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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -32.057539 0.0000000) to (27.762643 32.057539 5.4447022) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9830384 4.9319290 5.4447022 Created 309 atoms using lattice units in orthogonal box = (0.0000000 -32.057539 0.0000000) to (27.762643 32.057539 5.4447022) create_atoms CPU = 0.003 seconds 309 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9830384 4.9319290 5.4447022 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -32.057539 0.0000000) to (27.762643 32.057539 5.4447022) create_atoms CPU = 0.002 seconds 317 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 13 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 625 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.938 | 4.938 | 4.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3386.9202 0 -3386.9202 225562.46 400 0 -4184.8089 0 -4184.8089 15130.204 Loop time of 16.1781 on 1 procs for 400 steps with 625 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 = -3386.92022414638 -4184.80513890608 -4184.80893772955 Force two-norm initial, final = 963.62626 0.36491911 Force max component initial, final = 267.43400 0.13810211 Final line search alpha, max atom move = 0.81347613 0.11234277 Iterations, force evaluations = 400 772 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.753 | 15.753 | 15.753 | 0.0 | 97.37 Neigh | 0.24406 | 0.24406 | 0.24406 | 0.0 | 1.51 Comm | 0.10573 | 0.10573 | 0.10573 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07503 | | | 0.46 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5903.00 ave 5903 max 5903 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: 172018.0 ave 172018 max 172018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 172018 Ave neighs/atom = 275.22880 Neighbor list builds = 11 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 400 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.936 | 4.936 | 4.936 Mbytes Step Temp E_pair E_mol TotEng Press Volume 400 0 -4184.8089 0 -4184.8089 15130.204 9691.5916 442 0 -4207.2958 0 -4207.2958 377.43392 9713.4799 Loop time of 1.04323 on 1 procs for 42 steps with 625 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 = -4184.80893772956 -4207.29341093122 -4207.29577376463 Force two-norm initial, final = 1045.0964 10.961719 Force max component initial, final = 739.96613 7.8796690 Final line search alpha, max atom move = 0.00013593625 0.0010711327 Iterations, force evaluations = 42 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9735 | 0.9735 | 0.9735 | 0.0 | 93.32 Neigh | 0.042528 | 0.042528 | 0.042528 | 0.0 | 4.08 Comm | 0.0063898 | 0.0063898 | 0.0063898 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0208 | | | 1.99 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5708.00 ave 5708 max 5708 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: 169172.0 ave 169172 max 169172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169172 Ave neighs/atom = 270.67520 Neighbor list builds = 2 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.073 | 5.073 | 5.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4207.2958 0 -4207.2958 377.43392 Loop time of 6.716e-06 on 1 procs for 0 steps with 625 atoms 178.7% 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 | | 6.716e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5699.00 ave 5699 max 5699 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: 168818.0 ave 168818 max 168818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168818 Ave neighs/atom = 270.10880 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 5.073 | 5.073 | 5.073 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 -4207.2958 -4207.2958 28.159613 61.972269 5.5660969 377.43392 377.43392 -715.85678 519.47942 1328.6791 2.540929 3771.1641 Loop time of 6.846e-06 on 1 procs for 0 steps with 625 atoms 262.9% 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 | | 6.846e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5699.00 ave 5699 max 5699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84409.0 ave 84409 max 84409 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 168818.0 ave 168818 max 168818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168818 Ave neighs/atom = 270.10880 Neighbor list builds = 0 Dangerous builds = 0 625 -4207.29577376463 eV 2.54092903403412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17