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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -36.757236 0.0000000) to (31.832700 36.757236 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7135615 5.6549593 6.2429061 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -36.757236 0.0000000) to (31.832700 36.757236 6.2429061) create_atoms CPU = 0.003 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7135615 5.6549593 6.2429061 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.757236 0.0000000) to (31.832700 36.757236 6.2429061) create_atoms CPU = 0.002 seconds 630 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1254 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4807.6461 0 -4807.6461 140099.64 91 0 -5304.638 0 -5304.638 13341.277 Loop time of 15.0607 on 1 procs for 91 steps with 1254 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 = -4807.64611788381 -5304.63315267026 -5304.63797991951 Force two-norm initial, final = 1010.1771 0.22520441 Force max component initial, final = 221.43526 0.022864614 Final line search alpha, max atom move = 1.0000000 0.022864614 Iterations, force evaluations = 91 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.992 | 14.992 | 14.992 | 0.0 | 99.55 Neigh | 0.031803 | 0.031803 | 0.031803 | 0.0 | 0.21 Comm | 0.015574 | 0.015574 | 0.015574 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02109 | | | 0.14 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4799.00 ave 4799 max 4799 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: 97556.0 ave 97556 max 97556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97556 Ave neighs/atom = 77.795853 Neighbor list builds = 2 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -5304.638 0 -5304.638 13341.277 14609.425 96 0 -5305.1652 0 -5305.1652 -2.4781861 14729.029 Loop time of 0.771709 on 1 procs for 5 steps with 1254 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 = -5304.63797991952 -5305.16243374633 -5305.16519794473 Force two-norm initial, final = 213.10802 0.52434019 Force max component initial, final = 136.94936 0.36361194 Final line search alpha, max atom move = 7.7834443e-05 2.8301533e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76743 | 0.76743 | 0.76743 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062507 | 0.00062507 | 0.00062507 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003652 | | | 0.47 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4771.00 ave 4771 max 4771 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: 97372.0 ave 97372 max 97372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97372 Ave neighs/atom = 77.649123 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5305.1652 0 -5305.1652 -2.4781861 Loop time of 3.765e-06 on 1 procs for 0 steps with 1254 atoms 159.4% 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 | | 3.765e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4765.00 ave 4765 max 4765 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: 97080.0 ave 97080 max 97080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97080 Ave neighs/atom = 77.416268 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.777 | 4.777 | 4.777 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 -5305.1652 -5305.1652 31.940695 73.789826 6.2493274 -2.4781861 -2.4781861 -39.686724 28.158882 4.0932846 2.2631441 1225.3818 Loop time of 3.937e-06 on 1 procs for 0 steps with 1254 atoms 203.2% 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 | | 3.937e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4765.00 ave 4765 max 4765 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48540.0 ave 48540 max 48540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 97080.0 ave 97080 max 97080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97080 Ave neighs/atom = 77.416268 Neighbor list builds = 0 Dangerous builds = 0 1254 -5305.16519794473 eV 2.26314413263059 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16