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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -44.853331 0.0000000) to (31.716095 44.853331 4.9837035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8733508 6.0911931 4.9837035 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -44.853331 0.0000000) to (31.716095 44.853331 4.9837035) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8733508 6.0911931 4.9837035 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -44.853331 0.0000000) to (31.716095 44.853331 4.9837035) create_atoms CPU = 0.004 seconds 650 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 24 2 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1292 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5759.8792 0 -5759.8792 7743.1219 47 0 -5837.4251 0 -5837.4251 861.08216 Loop time of 2.05242 on 1 procs for 47 steps with 1292 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 = -5759.87918212615 -5837.41996456551 -5837.42509670629 Force two-norm initial, final = 49.295222 0.25741661 Force max component initial, final = 11.013365 0.053370880 Final line search alpha, max atom move = 1.0000000 0.053370880 Iterations, force evaluations = 47 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9608 | 1.9608 | 1.9608 | 0.0 | 95.54 Neigh | 0.062441 | 0.062441 | 0.062441 | 0.0 | 3.04 Comm | 0.015533 | 0.015533 | 0.015533 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01361 | | | 0.66 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195.00 ave 8195 max 8195 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: 225392.0 ave 225392 max 225392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225392 Ave neighs/atom = 174.45201 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.470 | 5.470 | 5.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -5837.4251 0 -5837.4251 861.08216 14179.359 49 0 -5837.4419 0 -5837.4419 71.694249 14185.794 Loop time of 0.101851 on 1 procs for 2 steps with 1292 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 = -5837.42509670627 -5837.44039905076 -5837.44189034134 Force two-norm initial, final = 28.956066 1.5718226 Force max component initial, final = 28.656565 1.5036871 Final line search alpha, max atom move = 0.00012879821 0.00019367220 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099109 | 0.099109 | 0.099109 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066846 | 0.00066846 | 0.00066846 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002073 | | | 2.04 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 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: 225332.0 ave 225332 max 225332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225332 Ave neighs/atom = 174.40557 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.608 | 5.608 | 5.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5837.4419 0 -5837.4419 71.694249 Loop time of 6.555e-06 on 1 procs for 0 steps with 1292 atoms 167.8% 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 | | 6.555e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 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: 225316.0 ave 225316 max 225316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225316 Ave neighs/atom = 174.39319 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.608 | 5.608 | 5.608 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 -5837.4419 -5837.4419 31.70613 89.801739 4.9822516 71.694249 71.694249 42.566986 170.00991 2.5058524 2.2966422 475.08884 Loop time of 7.397e-06 on 1 procs for 0 steps with 1292 atoms 256.9% 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 | | 7.397e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8213.00 ave 8213 max 8213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112658.0 ave 112658 max 112658 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225316.0 ave 225316 max 225316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225316 Ave neighs/atom = 174.39319 Neighbor list builds = 0 Dangerous builds = 0 1292 -5837.44189034134 eV 2.29664216589899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02