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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -42.432068 0.0000000) to (51.963503 42.432068 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6135368 6.1713487 6.6060342 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -42.432068 0.0000000) to (51.963503 42.432068 9.9090513) create_atoms CPU = 0.002 seconds 1324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6135368 6.1713487 6.6060342 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -42.432068 0.0000000) to (51.963503 42.432068 9.9090513) create_atoms CPU = 0.002 seconds 1324 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 2592 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8651 0 -8651 -3099.9484 34 0 -8672.5454 0 -8672.5454 -8964.1251 Loop time of 7.08497 on 1 procs for 34 steps with 2592 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8651.00000875622 -8672.53728099394 -8672.5453778684 Force two-norm initial, final = 11.039688 0.20751521 Force max component initial, final = 1.2617621 0.022467152 Final line search alpha, max atom move = 1.0000000 0.022467152 Iterations, force evaluations = 34 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0385 | 7.0385 | 7.0385 | 0.0 | 99.34 Neigh | 0.026175 | 0.026175 | 0.026175 | 0.0 | 0.37 Comm | 0.0074665 | 0.0074665 | 0.0074665 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01284 | | | 0.18 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5719.00 ave 5719 max 5719 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: 140292.0 ave 140292 max 140292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140292 Ave neighs/atom = 54.125000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -8672.5454 0 -8672.5454 -8964.1251 43697.309 41 0 -8673.6736 0 -8673.6736 -1854.8783 43259.708 Loop time of 1.3748 on 1 procs for 7 steps with 2592 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8672.54537786837 -8673.67123125034 -8673.67361991871 Force two-norm initial, final = 310.10990 0.29434172 Force max component initial, final = 235.25675 0.032990229 Final line search alpha, max atom move = 0.00013527248 4.4626702e-06 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3671 | 1.3671 | 1.3671 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092721 | 0.00092721 | 0.00092721 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006722 | | | 0.49 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5701.00 ave 5701 max 5701 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: 140412.0 ave 140412 max 140412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140412 Ave neighs/atom = 54.171296 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.250 | 5.250 | 5.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8673.6736 0 -8673.6736 -1854.8783 Loop time of 3.095e-06 on 1 procs for 0 steps with 2592 atoms 161.6% 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 | | 3.095e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5701.00 ave 5701 max 5701 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: 140618.0 ave 140618 max 140618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140618 Ave neighs/atom = 54.250772 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 17 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.250 | 5.250 | 5.250 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 -8673.6736 -8673.6736 51.761925 84.864136 9.8480209 -1854.8783 -1854.8783 -0.62375202 -5564.1704 0.15939416 2.5497558 1649.0103 Loop time of 3.168e-06 on 1 procs for 0 steps with 2592 atoms 189.4% 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 | | 3.168e-06 | | |100.00 Nlocal: 2592.00 ave 2592 max 2592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5701.00 ave 5701 max 5701 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70309.0 ave 70309 max 70309 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140618.0 ave 140618 max 140618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140618 Ave neighs/atom = 54.250772 Neighbor list builds = 0 Dangerous builds = 0 2592 -8673.67361991871 eV 2.54975575795591 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09