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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -50.867583 0.0000000) to (11.989604 50.867583 5.1123844) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498201 6.1657676 5.1123844 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -50.867583 0.0000000) to (11.989604 50.867583 5.1123844) create_atoms CPU = 0.003 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498201 6.1657676 5.1123844 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.867583 0.0000000) to (11.989604 50.867583 5.1123844) create_atoms CPU = 0.003 seconds 266 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.944 | 4.944 | 4.944 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1814.2082 0 -1814.2082 24748.708 75 0 -1863.5212 0 -1863.5212 5360.5071 Loop time of 2.01413 on 1 procs for 75 steps with 528 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 = -1814.20821818518 -1863.51947037307 -1863.52122837232 Force two-norm initial, final = 97.244573 0.12643859 Force max component initial, final = 30.305760 0.027432639 Final line search alpha, max atom move = 1.0000000 0.027432639 Iterations, force evaluations = 75 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9634 | 1.9634 | 1.9634 | 0.0 | 97.48 Neigh | 0.016479 | 0.016479 | 0.016479 | 0.0 | 0.82 Comm | 0.020627 | 0.020627 | 0.020627 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01359 | | | 0.67 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6015.00 ave 6015 max 6015 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: 109692.0 ave 109692 max 109692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109692 Ave neighs/atom = 207.75000 Neighbor list builds = 1 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.944 | 4.944 | 4.944 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -1863.5212 0 -1863.5212 5360.5071 6235.9043 80 0 -1863.5999 0 -1863.5999 -45.071964 6260.1471 Loop time of 0.107705 on 1 procs for 5 steps with 528 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 = -1863.52122837233 -1863.59944139123 -1863.5999212971 Force two-norm initial, final = 41.891112 0.59240881 Force max component initial, final = 38.117675 0.39272476 Final line search alpha, max atom move = 0.00061249639 0.00024054250 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10363 | 0.10363 | 0.10363 | 0.0 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095006 | 0.00095006 | 0.00095006 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003128 | | | 2.90 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6069.00 ave 6069 max 6069 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: 108924.0 ave 108924 max 108924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108924 Ave neighs/atom = 206.29545 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.082 | 5.082 | 5.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1863.5999 0 -1863.5999 -45.071964 Loop time of 6.716e-06 on 1 procs for 0 steps with 528 atoms 163.8% 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 | | 6.716e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6069.00 ave 6069 max 6069 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: 106836.0 ave 106836 max 106836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106836 Ave neighs/atom = 202.34091 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.082 | 5.082 | 5.082 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 -1863.5999 -1863.5999 11.985751 102.17688 5.1117153 -45.071964 -45.071964 -100.47881 -89.667947 54.930866 2.3550589 261.90363 Loop time of 8.771e-06 on 1 procs for 0 steps with 528 atoms 216.6% 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 | | 8.771e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6069.00 ave 6069 max 6069 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53418.0 ave 53418 max 53418 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106836.0 ave 106836 max 106836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106836 Ave neighs/atom = 202.34091 Neighbor list builds = 0 Dangerous builds = 0 528 -1863.5999212971 eV 2.35505887633528 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02