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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -40.288419 0.0000000) to (20.144210 40.288419 3.3116877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8110667 3.8110667 3.3116877 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -40.288419 0.0000000) to (20.144210 40.288419 3.3116877) create_atoms CPU = 0.001 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8110667 3.8110667 3.3116877 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -40.288419 0.0000000) to (20.144210 40.288419 3.3116877) create_atoms CPU = 0.001 seconds 298 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 594 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1656.2463 0 -1656.2463 321801.8 68 0 -2296.4668 0 -2296.4668 100389.02 Loop time of 1.88422 on 1 procs for 68 steps with 594 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 = -1656.2463473653 -2296.46466757558 -2296.46684682689 Force two-norm initial, final = 1251.4174 0.30530617 Force max component initial, final = 354.85727 0.027830501 Final line search alpha, max atom move = 1.0000000 0.027830501 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8377 | 1.8377 | 1.8377 | 0.0 | 97.53 Neigh | 0.01515 | 0.01515 | 0.01515 | 0.0 | 0.80 Comm | 0.018948 | 0.018948 | 0.018948 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01242 | | | 0.66 Nlocal: 594.000 ave 594 max 594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6117.00 ave 6117 max 6117 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: 116872.0 ave 116872 max 116872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116872 Ave neighs/atom = 196.75421 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.927 | 4.927 | 4.927 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -2296.4668 0 -2296.4668 100389.02 5375.3881 524 0 -2434.755 0 -2434.755 300.77886 6651.7382 Loop time of 6.76597 on 1 procs for 456 steps with 594 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 = -2296.46684682687 -2434.75342891126 -2434.75501616083 Force two-norm initial, final = 607.54813 3.8912749 Force max component initial, final = 473.90620 2.2656084 Final line search alpha, max atom move = 0.00021515253 0.00048745137 Iterations, force evaluations = 456 505 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2273 | 6.2273 | 6.2273 | 0.0 | 92.04 Neigh | 0.23674 | 0.23674 | 0.23674 | 0.0 | 3.50 Comm | 0.073441 | 0.073441 | 0.073441 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2284 | | | 3.38 Nlocal: 594.000 ave 594 max 594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6560.00 ave 6560 max 6560 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: 97812.0 ave 97812 max 97812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97812 Ave neighs/atom = 164.66667 Neighbor list builds = 17 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.691 | 4.691 | 4.691 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2434.755 0 -2434.755 300.77886 Loop time of 6.164e-06 on 1 procs for 0 steps with 594 atoms 194.7% 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 | | 6.164e-06 | | |100.00 Nlocal: 594.000 ave 594 max 594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6574.00 ave 6574 max 6574 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: 98060.0 ave 98060 max 98060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98060 Ave neighs/atom = 165.08418 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.691 | 4.691 | 4.691 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 -2434.755 -2434.755 24.16635 97.872554 2.8123098 300.77886 300.77886 654.66765 -119.94616 367.6151 2.3450892 943.69415 Loop time of 7.086e-06 on 1 procs for 0 steps with 594 atoms 254.0% 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 | | 7.086e-06 | | |100.00 Nlocal: 594.000 ave 594 max 594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6574.00 ave 6574 max 6574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49030.0 ave 49030 max 49030 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98060.0 ave 98060 max 98060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98060 Ave neighs/atom = 165.08418 Neighbor list builds = 0 Dangerous builds = 0 594 -2434.75501616083 eV 2.34508917330686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10