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 -53.400951 0.0000000) to (21.799589 53.400951 7.5515990) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2319012 4.6278153 5.0343993 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -53.400951 0.0000000) to (21.799589 53.400951 7.5515990) create_atoms CPU = 0.001 seconds 601 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2319012 4.6278153 5.0343993 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -53.400951 0.0000000) to (21.799589 53.400951 7.5515990) create_atoms CPU = 0.001 seconds 601 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 = 7 32 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 15 atoms, new total = 1187 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 = 7 32 3 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) = 5.801 | 5.801 | 5.801 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7592.8598 0 -7592.8598 10265.413 109 0 -7701.9657 0 -7701.9657 -16284.357 Loop time of 57.5368 on 1 procs for 109 steps with 1187 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 = -7592.8598419346 -7701.95823797809 -7701.96571968187 Force two-norm initial, final = 138.23887 0.41362590 Force max component initial, final = 46.854647 0.13025554 Final line search alpha, max atom move = 1.0000000 0.13025554 Iterations, force evaluations = 109 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 57.436 | 57.436 | 57.436 | 0.0 | 99.82 Neigh | 0.08437 | 0.08437 | 0.08437 | 0.0 | 0.15 Comm | 0.0077255 | 0.0077255 | 0.0077255 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00901 | | | 0.02 Nlocal: 1187.00 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4921.00 ave 4921 max 4921 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: 85456.0 ave 85456 max 85456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85456 Ave neighs/atom = 71.993260 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 7 32 3 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 : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.800 | 5.800 | 5.800 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -7701.9657 0 -7701.9657 -16284.357 17581.916 115 0 -7702.932 0 -7702.932 1513.7858 17432.994 Loop time of 2.68704 on 1 procs for 6 steps with 1187 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 = -7701.96571968189 -7702.93152650055 -7702.93195496066 Force two-norm initial, final = 318.92220 0.70467076 Force max component initial, final = 229.20259 0.13982097 Final line search alpha, max atom move = 0.00024340096 3.4032559e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.685 | 2.685 | 2.685 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031892 | 0.00031892 | 0.00031892 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001671 | | | 0.06 Nlocal: 1187.00 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4922.00 ave 4922 max 4922 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: 85318.0 ave 85318 max 85318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85318 Ave neighs/atom = 71.877001 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 = 7 32 3 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) = 5.938 | 5.938 | 5.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7702.932 0 -7702.932 1513.7858 Loop time of 1.668e-06 on 1 procs for 0 steps with 1187 atoms 179.9% 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 | | 1.668e-06 | | |100.00 Nlocal: 1187.00 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4931.00 ave 4931 max 4931 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: 86612.0 ave 86612 max 86612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86612 Ave neighs/atom = 72.967144 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 = 7 32 3 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) = 5.938 | 5.938 | 5.938 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 -7702.932 -7702.932 21.716388 106.8019 7.5163222 1513.7858 1513.7858 -11.963127 4551.8652 1.4553054 2.4692152 2390.8658 Loop time of 1.517e-06 on 1 procs for 0 steps with 1187 atoms 131.8% 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 | | 1.517e-06 | | |100.00 Nlocal: 1187.00 ave 1187 max 1187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4931.00 ave 4931 max 4931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43306.0 ave 43306 max 43306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86612.0 ave 86612 max 86612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86612 Ave neighs/atom = 72.967144 Neighbor list builds = 0 Dangerous builds = 0 1187 -7702.93195496066 eV 2.4692151865603 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:01