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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -42.381122 0.0000000) to (34.601703 42.381122 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763329 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.381122 0.0000000) to (34.601703 42.381122 7.0144993) create_atoms CPU = 0.004 seconds 877 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763329 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.381122 0.0000000) to (34.601703 42.381122 7.0144993) create_atoms CPU = 0.003 seconds 877 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 = 13 31 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1748 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_058735400462_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 = 13 31 3 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) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7317.9459 0 -7317.9459 25429.92 25 0 -7460.323 0 -7460.323 3593.6185 Loop time of 3.66924 on 1 procs for 25 steps with 1748 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7317.94591015599 -7460.31626504858 -7460.32304671266 Force two-norm initial, final = 156.31649 0.28384365 Force max component initial, final = 27.964659 0.038942024 Final line search alpha, max atom move = 1.0000000 0.038942024 Iterations, force evaluations = 25 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6353 | 3.6353 | 3.6353 | 0.0 | 99.07 Neigh | 0.020871 | 0.020871 | 0.020871 | 0.0 | 0.57 Comm | 0.0050587 | 0.0050587 | 0.0050587 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008042 | | | 0.22 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5220.00 ave 5220 max 5220 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: 101732.0 ave 101732 max 101732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101732 Ave neighs/atom = 58.199085 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 = 13 31 3 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -7460.323 0 -7460.323 3593.6185 20572.951 26 0 -7460.3287 0 -7460.3287 4625.6244 20560.686 Loop time of 0.260591 on 1 procs for 1 steps with 1748 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7460.32304671267 -7460.32304671267 -7460.32874330227 Force two-norm initial, final = 22.606503 6.0533193 Force max component initial, final = 22.108862 5.9049349 Final line search alpha, max atom move = 4.5230732e-05 0.00026708453 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.259 | 0.259 | 0.259 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034962 | 0.00034962 | 0.00034962 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001241 | | | 0.48 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5220.00 ave 5220 max 5220 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: 101690.0 ave 101690 max 101690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101690 Ave neighs/atom = 58.175057 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 = 13 31 3 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) = 5.193 | 5.193 | 5.193 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7460.3287 0 -7460.3287 4625.6244 Loop time of 6.295e-06 on 1 procs for 0 steps with 1748 atoms 174.7% 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 | | 6.295e-06 | | |100.00 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5220.00 ave 5220 max 5220 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: 101692.0 ave 101692 max 101692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101692 Ave neighs/atom = 58.176201 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 = 13 31 3 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) = 5.193 | 5.193 | 5.193 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 -7460.3287 -7460.3287 34.598081 84.762245 7.0110512 4625.6244 4625.6244 460.08959 13518.114 -101.33073 2.263823 1167.9267 Loop time of 6.566e-06 on 1 procs for 0 steps with 1748 atoms 304.6% 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 | | 6.566e-06 | | |100.00 Nlocal: 1748.00 ave 1748 max 1748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5220.00 ave 5220 max 5220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50846.0 ave 50846 max 50846 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101692.0 ave 101692 max 101692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101692 Ave neighs/atom = 58.176201 Neighbor list builds = 0 Dangerous builds = 0 1748 -7460.32874330227 eV 2.26382302663272 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04