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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -42.288374 0.0000000) to (51.792469 42.288374 9.8764362) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5917687 6.1510361 6.5842908 Created 1315 atoms using lattice units in orthogonal box = (0.0000000 -42.288374 0.0000000) to (51.792469 42.288374 9.8764362) create_atoms CPU = 0.002 seconds 1315 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5917687 6.1510361 6.5842908 Created 1321 atoms using lattice units in orthogonal box = (0.0000000 -42.288374 0.0000000) to (51.792469 42.288374 9.8764362) create_atoms CPU = 0.002 seconds 1321 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 20 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 2624 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.461 | 6.461 | 6.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8550.6624 0 -8550.6624 6236.2339 69 0 -8785.4877 0 -8785.4877 1323.872 Loop time of 2.70852 on 1 procs for 69 steps with 2624 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 = -8550.66240760831 -8785.47937441864 -8785.48765863075 Force two-norm initial, final = 68.665258 0.24813827 Force max component initial, final = 6.5106128 0.031210957 Final line search alpha, max atom move = 1.0000000 0.031210957 Iterations, force evaluations = 69 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5907 | 2.5907 | 2.5907 | 0.0 | 95.65 Neigh | 0.086888 | 0.086888 | 0.086888 | 0.0 | 3.21 Comm | 0.012941 | 0.012941 | 0.012941 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01802 | | | 0.67 Nlocal: 2624.00 ave 2624 max 2624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8966.00 ave 8966 max 8966 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: 452726.0 ave 452726 max 452726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452726 Ave neighs/atom = 172.53277 Neighbor list builds = 3 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.461 | 6.461 | 6.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -8785.4877 0 -8785.4877 1323.872 43263.122 73 0 -8785.6089 0 -8785.6089 -2.4964242 43330.462 Loop time of 0.162819 on 1 procs for 4 steps with 2624 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8785.4876586307 -8785.60664667342 -8785.60891086277 Force two-norm initial, final = 84.320896 0.34704978 Force max component initial, final = 79.112712 0.078457762 Final line search alpha, max atom move = 5.6350144e-05 4.4211062e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15852 | 0.15852 | 0.15852 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058078 | 0.00058078 | 0.00058078 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003718 | | | 2.28 Nlocal: 2624.00 ave 2624 max 2624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8960.00 ave 8960 max 8960 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: 453140.0 ave 453140 max 453140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 453140 Ave neighs/atom = 172.69055 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.599 | 6.599 | 6.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8785.6089 0 -8785.6089 -2.4964242 Loop time of 2.105e-06 on 1 procs for 0 steps with 2624 atoms 190.0% 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 | | 2.105e-06 | | |100.00 Nlocal: 2624.00 ave 2624 max 2624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8963.00 ave 8963 max 8963 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: 452804.0 ave 452804 max 452804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452804 Ave neighs/atom = 172.56250 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.599 | 6.599 | 6.599 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 -8785.6089 -8785.6089 51.799734 84.831947 9.8606684 -2.4964242 -2.4964242 -2.830627 -1.7622422 -2.8964034 2.6110237 2462.6577 Loop time of 2.828e-06 on 1 procs for 0 steps with 2624 atoms 247.5% 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 | | 2.828e-06 | | |100.00 Nlocal: 2624.00 ave 2624 max 2624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8963.00 ave 8963 max 8963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 226402.0 ave 226402 max 226402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 452804.0 ave 452804 max 452804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 452804 Ave neighs/atom = 172.56250 Neighbor list builds = 0 Dangerous builds = 0 2624 -8785.60891086277 eV 2.61102367644517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03