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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -47.074502 0.0000000) to (28.827127 47.074502 8.6917059) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2412959 5.3493752 5.7944706 Created 1051 atoms using lattice units in orthogonal box = (0.0000000 -47.074502 0.0000000) to (28.827127 47.074502 8.6917059) create_atoms CPU = 0.002 seconds 1051 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2412959 5.3493752 5.7944706 Created 1075 atoms using lattice units in orthogonal box = (0.0000000 -47.074502 0.0000000) to (28.827127 47.074502 8.6917059) create_atoms CPU = 0.001 seconds 1075 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2112 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.428 | 6.428 | 6.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8486.2559 0 -8486.2559 14954.528 46 0 -8533.5576 0 -8533.5576 13215.914 Loop time of 1.78573 on 1 procs for 46 steps with 2112 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8486.25590834324 -8533.5497403802 -8533.55759837033 Force two-norm initial, final = 58.226193 0.19465609 Force max component initial, final = 5.1083090 0.022048860 Final line search alpha, max atom move = 1.0000000 0.022048860 Iterations, force evaluations = 46 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7667 | 1.7667 | 1.7667 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0082937 | 0.0082937 | 0.0082937 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01079 | | | 0.60 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8755.00 ave 8755 max 8755 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: 420930.0 ave 420930 max 420930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420930 Ave neighs/atom = 199.30398 Neighbor list builds = 0 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.429 | 6.429 | 6.429 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -8533.5576 0 -8533.5576 13215.914 23589.684 54 0 -8534.6546 0 -8534.6546 1.5132797 23714.648 Loop time of 0.223235 on 1 procs for 8 steps with 2112 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 = -8533.55759837029 -8534.65423537413 -8534.65462362 Force two-norm initial, final = 385.53480 1.0825283 Force max component initial, final = 337.68159 0.46217695 Final line search alpha, max atom move = 0.00014758098 6.8208529e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21734 | 0.21734 | 0.21734 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00084068 | 0.00084068 | 0.00084068 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005052 | | | 2.26 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8923.00 ave 8923 max 8923 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: 418386.0 ave 418386 max 418386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418386 Ave neighs/atom = 198.09943 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.567 | 6.567 | 6.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8534.6546 0 -8534.6546 1.5132797 Loop time of 2.339e-06 on 1 procs for 0 steps with 2112 atoms 213.8% 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 | | 2.339e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8896.00 ave 8896 max 8896 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: 418192.0 ave 418192 max 418192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418192 Ave neighs/atom = 198.00758 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.567 | 6.567 | 6.567 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 -8534.6546 -8534.6546 28.763994 94.788749 8.6978256 1.5132797 1.5132797 30.473179 5.3136096 -31.24695 2.3704565 676.13328 Loop time of 2.973e-06 on 1 procs for 0 steps with 2112 atoms 201.8% 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 | | 2.973e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8896.00 ave 8896 max 8896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 209096.0 ave 209096 max 209096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 418192.0 ave 418192 max 418192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 418192 Ave neighs/atom = 198.00758 Neighbor list builds = 0 Dangerous builds = 0 2112 -8534.65462362 eV 2.37045653250875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02