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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -43.058264 0.0000000) to (52.735388 43.058264 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0269015 5.5360625 5.9426050 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -43.058264 0.0000000) to (52.735388 43.058264 8.9139075) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0269015 5.5360625 5.9426050 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -43.058264 0.0000000) to (52.735388 43.058264 8.9139075) create_atoms CPU = 0.002 seconds 1685 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 = 14 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3346 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_945691923444_005#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 = 14 22 3 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) = 6.981 | 6.981 | 6.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10335.621 0 -10335.621 69974.248 73 0 -10932.862 0 -10932.862 637.77504 Loop time of 3.28634 on 1 procs for 73 steps with 3346 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 = -10335.6207568435 -10932.8515530581 -10932.8615672229 Force two-norm initial, final = 659.31968 0.26624153 Force max component initial, final = 94.740325 0.016139669 Final line search alpha, max atom move = 1.0000000 0.016139669 Iterations, force evaluations = 73 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1088 | 3.1088 | 3.1088 | 0.0 | 94.60 Neigh | 0.14441 | 0.14441 | 0.14441 | 0.0 | 4.39 Comm | 0.013669 | 0.013669 | 0.013669 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01945 | | | 0.59 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10848.0 ave 10848 max 10848 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: 586864.0 ave 586864 max 586864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586864 Ave neighs/atom = 175.39271 Neighbor list builds = 4 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 = 14 22 3 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.980 | 6.980 | 6.980 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -10932.862 0 -10932.862 637.77504 40481.517 75 0 -10932.901 0 -10932.901 108.9313 40496.262 Loop time of 0.11182 on 1 procs for 2 steps with 3346 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 = -10932.8615672229 -10932.8913802672 -10932.9011112804 Force two-norm initial, final = 55.642036 5.8089378 Force max component initial, final = 55.131094 5.0007016 Final line search alpha, max atom move = 3.7380494e-05 0.00018692869 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10964 | 0.10964 | 0.10964 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033067 | 0.00033067 | 0.00033067 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001851 | | | 1.66 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10870.0 ave 10870 max 10870 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: 586684.0 ave 586684 max 586684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586684 Ave neighs/atom = 175.33891 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 = 14 22 3 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) = 7.118 | 7.118 | 7.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10932.901 0 -10932.901 108.9313 Loop time of 2.015e-06 on 1 procs for 0 steps with 3346 atoms 198.5% 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 | | 2.015e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10880.0 ave 10880 max 10880 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: 586570.0 ave 586570 max 586570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586570 Ave neighs/atom = 175.30484 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 = 14 22 3 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) = 7.118 | 7.118 | 7.118 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 -10932.901 -10932.901 52.706107 86.226911 8.9106867 108.9313 108.9313 115.61283 198.09918 13.081884 2.1836629 1868.8253 Loop time of 1.951e-06 on 1 procs for 0 steps with 3346 atoms 256.3% 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 | | 1.951e-06 | | |100.00 Nlocal: 3346.00 ave 3346 max 3346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10880.0 ave 10880 max 10880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 293285.0 ave 293285 max 293285 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 586570.0 ave 586570 max 586570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586570 Ave neighs/atom = 175.30484 Neighbor list builds = 0 Dangerous builds = 0 3346 -10932.9011112804 eV 2.18366286206241 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04