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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -40.782193 0.0000000) to (28.837365 40.782193 4.0380388) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5235083 3.5984288 4.0380388 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.782193 0.0000000) to (28.837365 40.782193 4.0380388) create_atoms CPU = 0.004 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5235083 3.5984288 4.0380388 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.782193 0.0000000) to (28.837365 40.782193 4.0380388) create_atoms CPU = 0.002 seconds 410 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 = 8 23 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 6 atoms, new total = 812 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_737567242631_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 = 8 23 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) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2308.2236 0 -2308.2236 236975.92 59 0 -3330.7567 0 -3330.7567 -1468.5908 Loop time of 1.39448 on 1 procs for 59 steps with 812 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 = -2308.22362664727 -3330.75420005514 -3330.75672873789 Force two-norm initial, final = 2739.5348 0.15808755 Force max component initial, final = 895.83474 0.022962313 Final line search alpha, max atom move = 1.0000000 0.022962313 Iterations, force evaluations = 59 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.333 | 1.333 | 1.333 | 0.0 | 95.59 Neigh | 0.034948 | 0.034948 | 0.034948 | 0.0 | 2.51 Comm | 0.014133 | 0.014133 | 0.014133 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0124 | | | 0.89 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5671.00 ave 5671 max 5671 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: 110664.0 ave 110664 max 110664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110664 Ave neighs/atom = 136.28571 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 23 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -3330.7567 0 -3330.7567 -1468.5908 9497.8791 61 0 -3330.7621 0 -3330.7621 -2.9969904 9489.8819 Loop time of 0.0654993 on 1 procs for 2 steps with 812 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3330.75672873788 -3330.76156479687 -3330.76209559885 Force two-norm initial, final = 16.457221 0.65562166 Force max component initial, final = 13.849465 0.47572864 Final line search alpha, max atom move = 0.00037620875 0.00017897328 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.063146 | 0.063146 | 0.063146 | 0.0 | 96.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056838 | 0.00056838 | 0.00056838 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001785 | | | 2.73 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5637.00 ave 5637 max 5637 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: 110604.0 ave 110604 max 110604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110604 Ave neighs/atom = 136.21182 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 = 8 23 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3330.7621 0 -3330.7621 -2.9969904 Loop time of 6.886e-06 on 1 procs for 0 steps with 812 atoms 261.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5637.00 ave 5637 max 5637 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: 110636.0 ave 110636 max 110636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110636 Ave neighs/atom = 136.25123 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 = 8 23 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) = 5.084 | 5.084 | 5.084 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 -3330.7621 -3330.7621 28.83777 81.55069 4.0352598 -2.9969904 -2.9969904 -68.111128 80.303767 -21.18361 2.2850588 392.00324 Loop time of 6.706e-06 on 1 procs for 0 steps with 812 atoms 238.6% 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 | | 6.706e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5637.00 ave 5637 max 5637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55318.0 ave 55318 max 55318 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110636.0 ave 110636 max 110636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110636 Ave neighs/atom = 136.25123 Neighbor list builds = 0 Dangerous builds = 0 812 -3330.76209559885 eV 2.28505878469623 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02