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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9099749 5.5148277 5.9032704 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) create_atoms CPU = 0.002 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9099749 5.5148277 5.9032704 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) create_atoms CPU = 0.002 seconds 1322 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 15 24 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2638 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_179025990738_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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.570 | 5.570 | 5.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9049.7002 0 -9049.7002 16261.827 83 0 -9234.8383 0 -9234.8383 14269.164 Loop time of 1.69989 on 1 procs for 83 steps with 2638 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9049.7002275028 -9234.82933788343 -9234.8383365266 Force two-norm initial, final = 80.755404 0.28540237 Force max component initial, final = 10.224927 0.085663705 Final line search alpha, max atom move = 1.0000000 0.085663705 Iterations, force evaluations = 83 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6291 | 1.6291 | 1.6291 | 0.0 | 95.83 Neigh | 0.040044 | 0.040044 | 0.040044 | 0.0 | 2.36 Comm | 0.011544 | 0.011544 | 0.011544 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01924 | | | 1.13 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7013.00 ave 7013 max 7013 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: 226046.0 ave 226046 max 226046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226046 Ave neighs/atom = 85.688400 Neighbor list builds = 2 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -9234.8383 0 -9234.8383 14269.164 31179.48 92 0 -9236.6859 0 -9236.6859 -264.31977 31458.059 Loop time of 0.121404 on 1 procs for 9 steps with 2638 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 = -9234.83833652669 -9236.6825565925 -9236.68585676293 Force two-norm initial, final = 520.79075 9.5573721 Force max component initial, final = 437.87341 7.0547055 Final line search alpha, max atom move = 7.2388070e-05 0.00051067652 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11576 | 0.11576 | 0.11576 | 0.0 | 95.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069266 | 0.00069266 | 0.00069266 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004957 | | | 4.08 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6857.00 ave 6857 max 6857 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: 226152.0 ave 226152 max 226152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226152 Ave neighs/atom = 85.728582 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.706 | 5.706 | 5.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9236.6859 0 -9236.6859 -264.31977 Loop time of 2.297e-06 on 1 procs for 0 steps with 2638 atoms 174.1% 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 | | 2.297e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6832.00 ave 6832 max 6832 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: 225652.0 ave 225652 max 225652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225652 Ave neighs/atom = 85.539045 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 5.706 | 5.706 | 5.706 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 -9236.6859 -9236.6859 46.494902 76.467729 8.8480666 -264.31977 -264.31977 -297.20287 -136.73386 -359.02259 2.2287899 1528.7227 Loop time of 2.842e-06 on 1 procs for 0 steps with 2638 atoms 246.3% 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 | | 2.842e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6832.00 ave 6832 max 6832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112826.0 ave 112826 max 112826 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225652.0 ave 225652 max 225652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225652 Ave neighs/atom = 85.539045 Neighbor list builds = 0 Dangerous builds = 0 2638 -9236.68585676293 eV 2.22878994723887 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02