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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -47.954811 0.0000000) to (29.366204 47.954811 8.8542437) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3393099 5.4494103 5.9028292 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -47.954811 0.0000000) to (29.366204 47.954811 8.8542437) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3393099 5.4494103 5.9028292 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -47.954811 0.0000000) to (29.366204 47.954811 8.8542437) create_atoms CPU = 0.002 seconds 1073 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 35 4 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 2105 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7429.4839 0 -7429.4839 2508.7038 4 0 -7435.3329 0 -7435.3329 1983.6221 Loop time of 0.865428 on 1 procs for 4 steps with 2105 atoms 38.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -7429.48385834826 -7435.33292506188 -7435.33292506188 Force two-norm initial, final = 14.256412 0.84720831 Force max component initial, final = 1.4705265 0.086687653 Final line search alpha, max atom move = 1.4901161e-08 1.2917467e-09 Iterations, force evaluations = 4 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85767 | 0.85767 | 0.85767 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0034812 | 0.0034812 | 0.0034812 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004272 | | | 0.49 Nlocal: 2105.00 ave 2105 max 2105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204.00 ave 5204 max 5204 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: 113404.0 ave 113404 max 113404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113404 Ave neighs/atom = 53.873634 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 35 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 4 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.054 | 5.054 | 5.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 4 0 -7435.3329 0 -7435.3329 1983.6221 24937.991 8 0 -7435.4741 0 -7435.4741 -301.27762 24978.914 Loop time of 0.0897477 on 1 procs for 4 steps with 2105 atoms 38.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7435.33292506189 -7435.4712616572 -7435.47414890443 Force two-norm initial, final = 82.023882 9.7201452 Force max component initial, final = 81.334080 7.6051867 Final line search alpha, max atom move = 7.7077280e-05 0.00058618710 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087426 | 0.087426 | 0.087426 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028442 | 0.00028442 | 0.00028442 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002037 | | | 2.27 Nlocal: 2105.00 ave 2105 max 2105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204.00 ave 5204 max 5204 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: 113404.0 ave 113404 max 113404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113404 Ave neighs/atom = 53.873634 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 35 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 7429.5717 0 7429.5717 -301.27762 Loop time of 2.267e-06 on 1 procs for 0 steps with 2105 atoms 220.6% 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 | | 2.267e-06 | | |100.00 Nlocal: 2105.00 ave 2105 max 2105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204.00 ave 5204 max 5204 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: 113400.0 ave 113400 max 113400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113400 Ave neighs/atom = 53.871734 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 11 35 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.192 | 5.192 | 5.192 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 7429.5717 -7435.4741 29.329911 96.238688 8.8493856 -301.27762 -301.27762 -487.20261 -34.091346 -382.5389 2.3713224 581.90356 Loop time of 2.726e-06 on 1 procs for 0 steps with 2105 atoms 293.5% 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 | | 2.726e-06 | | |100.00 Nlocal: 2105.00 ave 2105 max 2105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5204.00 ave 5204 max 5204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56700.0 ave 56700 max 56700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113400.0 ave 113400 max 113400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113400 Ave neighs/atom = 53.871734 Neighbor list builds = 0 Dangerous builds = 0 2105 7429.57173221897 eV 2.37132239980821 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01