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 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7906401 5.5720460 6.2546061 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7906401 5.5720460 6.2546061 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) create_atoms CPU = 0.001 seconds 676 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 = 8 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_260546967793_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 = 8 28 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5426.8211 0 -5426.8211 47143.768 141 0 -5687.4276 0 -5687.4276 7609.7069 Loop time of 21.4881 on 1 procs for 141 steps with 1344 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 = -5426.82112255722 -5687.4225995152 -5687.42757201485 Force two-norm initial, final = 324.06633 0.23632750 Force max component initial, final = 67.459108 0.027350001 Final line search alpha, max atom move = 1.0000000 0.027350001 Iterations, force evaluations = 141 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.429 | 21.429 | 21.429 | 0.0 | 99.72 Neigh | 0.021282 | 0.021282 | 0.021282 | 0.0 | 0.10 Comm | 0.018914 | 0.018914 | 0.018914 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01936 | | | 0.09 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6052.00 ave 6052 max 6052 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: 168448.0 ave 168448 max 168448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 168448 Ave neighs/atom = 125.33333 Neighbor list builds = 2 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 = 8 28 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 : 141 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press Volume 141 0 -5687.4276 0 -5687.4276 7609.7069 15821.851 146 0 -5687.7124 0 -5687.7124 -161.66494 15893.162 Loop time of 0.589956 on 1 procs for 5 steps with 1344 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 = -5687.42757201483 -5687.70906694114 -5687.71240476811 Force two-norm initial, final = 141.54892 3.5016628 Force max component initial, final = 99.570888 2.7224928 Final line search alpha, max atom move = 7.1793583e-05 0.00019545751 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58785 | 0.58785 | 0.58785 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032844 | 0.00032844 | 0.00032844 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001783 | | | 0.30 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5875.00 ave 5875 max 5875 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: 169280.0 ave 169280 max 169280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169280 Ave neighs/atom = 125.95238 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 = 8 28 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) = 5.221 | 5.221 | 5.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5687.7124 0 -5687.7124 -161.66494 Loop time of 1.805e-06 on 1 procs for 0 steps with 1344 atoms 166.2% 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 | | 1.805e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5860.00 ave 5860 max 5860 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: 167096.0 ave 167096 max 167096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167096 Ave neighs/atom = 124.32738 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 = 8 28 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) = 5.221 | 5.221 | 5.221 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 -5687.7124 -5687.7124 26.971074 93.949964 6.2721358 -161.66494 -161.66494 -273.925 8.0639396 -219.13375 2.2834393 1287.3597 Loop time of 2.076e-06 on 1 procs for 0 steps with 1344 atoms 192.7% 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 | | 2.076e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5860.00 ave 5860 max 5860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83548.0 ave 83548 max 83548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 167096.0 ave 167096 max 167096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167096 Ave neighs/atom = 124.32738 Neighbor list builds = 0 Dangerous builds = 0 1344 -5687.71240476811 eV 2.28343933032635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23