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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2267577 5.6609776 5.1100000 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) create_atoms CPU = 0.004 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2267577 5.6609776 5.1100000 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) create_atoms CPU = 0.003 seconds 532 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 ghost atom cutoff = 6 binsize = 3, bins = 10 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_087820130586_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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3658.591 0 -3658.591 10266.296 39 0 -3699.4788 0 -3699.4788 -6298.5009 Loop time of 2.91281 on 1 procs for 39 steps with 1048 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 = -3658.59103695191 -3699.4758208545 -3699.47884689413 Force two-norm initial, final = 46.503154 0.14142333 Force max component initial, final = 11.369016 0.024495043 Final line search alpha, max atom move = 1.0000000 0.024495043 Iterations, force evaluations = 39 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.883 | 2.883 | 2.883 | 0.0 | 98.98 Neigh | 0.013038 | 0.013038 | 0.013038 | 0.0 | 0.45 Comm | 0.0078141 | 0.0078141 | 0.0078141 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008975 | | | 0.31 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4414.00 ave 4414 max 4414 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: 80872.0 ave 80872 max 80872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80872 Ave neighs/atom = 77.167939 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3699.4788 0 -3699.4788 -6298.5009 12455.45 43 0 -3699.5721 0 -3699.5721 -2130.6705 12418.026 Loop time of 0.262936 on 1 procs for 4 steps with 1048 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 = -3699.47884689413 -3699.57072653324 -3699.57208911031 Force two-norm initial, final = 60.476031 2.2175113 Force max component initial, final = 57.847734 2.0937049 Final line search alpha, max atom move = 0.00016179742 0.00033875605 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26011 | 0.26011 | 0.26011 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005644 | 0.0005644 | 0.0005644 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002263 | | | 0.86 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 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: 80696.0 ave 80696 max 80696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80696 Ave neighs/atom = 77.000000 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3699.5721 0 -3699.5721 -2130.6705 Loop time of 5.873e-06 on 1 procs for 0 steps with 1048 atoms 170.3% 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 | | 5.873e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 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: 80744.0 ave 80744 max 80744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80744 Ave neighs/atom = 77.045802 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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.738 | 4.738 | 4.738 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 -3699.5721 -3699.5721 29.358443 83.034899 5.0939994 -2130.6705 -2130.6705 -91.225144 -6031.5021 -269.28443 2.3959152 637.28766 Loop time of 6.765e-06 on 1 procs for 0 steps with 1048 atoms 266.1% 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 | | 6.765e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4396.00 ave 4396 max 4396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40372.0 ave 40372 max 40372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80744.0 ave 80744 max 80744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80744 Ave neighs/atom = 77.045802 Neighbor list builds = 0 Dangerous builds = 0 1048 -3699.57208911031 eV 2.39591521550129 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03