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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -47.864159 0.0000000) to (58.621384 47.864159 9.9088223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6995867 6.1539633 6.6058816 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -47.864159 0.0000000) to (58.621384 47.864159 9.9088223) create_atoms CPU = 0.008 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6995867 6.1539633 6.6058816 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -47.864159 0.0000000) to (58.621384 47.864159 9.9088223) create_atoms CPU = 0.007 seconds 1686 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 3318 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.550 | 6.550 | 6.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11230.918 0 -11230.918 669.01918 163 0 -11280.173 0 -11280.173 -4655.0029 Loop time of 18.3155 on 1 procs for 163 steps with 3318 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11230.9177010797 -11280.1622814091 -11280.1734530994 Force two-norm initial, final = 36.148072 0.23105400 Force max component initial, final = 5.0548900 0.032196935 Final line search alpha, max atom move = 1.0000000 0.032196935 Iterations, force evaluations = 163 307 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.764 | 17.764 | 17.764 | 0.0 | 96.99 Neigh | 0.3766 | 0.3766 | 0.3766 | 0.0 | 2.06 Comm | 0.07604 | 0.07604 | 0.07604 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09903 | | | 0.54 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10312.0 ave 10312 max 10312 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: 467924.0 ave 467924 max 467924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467924 Ave neighs/atom = 141.02592 Neighbor list builds = 5 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 163 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.550 | 6.550 | 6.550 Mbytes Step Temp E_pair E_mol TotEng Press Volume 163 0 -11280.173 0 -11280.173 -4655.0029 55605.601 168 0 -11280.747 0 -11280.747 53.814836 55267.215 Loop time of 0.404357 on 1 procs for 5 steps with 3318 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11280.1734530993 -11280.7463303492 -11280.7472176107 Force two-norm initial, final = 285.50846 5.2257693 Force max component initial, final = 205.57252 3.7658082 Final line search alpha, max atom move = 0.00010302728 0.00038798098 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39591 | 0.39591 | 0.39591 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014867 | 0.0014867 | 0.0014867 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006958 | | | 1.72 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10072.0 ave 10072 max 10072 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: 467452.0 ave 467452 max 467452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 467452 Ave neighs/atom = 140.88366 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.688 | 6.688 | 6.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11280.747 0 -11280.747 53.814836 Loop time of 6.836e-06 on 1 procs for 0 steps with 3318 atoms 190.2% 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 | | 6.836e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10072.0 ave 10072 max 10072 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: 468652.0 ave 468652 max 468652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468652 Ave neighs/atom = 141.24533 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.688 | 6.688 | 6.688 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 -11280.747 -11280.747 58.594407 95.329463 9.8942816 53.814836 53.814836 109.11918 -42.89686 95.222192 2.4963162 2175.7303 Loop time of 7.046e-06 on 1 procs for 0 steps with 3318 atoms 241.3% 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 | | 7.046e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10072.0 ave 10072 max 10072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 234326.0 ave 234326 max 234326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 468652.0 ave 468652 max 468652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468652 Ave neighs/atom = 141.24533 Neighbor list builds = 0 Dangerous builds = 0 3318 -11280.7472176107 eV 2.49631620938821 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19