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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -49.045453 0.0000000) to (24.521291 49.045453 2.8700001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6949891 3.6949891 2.8700001 Created 293 atoms using lattice units in orthogonal box = (0.0000000 -49.045453 0.0000000) to (24.521291 49.045453 2.8700001) create_atoms CPU = 0.002 seconds 293 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6949891 3.6949891 2.8700001 Created 293 atoms using lattice units in orthogonal box = (0.0000000 -49.045453 0.0000000) to (24.521291 49.045453 2.8700001) create_atoms CPU = 0.001 seconds 293 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 32 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 578 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2449.2191 0 -2449.2191 1762.1401 22 0 -2462.7201 0 -2462.7201 -4465.7947 Loop time of 0.20427 on 1 procs for 22 steps with 578 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 = -2449.21905856586 -2462.71775827274 -2462.7200644291 Force two-norm initial, final = 30.664569 0.15789825 Force max component initial, final = 14.550745 0.022648047 Final line search alpha, max atom move = 1.0000000 0.022648047 Iterations, force evaluations = 22 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19567 | 0.19567 | 0.19567 | 0.0 | 95.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047369 | 0.0047369 | 0.0047369 | 0.0 | 2.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003859 | | | 1.89 Nlocal: 578.000 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4809.00 ave 4809 max 4809 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: 37184.0 ave 37184 max 37184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37184 Ave neighs/atom = 64.332180 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -2462.7201 0 -2462.7201 -4465.7947 6903.2562 27 0 -2462.7946 0 -2462.7946 1841.2379 6877.2016 Loop time of 0.0495868 on 1 procs for 5 steps with 578 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2462.7200644291 -2462.79412496291 -2462.79456286718 Force two-norm initial, final = 44.191348 0.19248753 Force max component initial, final = 38.902053 0.034904685 Final line search alpha, max atom move = 0.00025430864 8.8765631e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045153 | 0.045153 | 0.045153 | 0.0 | 91.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010402 | 0.0010402 | 0.0010402 | 0.0 | 2.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003394 | | | 6.84 Nlocal: 578.000 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4796.00 ave 4796 max 4796 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: 37354.0 ave 37354 max 37354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37354 Ave neighs/atom = 64.626298 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2462.7946 0 -2462.7946 1841.2379 Loop time of 8.43e-06 on 1 procs for 0 steps with 578 atoms 189.8% 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 | | 8.43e-06 | | |100.00 Nlocal: 578.000 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4796.00 ave 4796 max 4796 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: 37410.0 ave 37410 max 37410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37410 Ave neighs/atom = 64.723183 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.639 | 4.639 | 4.639 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 -2462.7946 -2462.7946 24.523137 98.090906 2.8589529 1841.2379 1841.2379 -2.7507377 5525.7057 0.75882176 2.3367122 265.70012 Loop time of 6.996e-06 on 1 procs for 0 steps with 578 atoms 214.4% 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 | | 6.996e-06 | | |100.00 Nlocal: 578.000 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4796.00 ave 4796 max 4796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18705.0 ave 18705 max 18705 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37410.0 ave 37410 max 37410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37410 Ave neighs/atom = 64.723183 Neighbor list builds = 0 Dangerous builds = 0 578 -2462.79450506718 eV 2.33671223656214 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00