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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8671916 4.8671916 3.5673230 Created 519 atoms using lattice units in orthogonal box = (0.0000000 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) create_atoms CPU = 0.001 seconds 519 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8671916 4.8671916 3.5673230 Created 521 atoms using lattice units in orthogonal box = (0.0000000 -57.521355 0.0000000) to (28.760677 57.521355 3.5673230) create_atoms CPU = 0.001 seconds 521 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1036 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3992.1173 0 -3992.1173 54621.282 95 0 -4360.8945 0 -4360.8945 26615.222 Loop time of 4.81644 on 1 procs for 95 steps with 1036 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 = -3992.11731781235 -4360.89096957734 -4360.89452405959 Force two-norm initial, final = 712.10500 0.24142609 Force max component initial, final = 242.76104 0.047157322 Final line search alpha, max atom move = 1.0000000 0.047157322 Iterations, force evaluations = 95 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7929 | 4.7929 | 4.7929 | 0.0 | 99.51 Neigh | 0.0047507 | 0.0047507 | 0.0047507 | 0.0 | 0.10 Comm | 0.0095838 | 0.0095838 | 0.0095838 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009187 | | | 0.19 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5260.00 ave 5260 max 5260 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: 57868.0 ave 57868 max 57868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57868 Ave neighs/atom = 55.857143 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -4360.8945 0 -4360.8945 26615.222 11803.224 135 0 -4365.5531 0 -4365.5531 640.04077 12240.015 Loop time of 1.07392 on 1 procs for 40 steps with 1036 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 = -4360.89452405959 -4365.55002111479 -4365.55305475187 Force two-norm initial, final = 386.59027 9.1449588 Force max component initial, final = 277.16623 5.4194277 Final line search alpha, max atom move = 0.00010092752 0.00054696937 Iterations, force evaluations = 40 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.048 | 1.048 | 1.048 | 0.0 | 97.59 Neigh | 0.014277 | 0.014277 | 0.014277 | 0.0 | 1.33 Comm | 0.0021499 | 0.0021499 | 0.0021499 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009459 | | | 0.88 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5212.00 ave 5212 max 5212 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: 63956.0 ave 63956 max 63956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63956 Ave neighs/atom = 61.733591 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.732 | 4.732 | 4.732 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4365.5531 0 -4365.5531 640.04077 Loop time of 1.61e-06 on 1 procs for 0 steps with 1036 atoms 186.3% 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 | | 1.61e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5212.00 ave 5212 max 5212 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: 64146.0 ave 64146 max 64146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64146 Ave neighs/atom = 61.916988 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.732 | 4.732 | 4.732 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 -4365.5531 -4365.5531 29.578148 118.12528 3.5032258 640.04077 640.04077 586.27378 728.39267 605.45585 2.3114205 449.24076 Loop time of 2.65e-06 on 1 procs for 0 steps with 1036 atoms 226.4% 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 | | 2.65e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5212.00 ave 5212 max 5212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32073.0 ave 32073 max 32073 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64146.0 ave 64146 max 64146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64146 Ave neighs/atom = 61.916988 Neighbor list builds = 0 Dangerous builds = 0 1036 -4365.55305475186 eV 2.31142049403739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06