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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -74.678499 0.0000000) to (37.339249 74.678499 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7107087 5.7107087 4.0500102 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678499 0.0000000) to (37.339249 74.678499 4.0500102) create_atoms CPU = 0.004 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7107087 5.7107087 4.0500102 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678499 0.0000000) to (37.339249 74.678499 4.0500102) create_atoms CPU = 0.003 seconds 682 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 40 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4462.4442 0 -4462.4442 21490.274 100 0 -4611.4005 0 -4611.4005 2444.4082 Loop time of 3.28618 on 1 procs for 100 steps with 1362 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 = -4462.44421177914 -4611.3961703495 -4611.40051459337 Force two-norm initial, final = 194.46122 0.15454602 Force max component initial, final = 52.340785 0.023430119 Final line search alpha, max atom move = 1.0000000 0.023430119 Iterations, force evaluations = 100 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1576 | 3.1576 | 3.1576 | 0.0 | 96.09 Neigh | 0.063562 | 0.063562 | 0.063562 | 0.0 | 1.93 Comm | 0.034545 | 0.034545 | 0.034545 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03043 | | | 0.93 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8113.00 ave 8113 max 8113 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: 162256.0 ave 162256 max 162256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162256 Ave neighs/atom = 119.13069 Neighbor list builds = 3 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -4611.4005 0 -4611.4005 2444.4082 22586.413 104 0 -4611.5048 0 -4611.5048 -86.231915 22659.896 Loop time of 0.108155 on 1 procs for 4 steps with 1362 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 = -4611.40051459337 -4611.50418353949 -4611.50484221907 Force two-norm initial, final = 68.915304 2.6577242 Force max component initial, final = 57.207298 2.3861148 Final line search alpha, max atom move = 0.00040915192 0.00097628345 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10381 | 0.10381 | 0.10381 | 0.0 | 95.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097994 | 0.00097994 | 0.00097994 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003366 | | | 3.11 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8104.00 ave 8104 max 8104 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: 165392.0 ave 165392 max 165392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165392 Ave neighs/atom = 121.43319 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4611.5048 0 -4611.5048 -86.231915 Loop time of 6.745e-06 on 1 procs for 0 steps with 1362 atoms 177.9% 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 | | 6.745e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8125.00 ave 8125 max 8125 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: 157744.0 ave 157744 max 157744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157744 Ave neighs/atom = 115.81791 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.217 | 5.217 | 5.217 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 -4611.5048 -4611.5048 37.291653 149.78456 4.0567593 -86.231915 -86.231915 -81.500237 -169.19411 -8.0013985 2.5861398 196.55976 Loop time of 6.836e-06 on 1 procs for 0 steps with 1362 atoms 248.7% 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 | | 6.836e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8125.00 ave 8125 max 8125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78872.0 ave 78872 max 78872 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 157744.0 ave 157744 max 157744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157744 Ave neighs/atom = 115.81791 Neighbor list builds = 0 Dangerous builds = 0 1362 -4611.50484221907 eV 2.58613979514965 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04