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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0731418 5.9047447 4.9780318 Created 686 atoms using lattice units in orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) create_atoms CPU = 0.005 seconds 686 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0731418 5.9047447 4.9780318 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.164368 0.0000000) to (32.643137 46.164368 4.9780318) create_atoms CPU = 0.005 seconds 694 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 22 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1376 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.914 | 5.914 | 5.914 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6034.6307 0 -6034.6307 5068.539 57 0 -6101.7065 0 -6101.7065 5703.414 Loop time of 4.96661 on 1 procs for 57 steps with 1376 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 = -6034.63066153928 -6101.70115970894 -6101.70651083049 Force two-norm initial, final = 27.929974 0.25351154 Force max component initial, final = 4.5400060 0.035791663 Final line search alpha, max atom move = 1.0000000 0.035791663 Iterations, force evaluations = 57 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8778 | 4.8778 | 4.8778 | 0.0 | 98.21 Neigh | 0.045714 | 0.045714 | 0.045714 | 0.0 | 0.92 Comm | 0.024575 | 0.024575 | 0.024575 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01857 | | | 0.37 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9937.00 ave 9937 max 9937 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: 340384.0 ave 340384 max 340384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340384 Ave neighs/atom = 247.37209 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.914 | 5.914 | 5.914 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -6101.7065 0 -6101.7065 5703.414 15003.288 60 0 -6101.8073 0 -6101.8073 1.3046168 15051.602 Loop time of 0.274069 on 1 procs for 3 steps with 1376 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 = -6101.70651083049 -6101.8050824553 -6101.80727480187 Force two-norm initial, final = 95.916277 0.94221576 Force max component initial, final = 73.712983 0.64960176 Final line search alpha, max atom move = 0.00014049426 9.1265318e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26902 | 0.26902 | 0.26902 | 0.0 | 98.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012143 | 0.0012143 | 0.0012143 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00383 | | | 1.40 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9937.00 ave 9937 max 9937 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: 342292.0 ave 342292 max 342292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342292 Ave neighs/atom = 248.75872 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.052 | 6.052 | 6.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6101.8073 0 -6101.8073 1.3046168 Loop time of 6.485e-06 on 1 procs for 0 steps with 1376 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9928.00 ave 9928 max 9928 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: 341900.0 ave 341900 max 341900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341900 Ave neighs/atom = 248.47384 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.052 | 6.052 | 6.052 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 -6101.8073 -6101.8073 32.658911 92.517097 4.9814873 1.3046168 1.3046168 66.539332 6.5697549 -69.195236 2.2918023 929.84217 Loop time of 7.287e-06 on 1 procs for 0 steps with 1376 atoms 274.5% 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 | | 7.287e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9928.00 ave 9928 max 9928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 170950.0 ave 170950 max 170950 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 341900.0 ave 341900 max 341900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341900 Ave neighs/atom = 248.47384 Neighbor list builds = 0 Dangerous builds = 0 1376 -6070.77895618984 eV 2.29180230641485 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06