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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8982931 5.0975504 4.9479041 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8982931 5.0975504 4.9479041 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -52.832658 0.0000000) to (37.355857 52.832658 4.9479041) create_atoms CPU = 0.002 seconds 916 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1808 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.979 | 5.979 | 5.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7381.5778 0 -7381.5778 9363.1094 31 0 -7423.8277 0 -7423.8277 -6108.2128 Loop time of 0.824707 on 1 procs for 31 steps with 1808 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 = -7381.57778232415 -7423.82122647083 -7423.82774714914 Force two-norm initial, final = 73.817914 0.28214696 Force max component initial, final = 16.618619 0.031311330 Final line search alpha, max atom move = 1.0000000 0.031311330 Iterations, force evaluations = 31 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81543 | 0.81543 | 0.81543 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004838 | 0.004838 | 0.004838 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004438 | | | 0.54 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10467.0 ave 10467 max 10467 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: 315096.0 ave 315096 max 315096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315096 Ave neighs/atom = 174.27876 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.983 | 5.983 | 5.983 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -7423.8277 0 -7423.8277 -6108.2128 19530.458 34 0 -7423.9102 0 -7423.9102 -2818.6921 19472.13 Loop time of 0.0780619 on 1 procs for 3 steps with 1808 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 = -7423.82774714913 -7423.90930675427 -7423.91015235258 Force two-norm initial, final = 69.896101 0.67998585 Force max component initial, final = 64.174497 0.59759168 Final line search alpha, max atom move = 0.00014820337 8.8565102e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076031 | 0.076031 | 0.076031 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039223 | 0.00039223 | 0.00039223 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001638 | | | 2.10 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10534.0 ave 10534 max 10534 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: 315624.0 ave 315624 max 315624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315624 Ave neighs/atom = 174.57080 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.120 | 6.120 | 6.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7423.9102 0 -7423.9102 -2818.6921 Loop time of 1.868e-06 on 1 procs for 0 steps with 1808 atoms 160.6% 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 | | 1.868e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10534.0 ave 10534 max 10534 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: 315728.0 ave 315728 max 315728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315728 Ave neighs/atom = 174.62832 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.120 | 6.120 | 6.120 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 -7423.9102 -7423.9102 37.328098 105.66532 4.9367955 -2818.6921 -2818.6921 49.133603 -8509.3869 4.1768693 2.3340704 551.614 Loop time of 2.172e-06 on 1 procs for 0 steps with 1808 atoms 230.2% 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 | | 2.172e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10534.0 ave 10534 max 10534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157864.0 ave 157864 max 157864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 315728.0 ave 315728 max 315728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315728 Ave neighs/atom = 174.62832 Neighbor list builds = 0 Dangerous builds = 0 1808 -7423.91015235258 eV 2.33407040830859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01