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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -37.761078 0.0000000) to (5.3397869 37.761078 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3397869 5.0343993 4.3599177 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -37.761078 0.0000000) to (5.3397869 37.761078 4.3599177) create_atoms CPU = 0.001 seconds 62 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3397869 5.0343993 4.3599177 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -37.761078 0.0000000) to (5.3397869 37.761078 4.3599177) create_atoms CPU = 0.000 seconds 62 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 120 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.786 | 4.786 | 4.786 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -777.48195 0 -777.48195 2300.3544 80 0 -780.9465 0 -780.9465 -2195.0094 Loop time of 4.63702 on 1 procs for 80 steps with 120 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 = -777.481949777812 -780.94585911385 -780.946496286434 Force two-norm initial, final = 4.1919788 0.10845457 Force max component initial, final = 1.4389465 0.025597247 Final line search alpha, max atom move = 0.99035205 0.025350286 Iterations, force evaluations = 80 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6329 | 4.6329 | 4.6329 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026238 | 0.0026238 | 0.0026238 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001535 | | | 0.03 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2224.00 ave 2224 max 2224 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: 7768.00 ave 7768 max 7768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7768 Ave neighs/atom = 64.733333 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.785 | 4.785 | 4.785 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -780.9465 0 -780.9465 -2195.0094 1758.2337 85 0 -780.98676 0 -780.98676 -2074.3606 1758.0885 Loop time of 0.236956 on 1 procs for 5 steps with 120 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 = -780.946496286433 -780.986570314982 -780.98675633752 Force two-norm initial, final = 16.304024 1.4065974 Force max component initial, final = 11.595597 1.1017442 Final line search alpha, max atom move = 0.030620336 0.033735778 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23639 | 0.23639 | 0.23639 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012132 | 0.00012132 | 0.00012132 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000448 | | | 0.19 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2120.00 ave 2120 max 2120 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: 8536.00 ave 8536 max 8536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8536 Ave neighs/atom = 71.133333 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.923 | 4.923 | 4.923 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -780.98676 0 -780.98676 -2074.3606 Loop time of 1.41e-06 on 1 procs for 0 steps with 120 atoms 141.8% 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 | | 1.41e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2120.00 ave 2120 max 2120 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: 8560.00 ave 8560 max 8560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8560 Ave neighs/atom = 71.333333 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 2 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.923 | 4.923 | 4.923 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 -780.98676 -780.98676 5.3584147 75.522156 4.3444022 -2074.3606 -2074.3606 -1007.5412 -4448.7096 -766.83087 2.6650002 191.36684 Loop time of 1.403e-06 on 1 procs for 0 steps with 120 atoms 142.6% 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 | | 1.403e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2120.00 ave 2120 max 2120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4280.00 ave 4280 max 4280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8560.00 ave 8560 max 8560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8560 Ave neighs/atom = 71.333333 Neighbor list builds = 0 Dangerous builds = 0 120 -780.98675633752 eV 2.66500019790994 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05