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 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8884161 5.2883889 6.2584463 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8884161 5.2883889 6.2584463 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.130412 0.0000000) to (39.910376 69.130412 6.2584463) create_atoms CPU = 0.003 seconds 1466 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 = 14 47 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 32 atoms, new total = 2900 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 = 14 47 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) = 5.780 | 5.780 | 5.780 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10193.341 0 -10193.341 1371.6383 71 0 -10234.538 0 -10234.538 -8387.9357 Loop time of 5.25786 on 1 procs for 71 steps with 2900 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 = -10193.340922643 -10234.5302082542 -10234.5376016169 Force two-norm initial, final = 46.646741 0.27391284 Force max component initial, final = 10.137112 0.061672193 Final line search alpha, max atom move = 1.0000000 0.061672193 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1974 | 5.1974 | 5.1974 | 0.0 | 98.85 Neigh | 0.032505 | 0.032505 | 0.032505 | 0.0 | 0.62 Comm | 0.012281 | 0.012281 | 0.012281 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01569 | | | 0.30 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9391.00 ave 9391 max 9391 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: 224604.0 ave 224604 max 224604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224604 Ave neighs/atom = 77.449655 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 47 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.780 | 5.780 | 5.780 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -10234.538 0 -10234.538 -8387.9357 34534.366 74 0 -10234.791 0 -10234.791 -3024.2974 34401.319 Loop time of 0.212868 on 1 procs for 3 steps with 2900 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 = -10234.5376016169 -10234.7851306171 -10234.7914708342 Force two-norm initial, final = 183.94569 9.4595824 Force max component initial, final = 147.88666 9.4502661 Final line search alpha, max atom move = 3.9625456e-05 0.00037447110 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21058 | 0.21058 | 0.21058 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034221 | 0.00034221 | 0.00034221 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001951 | | | 0.92 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9403.00 ave 9403 max 9403 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: 224612.0 ave 224612 max 224612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224612 Ave neighs/atom = 77.452414 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 = 14 47 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) = 5.918 | 5.918 | 5.918 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10234.791 0 -10234.791 -3024.2974 Loop time of 2.069e-06 on 1 procs for 0 steps with 2900 atoms 145.0% 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 | | 2.069e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9403.00 ave 9403 max 9403 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: 224644.0 ave 224644 max 224644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224644 Ave neighs/atom = 77.463448 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 = 14 47 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) = 5.918 | 5.918 | 5.918 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 -10234.791 -10234.791 39.810573 138.26082 6.249964 -3024.2974 -3024.2974 -13.441977 -9498.9821 439.53179 2.3067655 1069.1691 Loop time of 2.059e-06 on 1 procs for 0 steps with 2900 atoms 194.3% 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 | | 2.059e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9403.00 ave 9403 max 9403 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112322.0 ave 112322 max 112322 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224644.0 ave 224644 max 224644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224644 Ave neighs/atom = 77.463448 Neighbor list builds = 0 Dangerous builds = 0 2900 -10234.7914708342 eV 2.30676547524478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05