 6344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78682.0 ave 78682 max 78682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157364.0 ave 157364 max 157364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157364 Ave neighs/atom = 174.07522 Neighbor list builds = 0 Dangerous builds = 0 904 -3962.20956879085 eV 2.38516390207521 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03