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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -62.280835 0.0000000) to (31.140417 62.280835 3.6200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0497974 5.0497974 3.6200000 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.280835 0.0000000) to (31.140417 62.280835 3.6200000) create_atoms CPU = 0.003 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0497974 5.0497974 3.6200000 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.280835 0.0000000) to (31.140417 62.280835 3.6200000) create_atoms CPU = 0.002 seconds 594 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 ghost atom cutoff = 6 binsize = 3, 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_313717476091_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3781.0341 0 -3781.0341 85257.606 30 0 -4186.7035 0 -4186.7035 4517.1037 Loop time of 2.8992 on 1 procs for 30 steps with 1186 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 = -3781.03413940998 -4186.701958226 -4186.70354388787 Force two-norm initial, final = 1201.3114 1.4478031 Force max component initial, final = 567.46774 0.56098577 Final line search alpha, max atom move = 0.64660735 0.36273752 Iterations, force evaluations = 30 59 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8824 | 2.8824 | 2.8824 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0085096 | 0.0085096 | 0.0085096 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008277 | | | 0.29 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6018.00 ave 6018 max 6018 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: 92500.0 ave 92500 max 92500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92500 Ave neighs/atom = 77.993255 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -4186.7035 0 -4186.7035 4517.1037 14041.626 34 0 -4186.8399 0 -4186.8399 322.83903 14084.499 Loop time of 0.292825 on 1 procs for 4 steps with 1186 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 = -4186.70354388787 -4186.83649259671 -4186.8399089621 Force two-norm initial, final = 81.460543 5.4187938 Force max component initial, final = 71.163077 4.2879572 Final line search alpha, max atom move = 0.00011201056 0.00048029649 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28926 | 0.28926 | 0.28926 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080415 | 0.00080415 | 0.00080415 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002761 | | | 0.94 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6018.00 ave 6018 max 6018 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: 92012.0 ave 92012 max 92012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92012 Ave neighs/atom = 77.581788 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.768 | 4.768 | 4.768 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4186.8399 0 -4186.8399 322.83903 Loop time of 6.856e-06 on 1 procs for 0 steps with 1186 atoms 189.6% 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 | | 6.856e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6018.00 ave 6018 max 6018 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: 92012.0 ave 92012 max 92012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92012 Ave neighs/atom = 77.581788 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.768 | 4.768 | 4.768 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 -4186.8399 -4186.8399 31.104873 124.97161 3.6232777 322.83903 322.83903 191.5507 489.38013 287.58627 2.2868763 317.90349 Loop time of 7.306e-06 on 1 procs for 0 steps with 1186 atoms 273.7% 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 | | 7.306e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6018.00 ave 6018 max 6018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46006.0 ave 46006 max 46006 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92012.0 ave 92012 max 92012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92012 Ave neighs/atom = 77.581788 Neighbor list builds = 0 Dangerous builds = 0 1186 -4186.8399089621 eV 2.28687633866319 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03