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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -53.571108 0.0000000) to (43.740626 53.571108 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3926799 5.1369555 5.9114352 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -53.571108 0.0000000) to (43.740626 53.571108 8.8671528) create_atoms CPU = 0.011 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3926799 5.1369555 5.9114352 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.571108 0.0000000) to (43.740626 53.571108 8.8671528) create_atoms CPU = 0.007 seconds 1757 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 3493 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_313717476091_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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11180.739 0 -11180.739 96845.719 25 0 -12312.475 0 -12312.475 2206.5446 Loop time of 6.47862 on 1 procs for 25 steps with 3493 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 = -11180.7385349771 -12312.4742013547 -12312.4745313371 Force two-norm initial, final = 2059.4717 4.4806649 Force max component initial, final = 363.18070 0.82192642 Final line search alpha, max atom move = 0.060626992 0.049830926 Iterations, force evaluations = 25 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.452 | 6.452 | 6.452 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010134 | 0.010134 | 0.010134 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01648 | | | 0.25 Nlocal: 3493.00 ave 3493 max 3493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8446.00 ave 8446 max 8446 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: 271172.0 ave 271172 max 271172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271172 Ave neighs/atom = 77.632980 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -12312.475 0 -12312.475 2206.5446 41555.624 32 0 -12313.227 0 -12313.227 82.332184 41623.159 Loop time of 1.13074 on 1 procs for 7 steps with 3493 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 = -12312.4745313371 -12313.2256722003 -12313.2270507982 Force two-norm initial, final = 235.75462 6.0806948 Force max component initial, final = 229.41895 3.4263578 Final line search alpha, max atom move = 0.00016899389 0.00057903356 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.12 | 1.12 | 1.12 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017931 | 0.0017931 | 0.0017931 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008962 | | | 0.79 Nlocal: 3493.00 ave 3493 max 3493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8436.00 ave 8436 max 8436 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: 270234.0 ave 270234 max 270234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270234 Ave neighs/atom = 77.364443 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.836 | 5.836 | 5.836 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12313.227 0 -12313.227 82.332184 Loop time of 6.295e-06 on 1 procs for 0 steps with 3493 atoms 190.6% 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 | | 6.295e-06 | | |100.00 Nlocal: 3493.00 ave 3493 max 3493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8445.00 ave 8445 max 8445 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: 270140.0 ave 270140 max 270140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270140 Ave neighs/atom = 77.337532 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.836 | 5.836 | 5.836 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 -12313.227 -12313.227 43.639194 107.79006 8.8487029 82.332184 82.332184 131.58299 110.79828 4.6152757 2.1565313 1795.3804 Loop time of 6.445e-06 on 1 procs for 0 steps with 3493 atoms 232.7% 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 | | 6.445e-06 | | |100.00 Nlocal: 3493.00 ave 3493 max 3493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8445.00 ave 8445 max 8445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135070.0 ave 135070 max 135070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270140.0 ave 270140 max 270140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270140 Ave neighs/atom = 77.337532 Neighbor list builds = 0 Dangerous builds = 0 3493 -12313.2270507982 eV 2.15653134516425 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08