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 -40.686235 0.0000000) to (19.932103 40.686235 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3152275 4.8823482 5.9426050 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -40.686235 0.0000000) to (19.932103 40.686235 8.9139075) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3152275 4.8823482 5.9426050 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -40.686235 0.0000000) to (19.932103 40.686235 8.9139075) create_atoms CPU = 0.001 seconds 612 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 = 5 21 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 12 atoms, new total = 1200 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 = 5 21 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3871.5806 0 -3871.5806 28850.349 27 0 -3917.3186 0 -3917.3186 6230.4302 Loop time of 0.530301 on 1 procs for 27 steps with 1200 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 = -3871.58064620457 -3917.3148315284 -3917.31857732881 Force two-norm initial, final = 108.01422 0.15905461 Force max component initial, final = 14.623744 0.0081525072 Final line search alpha, max atom move = 1.0000000 0.0081525072 Iterations, force evaluations = 27 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52514 | 0.52514 | 0.52514 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024578 | 0.0024578 | 0.0024578 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002705 | | | 0.51 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6082.00 ave 6082 max 6082 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: 211128.0 ave 211128 max 211128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211128 Ave neighs/atom = 175.94000 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 21 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -3917.3186 0 -3917.3186 6230.4302 14457.685 32 0 -3917.5124 0 -3917.5124 -150.47149 14520.567 Loop time of 0.0735716 on 1 procs for 5 steps with 1200 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 = -3917.3185773288 -3917.51078045472 -3917.51238199593 Force two-norm initial, final = 105.64353 3.7107289 Force max component initial, final = 88.478431 3.6384350 Final line search alpha, max atom move = 0.00010408807 0.00037871769 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071596 | 0.071596 | 0.071596 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032362 | 0.00032362 | 0.00032362 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001652 | | | 2.25 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6082.00 ave 6082 max 6082 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: 210480.0 ave 210480 max 210480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210480 Ave neighs/atom = 175.40000 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 = 5 21 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) = 5.600 | 5.600 | 5.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3917.5124 0 -3917.5124 -150.47149 Loop time of 1.579e-06 on 1 procs for 0 steps with 1200 atoms 190.0% 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 | | 1.579e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6082.00 ave 6082 max 6082 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: 210456.0 ave 210456 max 210456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210456 Ave neighs/atom = 175.38000 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 = 5 21 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) = 5.600 | 5.600 | 5.600 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 -3917.5124 -3917.5124 19.939789 81.725501 8.9105685 -150.47149 -150.47149 -401.614 22.610988 -72.41146 2.3313336 620.11713 Loop time of 1.926e-06 on 1 procs for 0 steps with 1200 atoms 259.6% 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 | | 1.926e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6082.00 ave 6082 max 6082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105228.0 ave 105228 max 105228 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 210456.0 ave 210456 max 210456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 210456 Ave neighs/atom = 175.38000 Neighbor list builds = 0 Dangerous builds = 0 1200 -3917.51238199593 eV 2.33133359038896 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00