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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -58.235288 0.0000000) to (29.117644 58.235288 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4532868 4.4532868 3.1582519 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -58.235288 0.0000000) to (29.117644 58.235288 3.1582519) create_atoms CPU = 0.002 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4532868 4.4532868 3.1582519 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.235288 0.0000000) to (29.117644 58.235288 3.1582519) create_atoms CPU = 0.001 seconds 341 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 28 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 677 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3011.665 0 -3011.665 202203.78 160 0 -4309.0962 0 -4309.0962 -4181.2379 Loop time of 3.38942 on 1 procs for 160 steps with 677 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 = -3011.66502004477 -4309.09209329816 -4309.09616248679 Force two-norm initial, final = 2935.9471 0.36789249 Force max component initial, final = 1377.1552 0.084373133 Final line search alpha, max atom move = 0.53524926 0.045160657 Iterations, force evaluations = 160 294 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2725 | 3.2725 | 3.2725 | 0.0 | 96.55 Neigh | 0.041502 | 0.041502 | 0.041502 | 0.0 | 1.22 Comm | 0.044941 | 0.044941 | 0.044941 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0305 | | | 0.90 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6751.00 ave 6751 max 6751 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: 110470.0 ave 110470 max 110470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110470 Ave neighs/atom = 163.17578 Neighbor list builds = 3 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 160 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press Volume 160 0 -4309.0962 0 -4309.0962 -4181.2379 10710.734 205 0 -4316.4511 0 -4316.4511 805.59756 10685.695 Loop time of 0.581768 on 1 procs for 45 steps with 677 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 = -4309.09616248679 -4316.44777432767 -4316.45110873149 Force two-norm initial, final = 232.53776 10.103648 Force max component initial, final = 204.45509 6.1886291 Final line search alpha, max atom move = 0.00020905679 0.0012937749 Iterations, force evaluations = 45 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52207 | 0.52207 | 0.52207 | 0.0 | 89.74 Neigh | 0.028849 | 0.028849 | 0.028849 | 0.0 | 4.96 Comm | 0.0076731 | 0.0076731 | 0.0076731 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02318 | | | 3.98 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7947.00 ave 7947 max 7947 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: 109116.0 ave 109116 max 109116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109116 Ave neighs/atom = 161.17578 Neighbor list builds = 2 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4316.4511 0 -4316.4511 805.59756 Loop time of 6.625e-06 on 1 procs for 0 steps with 677 atoms 166.0% 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 | | 6.625e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7947.00 ave 7947 max 7947 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: 108910.0 ave 108910 max 108910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108910 Ave neighs/atom = 160.87149 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.089 | 5.089 | 5.089 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 -4316.4511 -4316.4511 29.793954 118.88185 3.0168871 805.59756 805.59756 789.53894 740.88519 886.36855 2.6233609 182.4969 Loop time of 8.66e-06 on 1 procs for 0 steps with 677 atoms 230.9% 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 | | 8.66e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7947.00 ave 7947 max 7947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54455.0 ave 54455 max 54455 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108910.0 ave 108910 max 108910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108910 Ave neighs/atom = 160.87149 Neighbor list builds = 0 Dangerous builds = 0 677 -4316.45110873149 eV 2.62336085713206 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04