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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -62.700239 0.0000000) to (25.597265 62.700239 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1433437 5.4340207 5.9114352 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -62.700239 0.0000000) to (25.597265 62.700239 8.8671528) create_atoms CPU = 0.007 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1433437 5.4340207 5.9114352 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -62.700239 0.0000000) to (25.597265 62.700239 8.8671528) create_atoms CPU = 0.005 seconds 1205 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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2402 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_313717476091_001#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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7328.9079 0 -7328.9079 91756.478 28 0 -8471.3291 0 -8471.3291 5862.3512 Loop time of 4.43743 on 1 procs for 28 steps with 2402 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 = -7328.9078833807 -8471.32072879767 -8471.32914830959 Force two-norm initial, final = 2570.5282 2.9005887 Force max component initial, final = 698.31098 0.66653001 Final line search alpha, max atom move = 0.15545359 0.10361448 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4169 | 4.4169 | 4.4169 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.008116 | 0.008116 | 0.008116 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01238 | | | 0.28 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6572.00 ave 6572 max 6572 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: 187136.0 ave 187136 max 187136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187136 Ave neighs/atom = 77.908410 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 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -8471.3291 0 -8471.3291 5862.3512 28462.756 34 0 -8471.7939 0 -8471.7939 -59.635705 28585.983 Loop time of 0.695486 on 1 procs for 6 steps with 2402 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8471.32914830959 -8471.79315341595 -8471.79392167784 Force two-norm initial, final = 208.93140 3.8231808 Force max component initial, final = 189.30546 2.4051713 Final line search alpha, max atom move = 0.00014170338 0.00034082090 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6885 | 0.6885 | 0.6885 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012353 | 0.0012353 | 0.0012353 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00575 | | | 0.83 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6586.00 ave 6586 max 6586 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: 186364.0 ave 186364 max 186364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186364 Ave neighs/atom = 77.587011 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 ghost atom cutoff = 6 binsize = 3, bins = 9 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.270 | 5.270 | 5.270 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8471.7939 0 -8471.7939 -59.635705 Loop time of 6.635e-06 on 1 procs for 0 steps with 2402 atoms 195.9% 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 | | 6.635e-06 | | |100.00 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6586.00 ave 6586 max 6586 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: 186296.0 ave 186296 max 186296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186296 Ave neighs/atom = 77.558701 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 ghost atom cutoff = 6 binsize = 3, bins = 9 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.270 | 5.270 | 5.270 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 -8471.7939 -8471.7939 25.604637 126.04249 8.8576301 -59.635705 -59.635705 -27.670308 -16.577431 -134.65938 2.1985557 884.98954 Loop time of 8.239e-06 on 1 procs for 0 steps with 2402 atoms 230.6% 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 | | 8.239e-06 | | |100.00 Nlocal: 2402.00 ave 2402 max 2402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6586.00 ave 6586 max 6586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93148.0 ave 93148 max 93148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186296.0 ave 186296 max 186296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186296 Ave neighs/atom = 77.558701 Neighbor list builds = 0 Dangerous builds = 0 2402 -8471.79392167784 eV 2.19855572712673 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05