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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -37.117092 0.0000000) to (21.429563 37.117092 4.9599800) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5920492 4.4187014 4.9599800 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -37.117092 0.0000000) to (21.429563 37.117092 4.9599800) create_atoms CPU = 0.001 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5920492 4.4187014 4.9599800 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.117092 0.0000000) to (21.429563 37.117092 4.9599800) create_atoms CPU = 0.001 seconds 339 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 672 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_924736622203_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2821.0972 0 -2821.0972 28295.89 46 0 -2868.6595 0 -2868.6595 7308.613 Loop time of 5.21392 on 1 procs for 46 steps with 672 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 = -2821.09724773609 -2868.65724265187 -2868.65945241135 Force two-norm initial, final = 71.357536 0.14517971 Force max component initial, final = 16.119772 0.029079465 Final line search alpha, max atom move = 1.0000000 0.029079465 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2034 | 5.2034 | 5.2034 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0055955 | 0.0055955 | 0.0055955 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004934 | | | 0.09 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3968.00 ave 3968 max 3968 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: 74314.0 ave 74314 max 74314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74314 Ave neighs/atom = 110.58631 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -2868.6595 0 -2868.6595 7308.613 7890.3666 49 0 -2868.747 0 -2868.747 150.74429 7923.0332 Loop time of 0.290323 on 1 procs for 3 steps with 672 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 = -2868.65945241135 -2868.74413699724 -2868.74697323304 Force two-norm initial, final = 64.084850 1.3207245 Force max component initial, final = 45.994087 0.93491099 Final line search alpha, max atom move = 0.00016433751 0.00015364095 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28917 | 0.28917 | 0.28917 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019395 | 0.00019395 | 0.00019395 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009548 | | | 0.33 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3962.00 ave 3962 max 3962 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: 73082.0 ave 73082 max 73082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73082 Ave neighs/atom = 108.75298 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.659 | 4.659 | 4.659 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2868.747 0 -2868.747 150.74429 Loop time of 2.561e-06 on 1 procs for 0 steps with 672 atoms 195.2% 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 | | 2.561e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3962.00 ave 3962 max 3962 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: 72986.0 ave 72986 max 72986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72986 Ave neighs/atom = 108.61012 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.659 | 4.659 | 4.659 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 -2868.747 -2868.747 21.43451 74.416119 4.9671914 150.74429 150.74429 127.76223 189.51877 134.95189 2.3287878 486.7479 Loop time of 2.17e-06 on 1 procs for 0 steps with 672 atoms 230.4% 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 | | 2.17e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3962.00 ave 3962 max 3962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36493.0 ave 36493 max 36493 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72986.0 ave 72986 max 72986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72986 Ave neighs/atom = 108.61012 Neighbor list builds = 0 Dangerous builds = 0 672 -2868.74697323304 eV 2.32878784732596 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05