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 = 4.1288715 4.1288715 4.1288715 Created orthogonal box = (0.0000000 -49.889344 0.0000000) to (61.101718 49.889344 10.113628) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8590688 6.1507410 6.7424189 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -49.889344 0.0000000) to (61.101718 49.889344 10.113628) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8590688 6.1507410 6.7424189 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -49.889344 0.0000000) to (61.101718 49.889344 10.113628) create_atoms CPU = 0.002 seconds 1756 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 14 22 3 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 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 3480 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_122703700223_003#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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 7.387 | 7.387 | 7.387 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12087.153 0 -12087.153 14850.358 93 0 -12899.693 0 -12899.693 -4900.5827 Loop time of 7.00472 on 1 procs for 93 steps with 3480 atoms 95.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12087.1529283216 -12899.6838026005 -12899.6933356003 Force two-norm initial, final = 552.38441 0.20648707 Force max component initial, final = 89.520358 0.016005866 Final line search alpha, max atom move = 1.0000000 0.016005866 Iterations, force evaluations = 93 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.8083 | 6.8083 | 6.8083 | 0.0 | 97.20 Neigh | 0.14925 | 0.14925 | 0.14925 | 0.0 | 2.13 Comm | 0.019108 | 0.019108 | 0.019108 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02804 | | | 0.40 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11671.0 ave 11671 max 11671 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: 624012.0 ave 624012 max 624012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 624012 Ave neighs/atom = 179.31379 Neighbor list builds = 4 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.391 | 7.391 | 7.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -12899.693 0 -12899.693 -4900.5827 61659.244 97 0 -12900.213 0 -12900.213 -217.89257 61373.467 Loop time of 0.278132 on 1 procs for 4 steps with 3480 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 = -12899.6933356004 -12900.2010978678 -12900.2133669555 Force two-norm initial, final = 330.21582 16.337251 Force max component initial, final = 228.04822 14.482002 Final line search alpha, max atom move = 3.3794581e-05 0.00048941318 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27378 | 0.27378 | 0.27378 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005925 | 0.0005925 | 0.0005925 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003757 | | | 1.35 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11682.0 ave 11682 max 11682 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: 621000.0 ave 621000 max 621000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621000 Ave neighs/atom = 178.44828 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 7.529 | 7.529 | 7.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12900.213 0 -12900.213 -217.89257 Loop time of 2.377e-06 on 1 procs for 0 steps with 3480 atoms 210.3% 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 | | 2.377e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11705.0 ave 11705 max 11705 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: 623890.0 ave 623890 max 623890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623890 Ave neighs/atom = 179.27874 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 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) = 7.529 | 7.529 | 7.529 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 -12900.213 -12900.213 61.065545 99.44397 10.106621 -217.89257 -217.89257 -122.02619 -376.78965 -154.86188 2.7146328 1889.651 Loop time of 2.571e-06 on 1 procs for 0 steps with 3480 atoms 272.3% 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 | | 2.571e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11705.0 ave 11705 max 11705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 311945.0 ave 311945 max 311945 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 623890.0 ave 623890 max 623890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 623890 Ave neighs/atom = 179.27874 Neighbor list builds = 0 Dangerous builds = 0 3480 -12900.2133669555 eV 2.71463278613515 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08