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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -47.132907 0.0000000) to (22.218666 47.132907 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6776138 5.7882518 5.0973115 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -47.132907 0.0000000) to (22.218666 47.132907 5.0973115) create_atoms CPU = 0.001 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6776138 5.7882518 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.132907 0.0000000) to (22.218666 47.132907 5.0973115) create_atoms CPU = 0.001 seconds 458 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 31 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 898 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3780.8015 0 -3780.8015 -6637.2087 398 0 -3813.7657 0 -3813.7657 -29484.102 Loop time of 29.7108 on 1 procs for 398 steps with 898 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 = -3780.8015497749 -3813.76208707222 -3813.76566410764 Force two-norm initial, final = 19.486513 0.18185661 Force max component initial, final = 9.1846643 0.038398443 Final line search alpha, max atom move = 1.0000000 0.038398443 Iterations, force evaluations = 398 770 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.568 | 29.568 | 29.568 | 0.0 | 99.52 Neigh | 0.069346 | 0.069346 | 0.069346 | 0.0 | 0.23 Comm | 0.038095 | 0.038095 | 0.038095 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03551 | | | 0.12 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4437.00 ave 4437 max 4437 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: 62538.0 ave 62538 max 62538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62538 Ave neighs/atom = 69.641425 Neighbor list builds = 13 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 398 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 398 0 -3813.7657 0 -3813.7657 -29484.102 10676.118 429 0 -3821.9418 0 -3821.9418 0.30452987 10465.697 Loop time of 1.51689 on 1 procs for 31 steps with 898 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 = -3813.76566410764 -3821.94127275506 -3821.94177768067 Force two-norm initial, final = 499.60148 1.7605571 Force max component initial, final = 456.08153 0.80498562 Final line search alpha, max atom move = 0.00056776054 0.00045703906 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5042 | 1.5042 | 1.5042 | 0.0 | 99.16 Neigh | 0.0048678 | 0.0048678 | 0.0048678 | 0.0 | 0.32 Comm | 0.0013788 | 0.0013788 | 0.0013788 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00649 | | | 0.43 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4492.00 ave 4492 max 4492 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: 61104.0 ave 61104 max 61104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61104 Ave neighs/atom = 68.044543 Neighbor list builds = 1 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.719 | 4.719 | 4.719 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3821.9418 0 -3821.9418 0.30452987 Loop time of 1.809e-06 on 1 procs for 0 steps with 898 atoms 110.6% 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 | | 1.809e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4492.00 ave 4492 max 4492 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: 61102.0 ave 61102 max 61102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61102 Ave neighs/atom = 68.042316 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.719 | 4.719 | 4.719 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 -3821.9418 -3821.9418 22.631036 93.308664 4.9561193 0.30452987 0.30452987 -59.03766 121.98265 -62.0314 2.2680489 1929.9423 Loop time of 2.144e-06 on 1 procs for 0 steps with 898 atoms 186.6% 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 | | 2.144e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4492.00 ave 4492 max 4492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30551.0 ave 30551 max 30551 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61102.0 ave 61102 max 61102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61102 Ave neighs/atom = 68.042316 Neighbor list builds = 0 Dangerous builds = 0 898 -3821.94177768067 eV 2.26804889742853 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31