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 = 2.8436425 2.8436425 2.8436425 Created orthogonal box = (0.0000000 -49.253333 0.0000000) to (20.107589 49.253333 6.9654732) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8258214 4.2686222 4.6436488 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -49.253333 0.0000000) to (20.107589 49.253333 6.9654732) create_atoms CPU = 0.003 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8258214 4.2686222 4.6436488 Created 602 atoms using lattice units in orthogonal box = (0.0000000 -49.253333 0.0000000) to (20.107589 49.253333 6.9654732) create_atoms CPU = 0.003 seconds 602 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 25 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1202 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_044341472608_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4617.1868 0 -4617.1868 67434.694 107 0 -4825.1386 0 -4825.1386 7176.7356 Loop time of 4.46858 on 1 procs for 107 steps with 1202 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4617.18679990656 -4825.13422983821 -4825.13861740886 Force two-norm initial, final = 222.94793 0.22879957 Force max component initial, final = 51.477963 0.036987704 Final line search alpha, max atom move = 1.0000000 0.036987704 Iterations, force evaluations = 107 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3451 | 4.3451 | 4.3451 | 0.0 | 97.24 Neigh | 0.05639 | 0.05639 | 0.05639 | 0.0 | 1.26 Comm | 0.036238 | 0.036238 | 0.036238 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03081 | | | 0.69 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7133.00 ave 7133 max 7133 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: 204532.0 ave 204532 max 204532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204532 Ave neighs/atom = 170.15973 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.497 | 5.497 | 5.497 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -4825.1386 0 -4825.1386 7176.7356 13796.733 111 0 -4825.3114 0 -4825.3114 400.67236 13847.781 Loop time of 0.130844 on 1 procs for 4 steps with 1202 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 = -4825.13861740886 -4825.30846062174 -4825.31140460842 Force two-norm initial, final = 114.35620 7.2176325 Force max component initial, final = 94.247608 6.7170319 Final line search alpha, max atom move = 0.00011928905 0.00080126834 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12676 | 0.12676 | 0.12676 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097047 | 0.00097047 | 0.00097047 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003111 | | | 2.38 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7125.00 ave 7125 max 7125 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: 204376.0 ave 204376 max 204376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204376 Ave neighs/atom = 170.02995 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4825.3114 0 -4825.3114 400.67236 Loop time of 6.836e-06 on 1 procs for 0 steps with 1202 atoms 160.9% 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 | | 6.836e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7125.00 ave 7125 max 7125 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: 204032.0 ave 204032 max 204032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204032 Ave neighs/atom = 169.74376 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.635 | 5.635 | 5.635 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 -4825.3114 -4825.3114 20.109746 98.818837 6.9684126 400.67236 400.67236 241.09018 779.61772 181.30917 2.2547393 792.82928 Loop time of 6.976e-06 on 1 procs for 0 steps with 1202 atoms 243.7% 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 | | 6.976e-06 | | |100.00 Nlocal: 1202.00 ave 1202 max 1202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7125.00 ave 7125 max 7125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102016.0 ave 102016 max 102016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 204032.0 ave 204032 max 204032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204032 Ave neighs/atom = 169.74376 Neighbor list builds = 0 Dangerous builds = 0 1202 -4825.31140460842 eV 2.25473925859819 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05