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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -43.006740 0.0000000) to (43.002695 43.006740 4.0453532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7083223 5.7083223 4.0453532 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -43.006740 0.0000000) to (43.002695 43.006740 4.0453532) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7083223 5.7083223 4.0453532 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -43.006740 0.0000000) to (43.002695 43.006740 4.0453532) create_atoms CPU = 0.000 seconds 454 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 28 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 900 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2988.8533 0 -2988.8533 6936.6325 72 0 -3017.8585 0 -3017.8585 -1334.9618 Loop time of 3.49756 on 1 procs for 72 steps with 900 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 = -2988.85333919916 -3017.85622346024 -3017.85849890308 Force two-norm initial, final = 17.623450 0.11287013 Force max component initial, final = 4.2418161 0.013608787 Final line search alpha, max atom move = 1.0000000 0.013608787 Iterations, force evaluations = 72 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4787 | 3.4787 | 3.4787 | 0.0 | 99.46 Neigh | 0.0053455 | 0.0053455 | 0.0053455 | 0.0 | 0.15 Comm | 0.0066591 | 0.0066591 | 0.0066591 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006864 | | | 0.20 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5096.00 ave 5096 max 5096 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: 49800.0 ave 49800 max 49800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49800 Ave neighs/atom = 55.333333 Neighbor list builds = 1 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3017.8585 0 -3017.8585 -1334.9618 14962.999 75 0 -3017.8769 0 -3017.8769 -98.820665 14937.526 Loop time of 0.152683 on 1 procs for 3 steps with 900 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 = -3017.85849890308 -3017.87596482439 -3017.87692419316 Force two-norm initial, final = 19.822987 0.21247998 Force max component initial, final = 18.509198 0.16911390 Final line search alpha, max atom move = 0.00019734800 3.3374290e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1514 | 0.1514 | 0.1514 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021921 | 0.00021921 | 0.00021921 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001066 | | | 0.70 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5089.00 ave 5089 max 5089 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: 49128.0 ave 49128 max 49128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49128 Ave neighs/atom = 54.586667 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.689 | 4.689 | 4.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3017.8769 0 -3017.8769 -98.820665 Loop time of 2.383e-06 on 1 procs for 0 steps with 900 atoms 167.9% 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 | | 2.383e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5089.00 ave 5089 max 5089 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: 49128.0 ave 49128 max 49128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49128 Ave neighs/atom = 54.586667 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.689 | 4.689 | 4.689 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 -3017.8769 -3017.8769 43.020799 86.01348 4.0367669 -98.820665 -98.820665 -6.1078446 -272.25375 -18.100402 2.5433499 171.63397 Loop time of 2.261e-06 on 1 procs for 0 steps with 900 atoms 221.1% 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 | | 2.261e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5089.00 ave 5089 max 5089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24564.0 ave 24564 max 24564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49128.0 ave 49128 max 49128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49128 Ave neighs/atom = 54.586667 Neighbor list builds = 0 Dangerous builds = 0 900 -3017.87692419316 eV 2.54334991514791 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03