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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -49.644398 0.0000000) to (13.511494 49.644398 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7906401 5.5160442 5.8968993 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.644398 0.0000000) to (13.511494 49.644398 8.8453489) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7906401 5.5160442 5.8968993 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.644398 0.0000000) to (13.511494 49.644398 8.8453489) create_atoms CPU = 0.001 seconds 507 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 = 5 34 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 0 atoms, new total = 1010 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_150993986463_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 = 5 34 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4108.3043 0 -4108.3043 47364.121 306 0 -4290.4766 0 -4290.4766 6924.5109 Loop time of 21.6236 on 1 procs for 306 steps with 1010 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 = -4108.30434350664 -4290.47271131342 -4290.47656919496 Force two-norm initial, final = 198.83677 0.21299803 Force max component initial, final = 70.213038 0.068340700 Final line search alpha, max atom move = 1.0000000 0.068340700 Iterations, force evaluations = 306 587 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.508 | 21.508 | 21.508 | 0.0 | 99.47 Neigh | 0.059171 | 0.059171 | 0.059171 | 0.0 | 0.27 Comm | 0.025315 | 0.025315 | 0.025315 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03079 | | | 0.14 Nlocal: 1010.00 ave 1010 max 1010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3999.00 ave 3999 max 3999 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: 69826.0 ave 69826 max 69826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69826 Ave neighs/atom = 69.134653 Neighbor list builds = 9 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 = 5 34 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 : 306 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 306 0 -4290.4766 0 -4290.4766 6924.5109 11866.389 314 0 -4290.9975 0 -4290.9975 5.9304988 11914.328 Loop time of 0.359001 on 1 procs for 8 steps with 1010 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4290.47656919495 -4290.99419257762 -4290.99745254845 Force two-norm initial, final = 126.69277 0.77518540 Force max component initial, final = 98.311321 0.43897685 Final line search alpha, max atom move = 0.00015768002 6.9217878e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35641 | 0.35641 | 0.35641 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039888 | 0.00039888 | 0.00039888 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002194 | | | 0.61 Nlocal: 1010.00 ave 1010 max 1010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3994.00 ave 3994 max 3994 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: 69778.0 ave 69778 max 69778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69778 Ave neighs/atom = 69.087129 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 = 5 34 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) = 4.680 | 4.680 | 4.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4290.9975 0 -4290.9975 5.9304988 Loop time of 2.051e-06 on 1 procs for 0 steps with 1010 atoms 146.3% 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 | | 2.051e-06 | | |100.00 Nlocal: 1010.00 ave 1010 max 1010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3994.00 ave 3994 max 3994 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: 69584.0 ave 69584 max 69584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69584 Ave neighs/atom = 68.895050 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 = 5 34 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) = 4.680 | 4.680 | 4.680 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 -4290.9975 -4290.9975 13.427803 99.728624 8.8970241 5.9304988 5.9304988 11.530392 59.292806 -53.031701 2.2983738 6100.127 Loop time of 2.289e-06 on 1 procs for 0 steps with 1010 atoms 174.7% 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 | | 2.289e-06 | | |100.00 Nlocal: 1010.00 ave 1010 max 1010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3994.00 ave 3994 max 3994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34792.0 ave 34792 max 34792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69584.0 ave 69584 max 69584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69584 Ave neighs/atom = 68.895050 Neighbor list builds = 0 Dangerous builds = 0 1010 -4290.99745254845 eV 2.29837378324666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22