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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -58.256182 0.0000000) to (20.596671 58.256182 4.4419922) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2689157 5.4191797 4.4419922 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -58.256182 0.0000000) to (20.596671 58.256182 4.4419922) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2689157 5.4191797 4.4419922 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -58.256182 0.0000000) to (20.596671 58.256182 4.4419922) create_atoms CPU = 0.001 seconds 345 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 4 21 1 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 688 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.418 | 5.418 | 5.418 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3846.4677 0 -3846.4677 149903.26 211 0 -4663.4641 0 -4663.4641 4996.8426 Loop time of 5.59307 on 1 procs for 211 steps with 688 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 = -3846.46771683051 -4663.45973423137 -4663.46407624123 Force two-norm initial, final = 1741.8741 0.37851088 Force max component initial, final = 664.63140 0.029945169 Final line search alpha, max atom move = 1.0000000 0.029945169 Iterations, force evaluations = 211 380 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3932 | 5.3932 | 5.3932 | 0.0 | 96.43 Neigh | 0.13887 | 0.13887 | 0.13887 | 0.0 | 2.48 Comm | 0.040661 | 0.040661 | 0.040661 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02033 | | | 0.36 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9800.00 ave 9800 max 9800 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: 283130.0 ave 283130 max 283130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283130 Ave neighs/atom = 411.52616 Neighbor list builds = 9 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 211 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.418 | 5.418 | 5.418 Mbytes Step Temp E_pair E_mol TotEng Press Volume 211 0 -4663.4641 0 -4663.4641 4996.8426 10659.745 236 0 -4677.2372 0 -4677.2372 -69.986519 10658.81 Loop time of 0.415716 on 1 procs for 25 steps with 688 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 = -4663.4640762412 -4677.2356334961 -4677.23721089072 Force two-norm initial, final = 909.30790 4.6109817 Force max component initial, final = 767.93717 2.1154476 Final line search alpha, max atom move = 0.00018737198 0.00039637560 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40354 | 0.40354 | 0.40354 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021882 | 0.0021882 | 0.0021882 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009992 | | | 2.40 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9800.00 ave 9800 max 9800 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: 280454.0 ave 280454 max 280454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280454 Ave neighs/atom = 407.63663 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.556 | 5.556 | 5.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4677.2372 0 -4677.2372 -69.986519 Loop time of 3.943e-06 on 1 procs for 0 steps with 688 atoms 126.8% 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 | | 3.943e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9872.00 ave 9872 max 9872 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: 284488.0 ave 284488 max 284488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284488 Ave neighs/atom = 413.50000 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.556 | 5.556 | 5.556 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 -4677.2372 -4677.2372 20.268054 115.59021 4.5496251 -69.986519 -69.986519 123.89352 -8.1650942 -325.68799 2.5506346 5505.9157 Loop time of 2.602e-06 on 1 procs for 0 steps with 688 atoms 230.6% 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 | | 2.602e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9872.00 ave 9872 max 9872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 142244.0 ave 142244 max 142244 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 284488.0 ave 284488 max 284488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 284488 Ave neighs/atom = 413.50000 Neighbor list builds = 0 Dangerous builds = 0 688 -4677.23721089072 eV 2.55063456601821 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06