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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -48.884234 0.0000000) to (59.865761 48.884234 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7405524 6.0263247 6.6060342 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -48.884234 0.0000000) to (59.865761 48.884234 9.9090513) create_atoms CPU = 0.002 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7405524 6.0263247 6.6060342 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -48.884234 0.0000000) to (59.865761 48.884234 9.9090513) create_atoms CPU = 0.002 seconds 1757 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 20 32 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 3467 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.243 | 5.243 | 5.243 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11550.716 0 -11550.716 1392.985 58 0 -11612.929 0 -11612.929 -4302.8109 Loop time of 9.38502 on 1 procs for 58 steps with 3467 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11550.7156067988 -11612.9200166743 -11612.928985353 Force two-norm initial, final = 36.611385 0.23022921 Force max component initial, final = 5.3274576 0.065961690 Final line search alpha, max atom move = 1.0000000 0.065961690 Iterations, force evaluations = 58 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3425 | 9.3425 | 9.3425 | 0.0 | 99.55 Neigh | 0.017144 | 0.017144 | 0.017144 | 0.0 | 0.18 Comm | 0.0084919 | 0.0084919 | 0.0084919 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01693 | | | 0.18 Nlocal: 3467.00 ave 3467 max 3467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7178.00 ave 7178 max 7178 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: 188738.0 ave 188738 max 188738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188738 Ave neighs/atom = 54.438419 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 20 32 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -11612.929 0 -11612.929 -4302.8109 57997.516 62 0 -11613.342 0 -11613.342 -485.99798 57689.976 Loop time of 0.633652 on 1 procs for 4 steps with 3467 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 = -11612.928985353 -11613.3421607406 -11613.3422043335 Force two-norm initial, final = 218.93011 0.35781960 Force max component initial, final = 155.94066 0.13247268 Final line search alpha, max atom move = 0.0010790704 0.00014294735 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63007 | 0.63007 | 0.63007 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044001 | 0.00044001 | 0.00044001 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003145 | | | 0.50 Nlocal: 3467.00 ave 3467 max 3467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7496.00 ave 7496 max 7496 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: 188104.0 ave 188104 max 188104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188104 Ave neighs/atom = 54.255552 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.383 | 5.383 | 5.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11613.342 0 -11613.342 -485.99798 Loop time of 2.255e-06 on 1 procs for 0 steps with 3467 atoms 177.4% 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 | | 2.255e-06 | | |100.00 Nlocal: 3467.00 ave 3467 max 3467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7520.00 ave 7520 max 7520 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: 188290.0 ave 188290 max 188290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188290 Ave neighs/atom = 54.309201 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 20 32 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.383 | 5.383 | 5.383 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 -11613.342 -11613.342 59.701732 97.768469 9.8835876 -485.99798 -485.99798 3.668975 -1462.1732 0.51031228 2.4561626 1923.9377 Loop time of 2.442e-06 on 1 procs for 0 steps with 3467 atoms 204.8% 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 | | 2.442e-06 | | |100.00 Nlocal: 3467.00 ave 3467 max 3467 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7520.00 ave 7520 max 7520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94145.0 ave 94145 max 94145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188290.0 ave 188290 max 188290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188290 Ave neighs/atom = 54.309201 Neighbor list builds = 0 Dangerous builds = 0 3467 -11613.3422043335 eV 2.45616262287343 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10