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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -57.624884 0.0000000) to (40.746946 57.624884 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0816338 5.5904738 4.9780318 Created 1071 atoms using lattice units in orthogonal box = (0.0000000 -57.624884 0.0000000) to (40.746946 57.624884 4.9780318) create_atoms CPU = 0.006 seconds 1071 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0816338 5.5904738 4.9780318 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -57.624884 0.0000000) to (40.746946 57.624884 4.9780318) create_atoms CPU = 0.003 seconds 1079 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 ghost atom cutoff = 6 binsize = 3, bins = 14 39 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2144 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_937008984446_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 ghost atom cutoff = 6 binsize = 3, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8168.1176 0 -8168.1176 196318.81 79 0 -9519.9 0 -9519.9 4576.2603 Loop time of 11.5309 on 1 procs for 79 steps with 2144 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8168.11757594168 -9519.89192714964 -9519.9000321996 Force two-norm initial, final = 2492.2629 0.26922206 Force max component initial, final = 313.97435 0.067699502 Final line search alpha, max atom move = 1.0000000 0.067699502 Iterations, force evaluations = 79 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.475 | 11.475 | 11.475 | 0.0 | 99.52 Neigh | 0.013989 | 0.013989 | 0.013989 | 0.0 | 0.12 Comm | 0.021169 | 0.021169 | 0.021169 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02029 | | | 0.18 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8419.00 ave 8419 max 8419 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: 167278.0 ave 167278 max 167278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167278 Ave neighs/atom = 78.021455 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -9519.9 0 -9519.9 4576.2603 23377.216 82 0 -9520.0196 0 -9520.0196 -0.4110291 23433.468 Loop time of 0.482699 on 1 procs for 3 steps with 2144 atoms 96.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9519.90003219957 -9520.01674501923 -9520.01960419503 Force two-norm initial, final = 127.87035 1.4670054 Force max component initial, final = 108.26616 1.1646540 Final line search alpha, max atom move = 5.7768270e-05 6.7280048e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4798 | 0.4798 | 0.4798 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049075 | 0.00049075 | 0.00049075 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002405 | | | 0.50 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8552.00 ave 8552 max 8552 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: 167456.0 ave 167456 max 167456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167456 Ave neighs/atom = 78.104478 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 ghost atom cutoff = 6 binsize = 3, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.361 | 5.361 | 5.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9520.0196 0 -9520.0196 -0.4110291 Loop time of 2.425e-06 on 1 procs for 0 steps with 2144 atoms 164.9% 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 | | 2.425e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8552.00 ave 8552 max 8552 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: 167344.0 ave 167344 max 167344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167344 Ave neighs/atom = 78.052239 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 ghost atom cutoff = 6 binsize = 3, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.361 | 5.361 | 5.361 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 -9520.0196 -9520.0196 40.823945 115.32624 4.977296 -0.4110291 -0.4110291 -34.497503 79.681736 -46.417321 2.3445051 1004.6001 Loop time of 2.72e-06 on 1 procs for 0 steps with 2144 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 | | 2.72e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8552.00 ave 8552 max 8552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83672.0 ave 83672 max 83672 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 167344.0 ave 167344 max 167344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167344 Ave neighs/atom = 78.052239 Neighbor list builds = 0 Dangerous builds = 0 2144 -9520.01960419503 eV 2.34450512445105 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12