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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -42.349098 0.0000000) to (29.945334 42.349098 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8102887 6.3207608 5.1737657 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -42.349098 0.0000000) to (29.945334 42.349098 5.1737657) create_atoms CPU = 0.001 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8102887 6.3207608 5.1737657 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -42.349098 0.0000000) to (29.945334 42.349098 5.1737657) create_atoms CPU = 0.001 seconds 538 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1068 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_249706810527_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.012 | 5.012 | 5.012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3892.4136 0 -3892.4136 59071.719 648 0 -4226.4496 0 -4226.4496 -69575.158 Loop time of 9.75135 on 1 procs for 648 steps with 1068 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3892.41363295729 -4226.44631294935 -4226.44963155495 Force two-norm initial, final = 645.20443 0.19806413 Force max component initial, final = 205.87902 0.036969849 Final line search alpha, max atom move = 1.0000000 0.036969849 Iterations, force evaluations = 648 1205 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4644 | 9.4644 | 9.4644 | 0.0 | 97.06 Neigh | 0.14157 | 0.14157 | 0.14157 | 0.0 | 1.45 Comm | 0.077295 | 0.077295 | 0.077295 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06811 | | | 0.70 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6036.00 ave 6036 max 6036 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: 144008.0 ave 144008 max 144008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 144008 Ave neighs/atom = 134.83895 Neighbor list builds = 15 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 648 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.010 | 5.010 | 5.010 Mbytes Step Temp E_pair E_mol TotEng Press Volume 648 0 -4226.4496 0 -4226.4496 -69575.158 13122.304 695 0 -4253.7955 0 -4253.7955 69.797404 12477.372 Loop time of 0.429754 on 1 procs for 47 steps with 1068 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 = -4226.44963155496 -4253.79411515182 -4253.79551975223 Force two-norm initial, final = 1111.6329 5.9738071 Force max component initial, final = 922.02925 4.4070006 Final line search alpha, max atom move = 0.00063651828 0.0028051364 Iterations, force evaluations = 47 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40279 | 0.40279 | 0.40279 | 0.0 | 93.73 Neigh | 0.0097968 | 0.0097968 | 0.0097968 | 0.0 | 2.28 Comm | 0.0027759 | 0.0027759 | 0.0027759 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01439 | | | 3.35 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6194.00 ave 6194 max 6194 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: 148840.0 ave 148840 max 148840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148840 Ave neighs/atom = 139.36330 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4253.7955 0 -4253.7955 69.797404 Loop time of 1.895e-06 on 1 procs for 0 steps with 1068 atoms 158.3% 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 | | 1.895e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254.00 ave 6254 max 6254 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: 149832.0 ave 149832 max 149832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149832 Ave neighs/atom = 140.29213 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.149 | 5.149 | 5.149 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 -4253.7955 -4253.7955 30.310042 83.266308 4.9438727 69.797404 69.797404 -21.009884 556.32104 -325.91895 2.2894604 3303.3042 Loop time of 2.915e-06 on 1 procs for 0 steps with 1068 atoms 240.1% 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 | | 2.915e-06 | | |100.00 Nlocal: 1068.00 ave 1068 max 1068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6254.00 ave 6254 max 6254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 74916.0 ave 74916 max 74916 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 149832.0 ave 149832 max 149832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149832 Ave neighs/atom = 140.29213 Neighbor list builds = 0 Dangerous builds = 0 1068 -4253.79551975223 eV 2.28946043125072 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10