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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -40.052304 0.0000000) to (28.319031 40.052304 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2442649 5.4387744 4.4499063 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -40.052304 0.0000000) to (28.319031 40.052304 4.4499063) create_atoms CPU = 0.003 seconds 326 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2442649 5.4387744 4.4499063 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -40.052304 0.0000000) to (28.319031 40.052304 4.4499063) create_atoms CPU = 0.003 seconds 326 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 28 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 648 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4332.3881 0 -4332.3881 26019.869 54 0 -4386.6097 0 -4386.6097 12428.08 Loop time of 3.58649 on 1 procs for 54 steps with 648 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 = -4332.38813242787 -4386.60596346347 -4386.60968497133 Force two-norm initial, final = 34.451389 0.17741341 Force max component initial, final = 7.7810593 0.025641367 Final line search alpha, max atom move = 1.0000000 0.025641367 Iterations, force evaluations = 54 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5639 | 3.5639 | 3.5639 | 0.0 | 99.37 Neigh | 0.0061123 | 0.0061123 | 0.0061123 | 0.0 | 0.17 Comm | 0.0075868 | 0.0075868 | 0.0075868 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008865 | | | 0.25 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3002.00 ave 3002 max 3002 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: 37280.0 ave 37280 max 37280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37280 Ave neighs/atom = 57.530864 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.488 | 4.488 | 4.488 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -4386.6097 0 -4386.6097 12428.08 10094.545 57 0 -4386.7286 0 -4386.7286 3011.9925 10130.415 Loop time of 0.182826 on 1 procs for 3 steps with 648 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 = -4386.60968497133 -4386.72745062254 -4386.72861674818 Force two-norm initial, final = 93.731956 1.6777033 Force max component initial, final = 73.856002 1.3832154 Final line search alpha, max atom move = 0.00019975393 0.00027630270 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18117 | 0.18117 | 0.18117 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032458 | 0.00032458 | 0.00032458 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001331 | | | 0.73 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3004.00 ave 3004 max 3004 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: 37264.0 ave 37264 max 37264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37264 Ave neighs/atom = 57.506173 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.626 | 4.626 | 4.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4386.7286 0 -4386.7286 3011.9925 Loop time of 6.676e-06 on 1 procs for 0 steps with 648 atoms 164.8% 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 | | 6.676e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3004.00 ave 3004 max 3004 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: 37264.0 ave 37264 max 37264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37264 Ave neighs/atom = 57.506173 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.626 | 4.626 | 4.626 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 -4386.7286 -4386.7286 28.38483 80.104607 4.4553666 3011.9925 3011.9925 -147.45788 9402.4664 -219.03096 2.3396902 441.20861 Loop time of 6.795e-06 on 1 procs for 0 steps with 648 atoms 250.2% 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 | | 6.795e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3004.00 ave 3004 max 3004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18632.0 ave 18632 max 18632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37264.0 ave 37264 max 37264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37264 Ave neighs/atom = 57.506173 Neighbor list builds = 0 Dangerous builds = 0 648 -4386.72861674818 eV 2.33969024217297 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04