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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -36.150127 0.0000000) to (18.075063 36.150127 3.6150127) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0610177 5.0610177 3.6150127 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -36.150127 0.0000000) to (18.075063 36.150127 3.6150127) create_atoms CPU = 0.002 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0610177 5.0610177 3.6150127 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.150127 0.0000000) to (18.075063 36.150127 3.6150127) create_atoms CPU = 0.001 seconds 202 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 400 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1359.7115 0 -1359.7115 35305.267 42 0 -1407.83 0 -1407.83 7262.3324 Loop time of 4.81473 on 1 procs for 42 steps with 400 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1359.71149026327 -1407.82895208199 -1407.82997320206 Force two-norm initial, final = 100.35236 0.12013714 Force max component initial, final = 33.585024 0.035412083 Final line search alpha, max atom move = 1.0000000 0.035412083 Iterations, force evaluations = 42 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8021 | 4.8021 | 4.8021 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.006988 | 0.006988 | 0.006988 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005641 | | | 0.12 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3850.00 ave 3850 max 3850 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: 53112.0 ave 53112 max 53112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53112 Ave neighs/atom = 132.78000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1407.83 0 -1407.83 7262.3324 4724.213 48 0 -1407.9438 0 -1407.9438 -337.9386 4749.4314 Loop time of 0.491645 on 1 procs for 6 steps with 400 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 = -1407.82997320206 -1407.94274601994 -1407.94381962518 Force two-norm initial, final = 43.199361 1.9315954 Force max component initial, final = 35.713371 1.4580920 Final line search alpha, max atom move = 0.00054931724 0.00080095509 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48868 | 0.48868 | 0.48868 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066173 | 0.00066173 | 0.00066173 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002301 | | | 0.47 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3810.00 ave 3810 max 3810 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: 53080.0 ave 53080 max 53080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53080 Ave neighs/atom = 132.70000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1407.9438 0 -1407.9438 -337.9386 Loop time of 6.505e-06 on 1 procs for 0 steps with 400 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3795.00 ave 3795 max 3795 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: 53016.0 ave 53016 max 53016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53016 Ave neighs/atom = 132.54000 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.593 | 4.593 | 4.593 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 -1407.9438 -1407.9438 18.031325 72.657941 3.6251911 -337.9386 -337.9386 -490.68352 -409.785 -113.34728 2.2684192 151.44839 Loop time of 6.355e-06 on 1 procs for 0 steps with 400 atoms 283.2% 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 | | 6.355e-06 | | |100.00 Nlocal: 400.000 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3795.00 ave 3795 max 3795 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26508.0 ave 26508 max 26508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53016.0 ave 53016 max 53016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53016 Ave neighs/atom = 132.54000 Neighbor list builds = 0 Dangerous builds = 0 400 -1407.94381962518 eV 2.26841921603018 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05