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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -42.663965 0.0000000) to (21.331983 42.663965 3.6584048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0192900 5.0192900 3.6584048 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.663965 0.0000000) to (21.331983 42.663965 3.6584048) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0192900 5.0192900 3.6584048 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.663965 0.0000000) to (21.331983 42.663965 3.6584048) create_atoms CPU = 0.000 seconds 274 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1586.5294 0 -1586.5294 215223.37 183 0 -2121.3886 0 -2121.3886 1208.8504 Loop time of 1.53604 on 1 procs for 183 steps with 546 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1586.52943891889 -2121.38670999936 -2121.38858798964 Force two-norm initial, final = 1347.9438 0.14302533 Force max component initial, final = 536.34518 0.033057818 Final line search alpha, max atom move = 1.0000000 0.033057818 Iterations, force evaluations = 183 349 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4981 | 1.4981 | 1.4981 | 0.0 | 97.53 Neigh | 0.010187 | 0.010187 | 0.010187 | 0.0 | 0.66 Comm | 0.015999 | 0.015999 | 0.015999 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01176 | | | 0.77 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4874.00 ave 4874 max 4874 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: 75276.0 ave 75276 max 75276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75276 Ave neighs/atom = 137.86813 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 183 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press Volume 183 0 -2121.3886 0 -2121.3886 1208.8504 6659.0794 243 0 -2129.9129 0 -2129.9129 -302.77102 6657.2223 Loop time of 0.284478 on 1 procs for 60 steps with 546 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2121.38858798964 -2129.91185573129 -2129.91285009136 Force two-norm initial, final = 223.96660 3.1124737 Force max component initial, final = 166.26092 1.5733359 Final line search alpha, max atom move = 0.00037153377 0.00058454740 Iterations, force evaluations = 60 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25293 | 0.25293 | 0.25293 | 0.0 | 88.91 Neigh | 0.018176 | 0.018176 | 0.018176 | 0.0 | 6.39 Comm | 0.0026048 | 0.0026048 | 0.0026048 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01077 | | | 3.79 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4889.00 ave 4889 max 4889 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: 76916.0 ave 76916 max 76916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76916 Ave neighs/atom = 140.87179 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2129.9129 0 -2129.9129 -302.77102 Loop time of 2.342e-06 on 1 procs for 0 steps with 546 atoms 170.8% 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 | | 2.342e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4889.00 ave 4889 max 4889 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: 76960.0 ave 76960 max 76960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76960 Ave neighs/atom = 140.95238 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.641 | 4.641 | 4.641 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 -2129.9129 -2129.9129 21.415177 81.051538 3.8353952 -302.77102 -302.77102 -278.72544 -359.67379 -269.91383 2.2360474 299.2116 Loop time of 2.313e-06 on 1 procs for 0 steps with 546 atoms 216.2% 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 | | 2.313e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4889.00 ave 4889 max 4889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38480.0 ave 38480 max 38480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76960.0 ave 76960 max 76960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76960 Ave neighs/atom = 140.95238 Neighbor list builds = 0 Dangerous builds = 0 546 -2129.91285009136 eV 2.2360473887517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02