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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -39.558195 0.0000000) to (8.0747828 39.558195 8.8454813) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8448697 5.2744260 5.8969875 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.558195 0.0000000) to (8.0747828 39.558195 8.8454813) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8448697 5.2744260 5.8969875 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.558195 0.0000000) to (8.0747828 39.558195 8.8454813) create_atoms CPU = 0.001 seconds 242 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 30 4 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 482 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_137964310702_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1962.8891 0 -1962.8891 48512.944 63 0 -2037.2594 0 -2037.2594 13896.046 Loop time of 3.39233 on 1 procs for 63 steps with 482 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1962.88910224242 -2037.25771271844 -2037.25944248467 Force two-norm initial, final = 107.77194 0.16367513 Force max component initial, final = 25.335096 0.028546080 Final line search alpha, max atom move = 1.0000000 0.028546080 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3865 | 3.3865 | 3.3865 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002705 | 0.002705 | 0.002705 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003106 | | | 0.09 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2360.00 ave 2360 max 2360 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: 26064.0 ave 26064 max 26064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26064 Ave neighs/atom = 54.074689 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 30 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.814 | 4.814 | 4.814 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2037.2594 0 -2037.2594 13896.046 5650.9151 67 0 -2037.461 0 -2037.461 -1.8029917 5697.664 Loop time of 0.197536 on 1 procs for 4 steps with 482 atoms 94.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2037.25944248466 -2037.46089804472 -2037.46096973852 Force two-norm initial, final = 84.919479 0.35746326 Force max component initial, final = 50.646690 0.14568392 Final line search alpha, max atom move = 0.0018108346 0.00026380948 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19657 | 0.19657 | 0.19657 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008145 | | | 0.41 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2423.00 ave 2423 max 2423 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: 26020.0 ave 26020 max 26020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26020 Ave neighs/atom = 53.983402 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 30 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.952 | 4.952 | 4.952 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2037.461 0 -2037.461 -1.8029917 Loop time of 2.306e-06 on 1 procs for 0 steps with 482 atoms 130.1% 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 | | 2.306e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2416.00 ave 2416 max 2416 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: 25992.0 ave 25992 max 25992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25992 Ave neighs/atom = 53.925311 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 30 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.952 | 4.952 | 4.952 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 -2037.461 -2037.461 8.0967225 79.353968 8.8678622 -1.8029917 -1.8029917 -30.004357 -16.474419 41.069801 2.2967712 206.65328 Loop time of 2.195e-06 on 1 procs for 0 steps with 482 atoms 227.8% 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 | | 2.195e-06 | | |100.00 Nlocal: 482.000 ave 482 max 482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2416.00 ave 2416 max 2416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12996.0 ave 12996 max 12996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25992.0 ave 25992 max 25992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25992 Ave neighs/atom = 53.925311 Neighbor list builds = 0 Dangerous builds = 0 482 -2037.46096973852 eV 2.29677117818875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03