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 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5724642 6.1919427 5.0973115 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5724642 6.1919427 5.0973115 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -46.158119 0.0000000) to (32.638719 46.158119 5.0973115) create_atoms CPU = 0.001 seconds 660 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 = 11 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 0 atoms, new total = 1316 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 = 11 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5223.7743 0 -5223.7743 98355.345 547 0 -5624.6606 0 -5624.6606 -9373.1607 Loop time of 63.7935 on 1 procs for 547 steps with 1316 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 = -5223.77432148946 -5624.65541463048 -5624.66061099986 Force two-norm initial, final = 419.27529 0.20440560 Force max component initial, final = 115.09905 0.016746765 Final line search alpha, max atom move = 1.0000000 0.016746765 Iterations, force evaluations = 547 983 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.433 | 63.433 | 63.433 | 0.0 | 99.43 Neigh | 0.20347 | 0.20347 | 0.20347 | 0.0 | 0.32 Comm | 0.080355 | 0.080355 | 0.080355 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07668 | | | 0.12 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5572.00 ave 5572 max 5572 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: 89488.0 ave 89488 max 89488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89488 Ave neighs/atom = 68.000000 Neighbor list builds = 25 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 = 11 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 : 547 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.658 | 4.658 | 4.658 Mbytes Step Temp E_pair E_mol TotEng Press Volume 547 0 -5624.6606 0 -5624.6606 -9373.1607 15358.626 579 0 -5638.4989 0 -5638.4989 -20.384592 15250.73 Loop time of 2.76867 on 1 procs for 32 steps with 1316 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 = -5624.66061099986 -5638.49412786342 -5638.49892430807 Force two-norm initial, final = 739.21377 2.2375875 Force max component initial, final = 678.28023 1.9613364 Final line search alpha, max atom move = 9.3987693e-05 0.00018434148 Iterations, force evaluations = 32 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7475 | 2.7475 | 2.7475 | 0.0 | 99.23 Neigh | 0.0080993 | 0.0080993 | 0.0080993 | 0.0 | 0.29 Comm | 0.0019446 | 0.0019446 | 0.0019446 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01114 | | | 0.40 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5703.00 ave 5703 max 5703 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: 84240.0 ave 84240 max 84240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84240 Ave neighs/atom = 64.012158 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 = 11 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) = 4.797 | 4.797 | 4.797 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5638.4989 0 -5638.4989 -20.384592 Loop time of 1.901e-06 on 1 procs for 0 steps with 1316 atoms 157.8% 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 | | 1.901e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5723.00 ave 5723 max 5723 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: 86800.0 ave 86800 max 86800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86800 Ave neighs/atom = 65.957447 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 = 11 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) = 4.797 | 4.797 | 4.797 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 -5638.4989 -5638.4989 32.913613 93.851747 4.9371091 -20.384592 -20.384592 -207.78503 50.216426 96.414828 2.4527854 0.085288743 Loop time of 1.69e-06 on 1 procs for 0 steps with 1316 atoms 177.5% 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 | | 1.69e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5723.00 ave 5723 max 5723 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43400.0 ave 43400 max 43400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86800.0 ave 86800 max 86800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86800 Ave neighs/atom = 65.957447 Neighbor list builds = 0 Dangerous builds = 0 1316 -5638.49892430807 eV 2.45278538287427 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:07