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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -29.169879 0.0000000) to (25.261857 29.169879 4.9542577) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5341794 4.4876738 4.9542577 Created 311 atoms using lattice units in orthogonal box = (0.0000000 -29.169879 0.0000000) to (25.261857 29.169879 4.9542577) create_atoms CPU = 0.002 seconds 311 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5341794 4.4876738 4.9542577 Created 318 atoms using lattice units in orthogonal box = (0.0000000 -29.169879 0.0000000) to (25.261857 29.169879 4.9542577) create_atoms CPU = 0.002 seconds 318 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 15 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 625 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_820335782779_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.908 | 4.908 | 4.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2541.3117 0 -2541.3117 42585.856 343 0 -2729.7221 0 -2729.7221 -15080.397 Loop time of 7.94717 on 1 procs for 343 steps with 625 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 = -2541.31170888373 -2729.71960578211 -2729.72208132014 Force two-norm initial, final = 232.10930 0.26479272 Force max component initial, final = 97.008283 0.11338924 Final line search alpha, max atom move = 1.0000000 0.11338924 Iterations, force evaluations = 343 650 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7031 | 7.7031 | 7.7031 | 0.0 | 96.93 Neigh | 0.11091 | 0.11091 | 0.11091 | 0.0 | 1.40 Comm | 0.073145 | 0.073145 | 0.073145 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06002 | | | 0.76 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4700.00 ave 4700 max 4700 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: 103582.0 ave 103582 max 103582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103582 Ave neighs/atom = 165.73120 Neighbor list builds = 7 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 343 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 343 0 -2729.7221 0 -2729.7221 -15080.397 7301.4395 365 0 -2732.284 0 -2732.284 -9.0839559 7239.6044 Loop time of 0.306977 on 1 procs for 22 steps with 625 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 = -2729.72208132014 -2732.28158861552 -2732.28397503175 Force two-norm initial, final = 234.84824 3.8562764 Force max component initial, final = 227.43253 1.8930244 Final line search alpha, max atom move = 0.00031470455 0.00059574340 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27909 | 0.27909 | 0.27909 | 0.0 | 90.91 Neigh | 0.016296 | 0.016296 | 0.016296 | 0.0 | 5.31 Comm | 0.0026054 | 0.0026054 | 0.0026054 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00899 | | | 2.93 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4879.00 ave 4879 max 4879 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: 103416.0 ave 103416 max 103416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103416 Ave neighs/atom = 165.46560 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2732.284 0 -2732.284 -9.0839559 Loop time of 6.084e-06 on 1 procs for 0 steps with 625 atoms 180.8% 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 | | 6.084e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4867.00 ave 4867 max 4867 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: 103400.0 ave 103400 max 103400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103400 Ave neighs/atom = 165.44000 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.047 | 5.047 | 5.047 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 -2732.284 -2732.284 25.370708 57.077316 4.9994094 -9.0839559 -9.0839559 -241.77485 409.87426 -195.35129 2.3192301 2935.6759 Loop time of 7.236e-06 on 1 procs for 0 steps with 625 atoms 248.8% 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 | | 7.236e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4867.00 ave 4867 max 4867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51700.0 ave 51700 max 51700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103400.0 ave 103400 max 103400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103400 Ave neighs/atom = 165.44000 Neighbor list builds = 0 Dangerous builds = 0 625 -2732.28397503175 eV 2.3192300806534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08