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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -43.659859 0.0000000) to (53.472188 43.659859 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1274701 5.3827223 5.9005197 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.659859 0.0000000) to (53.472188 43.659859 8.8507796) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1274701 5.3827223 5.9005197 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.659859 0.0000000) to (53.472188 43.659859 8.8507796) create_atoms CPU = 0.003 seconds 1756 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 = 18 30 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 4 atoms, new total = 3502 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_087820130586_000#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 = 18 30 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) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11708.905 0 -11708.905 45693.894 23 0 -12355.503 0 -12355.503 5424.4767 Loop time of 2.21282 on 1 procs for 23 steps with 3502 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 = -11708.9048043842 -12355.4926874981 -12355.5033177224 Force two-norm initial, final = 544.26172 0.34148593 Force max component initial, final = 97.902751 0.085668329 Final line search alpha, max atom move = 1.0000000 0.085668329 Iterations, force evaluations = 23 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2001 | 2.2001 | 2.2001 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046023 | 0.0046023 | 0.0046023 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008107 | | | 0.37 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8335.00 ave 8335 max 8335 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: 272692.0 ave 272692 max 272692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272692 Ave neighs/atom = 77.867504 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 = 18 30 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -12355.503 0 -12355.503 5424.4767 41325.851 30 0 -12356.218 0 -12356.218 5.9154327 41482.673 Loop time of 0.617489 on 1 procs for 7 steps with 3502 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12355.5033177225 -12356.2170487245 -12356.2179198825 Force two-norm initial, final = 291.51383 1.8529859 Force max component initial, final = 268.35128 1.4750093 Final line search alpha, max atom move = 8.2256170e-05 0.00012132862 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61073 | 0.61073 | 0.61073 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077981 | 0.00077981 | 0.00077981 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005981 | | | 0.97 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8275.00 ave 8275 max 8275 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: 271176.0 ave 271176 max 271176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271176 Ave neighs/atom = 77.434609 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 = 18 30 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) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12356.218 0 -12356.218 5.9154327 Loop time of 2.344e-06 on 1 procs for 0 steps with 3502 atoms 170.6% 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 | | 2.344e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8275.00 ave 8275 max 8275 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: 270850.0 ave 270850 max 270850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270850 Ave neighs/atom = 77.341519 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 = 18 30 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) = 5.824 | 5.824 | 5.824 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 -12356.218 -12356.218 53.440369 87.833099 8.8376964 5.9154327 5.9154327 -37.012824 -2.1256395 56.884762 2.2568936 1595.1535 Loop time of 2.775e-06 on 1 procs for 0 steps with 3502 atoms 252.3% 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 | | 2.775e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8275.00 ave 8275 max 8275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 135425.0 ave 135425 max 135425 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 270850.0 ave 270850 max 270850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270850 Ave neighs/atom = 77.341519 Neighbor list builds = 0 Dangerous builds = 0 3502 -12356.2179198825 eV 2.25689362625382 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03