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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -51.123823 0.0000000) to (25.561911 51.123823 3.6150002) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0899058 4.0899058 3.6150002 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -51.123823 0.0000000) to (25.561911 51.123823 3.6150002) create_atoms CPU = 0.002 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0899058 4.0899058 3.6150002 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -51.123823 0.0000000) to (25.561911 51.123823 3.6150002) create_atoms CPU = 0.001 seconds 402 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 27 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2749.4011 0 -2749.4011 3722.7568 54 0 -2808.9197 0 -2808.9197 -1956.3208 Loop time of 1.3775 on 1 procs for 54 steps with 796 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 = -2749.4011357568 -2808.91691125698 -2808.91970552206 Force two-norm initial, final = 40.607526 0.15737784 Force max component initial, final = 9.8536508 0.023661847 Final line search alpha, max atom move = 1.0000000 0.023661847 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3297 | 1.3297 | 1.3297 | 0.0 | 96.53 Neigh | 0.018698 | 0.018698 | 0.018698 | 0.0 | 1.36 Comm | 0.017248 | 0.017248 | 0.017248 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01188 | | | 0.86 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7257.00 ave 7257 max 7257 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: 131004.0 ave 131004 max 131004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131004 Ave neighs/atom = 164.57789 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.974 | 4.974 | 4.974 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2808.9197 0 -2808.9197 -1956.3208 9448.3279 59 0 -2808.9486 0 -2808.9486 23.870518 9434.5736 Loop time of 0.126695 on 1 procs for 5 steps with 796 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 = -2808.91970552207 -2808.94859054812 -2808.94859707064 Force two-norm initial, final = 22.491000 0.35133895 Force max component initial, final = 18.328034 0.26638684 Final line search alpha, max atom move = 0.0029300915 0.00078053783 Iterations, force evaluations = 5 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12098 | 0.12098 | 0.12098 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014112 | 0.0014112 | 0.0014112 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004299 | | | 3.39 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7278.00 ave 7278 max 7278 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: 133036.0 ave 133036 max 133036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133036 Ave neighs/atom = 167.13065 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2808.9486 0 -2808.9486 23.870518 Loop time of 6.395e-06 on 1 procs for 0 steps with 796 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7288.00 ave 7288 max 7288 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: 134568.0 ave 134568 max 134568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134568 Ave neighs/atom = 169.05528 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.112 | 5.112 | 5.112 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 -2808.9486 -2808.9486 25.538007 101.93972 3.6240305 23.870518 23.870518 1.4410382 24.819777 45.35074 2.3364772 208.563 Loop time of 6.756e-06 on 1 procs for 0 steps with 796 atoms 266.4% 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 | | 6.756e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7288.00 ave 7288 max 7288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67284.0 ave 67284 max 67284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134568.0 ave 134568 max 134568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134568 Ave neighs/atom = 169.05528 Neighbor list builds = 0 Dangerous builds = 0 796 -2808.94859707064 eV 2.33647718911607 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01