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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -58.168557 0.0000000) to (29.084279 58.168557 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2482654 4.2482654 3.0829274 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -58.168557 0.0000000) to (29.084279 58.168557 3.0829274) create_atoms CPU = 0.001 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2482654 4.2482654 3.0829274 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -58.168557 0.0000000) to (29.084279 58.168557 3.0829274) create_atoms CPU = 0.000 seconds 357 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 713 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4301.1528 0 -4301.1528 103974.89 73 0 -4629.4766 0 -4629.4766 8532.3205 Loop time of 27.4752 on 1 procs for 73 steps with 713 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 = -4301.15276657871 -4629.47229341 -4629.47660795877 Force two-norm initial, final = 782.43900 0.30234696 Force max component initial, final = 281.62376 0.061823938 Final line search alpha, max atom move = 1.0000000 0.061823938 Iterations, force evaluations = 73 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.457 | 27.457 | 27.457 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010602 | 0.010602 | 0.010602 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007347 | | | 0.03 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5662.00 ave 5662 max 5662 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: 46558.0 ave 46558 max 46558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46558 Ave neighs/atom = 65.298738 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 35 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -4629.4766 0 -4629.4766 8532.3205 10431.335 98 0 -4631.1219 0 -4631.1219 -484.14248 10459.061 Loop time of 5.18215 on 1 procs for 25 steps with 713 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 = -4629.47660795878 -4631.11884156209 -4631.12185019343 Force two-norm initial, final = 198.55604 6.0306132 Force max component initial, final = 194.78460 3.7294803 Final line search alpha, max atom move = 0.00061869240 0.0023074011 Iterations, force evaluations = 25 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1114 | 5.1114 | 5.1114 | 0.0 | 98.63 Neigh | 0.063192 | 0.063192 | 0.063192 | 0.0 | 1.22 Comm | 0.001421 | 0.001421 | 0.001421 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006125 | | | 0.12 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5630.00 ave 5630 max 5630 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: 53890.0 ave 53890 max 53890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53890 Ave neighs/atom = 75.582048 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.825 | 5.825 | 5.825 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4631.1219 0 -4631.1219 -484.14248 Loop time of 1.956e-06 on 1 procs for 0 steps with 713 atoms 153.4% 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 | | 1.956e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5630.00 ave 5630 max 5630 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: 54000.0 ave 54000 max 54000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54000 Ave neighs/atom = 75.736325 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 36 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.825 | 5.825 | 5.825 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 -4631.1219 -4631.1219 29.183856 118.48469 3.0247382 -484.14248 -484.14248 -573.25831 -576.46786 -302.70126 2.5416227 976.86281 Loop time of 1.969e-06 on 1 procs for 0 steps with 713 atoms 203.1% 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 | | 1.969e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5630.00 ave 5630 max 5630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27000.0 ave 27000 max 27000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54000.0 ave 54000 max 54000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54000 Ave neighs/atom = 75.736325 Neighbor list builds = 0 Dangerous builds = 0 713 -4631.12185019344 eV 2.54162271509424 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:33