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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -41.416414 0.0000000) to (35.867666 41.416414 7.0342281) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4377863 6.3717559 7.0342281 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -41.416414 0.0000000) to (35.867666 41.416414 7.0342281) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4377863 6.3717559 7.0342281 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -41.416414 0.0000000) to (35.867666 41.416414 7.0342281) create_atoms CPU = 0.001 seconds 630 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 17 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1248 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3098.1828 0 -3098.1828 25318.871 122 0 -3342.3945 0 -3342.3945 4827.4932 Loop time of 2.8047 on 1 procs for 122 steps with 1248 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3098.18279907881 -3342.39165636624 -3342.39445016707 Force two-norm initial, final = 230.58410 0.16403852 Force max component initial, final = 51.018406 0.021808057 Final line search alpha, max atom move = 1.0000000 0.021808057 Iterations, force evaluations = 122 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6912 | 2.6912 | 2.6912 | 0.0 | 95.95 Neigh | 0.076367 | 0.076367 | 0.076367 | 0.0 | 2.72 Comm | 0.020415 | 0.020415 | 0.020415 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01675 | | | 0.60 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8250.00 ave 8250 max 8250 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: 281152.0 ave 281152 max 281152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281152 Ave neighs/atom = 225.28205 Neighbor list builds = 4 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -3342.3945 0 -3342.3945 4827.4932 20898.834 127 0 -3342.6601 0 -3342.6601 110.25146 21031.106 Loop time of 0.0925517 on 1 procs for 5 steps with 1248 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3342.39445016705 -3342.65825735677 -3342.6600708263 Force two-norm initial, final = 117.58098 2.9997310 Force max component initial, final = 93.435833 2.7216650 Final line search alpha, max atom move = 0.00016511677 0.00044939254 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089302 | 0.089302 | 0.089302 | 0.0 | 96.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055041 | 0.00055041 | 0.00055041 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002699 | | | 2.92 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8189.00 ave 8189 max 8189 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: 281336.0 ave 281336 max 281336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281336 Ave neighs/atom = 225.42949 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.630 | 5.630 | 5.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3342.6601 0 -3342.6601 110.25146 Loop time of 2.527e-06 on 1 procs for 0 steps with 1248 atoms 158.3% 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 | | 2.527e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8178.00 ave 8178 max 8178 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: 280780.0 ave 280780 max 280780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280780 Ave neighs/atom = 224.98397 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.630 | 5.630 | 5.630 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 -3342.6601 -3342.6601 35.937475 83.179619 7.0355431 110.25146 110.25146 34.365604 208.20797 88.180796 2.5866156 1136.2215 Loop time of 2.702e-06 on 1 procs for 0 steps with 1248 atoms 333.1% 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 | | 2.702e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8178.00 ave 8178 max 8178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140390.0 ave 140390 max 140390 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280780.0 ave 280780 max 280780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280780 Ave neighs/atom = 224.98397 Neighbor list builds = 0 Dangerous builds = 0 1248 -3342.6600708263 eV 2.5866155501839 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03