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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -62.939976 0.0000000) to (31.468159 62.939976 3.6580991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1029447 5.1029447 3.6580991 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.939976 0.0000000) to (31.468159 62.939976 3.6580991) create_atoms CPU = 0.001 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1029447 5.1029447 3.6580991 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.939976 0.0000000) to (31.468159 62.939976 3.6580991) create_atoms CPU = 0.001 seconds 594 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1180 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4551.2062 0 -4551.2062 8393.4661 236 0 -4594.7707 0 -4594.7707 -6378.6403 Loop time of 3.73984 on 1 procs for 236 steps with 1180 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 = -4551.2062293857 -4594.76675576848 -4594.77072669741 Force two-norm initial, final = 31.684276 0.23466696 Force max component initial, final = 9.1174217 0.024300471 Final line search alpha, max atom move = 1.0000000 0.024300471 Iterations, force evaluations = 236 454 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6533 | 3.6533 | 3.6533 | 0.0 | 97.69 Neigh | 0.035873 | 0.035873 | 0.035873 | 0.0 | 0.96 Comm | 0.027429 | 0.027429 | 0.027429 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0232 | | | 0.62 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7551.00 ave 7551 max 7551 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: 163652.0 ave 163652 max 163652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163652 Ave neighs/atom = 138.68814 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 236 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.045 | 5.045 | 5.045 Mbytes Step Temp E_pair E_mol TotEng Press Volume 236 0 -4594.7707 0 -4594.7707 -6378.6403 14490.5 267 0 -4601.2595 0 -4601.2595 -17991.416 14677.261 Loop time of 0.272673 on 1 procs for 31 steps with 1180 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 = -4594.77072669751 -4601.25880639067 -4601.25953672812 Force two-norm initial, final = 362.01135 3.8073382 Force max component initial, final = 338.04201 3.4061611 Final line search alpha, max atom move = 0.0016243805 0.0055329017 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26198 | 0.26198 | 0.26198 | 0.0 | 96.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017944 | 0.0017944 | 0.0017944 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008898 | | | 3.26 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7559.00 ave 7559 max 7559 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: 163800.0 ave 163800 max 163800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163800 Ave neighs/atom = 138.81356 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4601.2595 0 -4601.2595 -17991.416 Loop time of 1.841e-06 on 1 procs for 0 steps with 1180 atoms 108.6% 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 | | 1.841e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7601.00 ave 7601 max 7601 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: 163636.0 ave 163636 max 163636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163636 Ave neighs/atom = 138.67458 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.184 | 5.184 | 5.184 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 -4601.2595 -4601.2595 30.935507 125.87995 3.769044 -17991.416 -17991.416 81.7169 -53672.869 -383.0948 2.2627259 392.17994 Loop time of 1.613e-06 on 1 procs for 0 steps with 1180 atoms 186.0% 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 | | 1.613e-06 | | |100.00 Nlocal: 1180.00 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7601.00 ave 7601 max 7601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81818.0 ave 81818 max 81818 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163636.0 ave 163636 max 163636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163636 Ave neighs/atom = 138.67458 Neighbor list builds = 0 Dangerous builds = 0 1180 -4434.3820205105 eV 2.26272592384891 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04