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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1307403 6.1929829 5.1068645 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068645) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1307403 6.1929829 5.1068645 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.112284 0.0000000) to (14.888941 42.112284 5.1068645) create_atoms CPU = 0.001 seconds 274 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 542 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2222.4851 0 -2222.4851 32198.659 390 0 -2302.3232 0 -2302.3232 -1573.0068 Loop time of 34.2499 on 1 procs for 390 steps with 542 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 = -2222.48514260122 -2302.3209988226 -2302.32323937345 Force two-norm initial, final = 147.85719 0.15511103 Force max component initial, final = 47.139974 0.034566181 Final line search alpha, max atom move = 1.0000000 0.034566181 Iterations, force evaluations = 390 753 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.146 | 34.146 | 34.146 | 0.0 | 99.70 Neigh | 0.040988 | 0.040988 | 0.040988 | 0.0 | 0.12 Comm | 0.034741 | 0.034741 | 0.034741 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02828 | | | 0.08 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3911.00 ave 3911 max 3911 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: 63020.0 ave 63020 max 63020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63020 Ave neighs/atom = 116.27306 Neighbor list builds = 9 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 390 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press Volume 390 0 -2302.3232 0 -2302.3232 -1573.0068 6404.0827 409 0 -2304.4351 0 -2304.4351 -5.3564137 6394.7291 Loop time of 1.06081 on 1 procs for 19 steps with 542 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 = -2302.32323937345 -2304.43477914005 -2304.43507959374 Force two-norm initial, final = 170.48506 0.68578599 Force max component initial, final = 130.48105 0.19943687 Final line search alpha, max atom move = 0.00065894296 0.00013141752 Iterations, force evaluations = 19 20 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0563 | 1.0563 | 1.0563 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072963 | 0.00072963 | 0.00072963 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003822 | | | 0.36 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3874.00 ave 3874 max 3874 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: 62764.0 ave 62764 max 62764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62764 Ave neighs/atom = 115.80074 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2304.4351 0 -2304.4351 -5.3564137 Loop time of 2.055e-06 on 1 procs for 0 steps with 542 atoms 146.0% 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 | | 2.055e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3898.00 ave 3898 max 3898 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: 61920.0 ave 61920 max 61920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61920 Ave neighs/atom = 114.24354 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.648 | 4.648 | 4.648 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 -2304.4351 -2304.4351 15.135837 84.234354 5.0156414 -5.3564137 -5.3564137 -50.796793 0.37435204 34.3532 2.3444623 854.65189 Loop time of 2.341e-06 on 1 procs for 0 steps with 542 atoms 170.9% 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 | | 2.341e-06 | | |100.00 Nlocal: 542.000 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3898.00 ave 3898 max 3898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30960.0 ave 30960 max 30960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61920.0 ave 61920 max 61920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61920 Ave neighs/atom = 114.24354 Neighbor list builds = 0 Dangerous builds = 0 542 -2304.43507959374 eV 2.34446234726769 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35