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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -41.805099 0.0000000) to (29.558116 41.805099 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7351568 6.2390281 5.1068646 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.805099 0.0000000) to (29.558116 41.805099 5.1068646) create_atoms CPU = 0.001 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7351568 6.2390281 5.1068646 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.805099 0.0000000) to (29.558116 41.805099 5.1068646) 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 10 28 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1064 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_150993986463_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 ghost atom cutoff = 6 binsize = 3, bins = 10 28 2 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4473.5795 0 -4473.5795 5350.5318 342 0 -4525.1125 0 -4525.1125 -6489.0595 Loop time of 38.0458 on 1 procs for 342 steps with 1064 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 = -4473.57952589419 -4525.1104102494 -4525.11253833079 Force two-norm initial, final = 38.404911 0.64797667 Force max component initial, final = 10.514298 0.26608224 Final line search alpha, max atom move = 0.31728956 0.084425117 Iterations, force evaluations = 342 651 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.841 | 37.841 | 37.841 | 0.0 | 99.46 Neigh | 0.10539 | 0.10539 | 0.10539 | 0.0 | 0.28 Comm | 0.049912 | 0.049912 | 0.049912 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04951 | | | 0.13 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4591.00 ave 4591 max 4591 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: 69720.0 ave 69720 max 69720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69720 Ave neighs/atom = 65.526316 Neighbor list builds = 10 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 = 10 28 2 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 : 342 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press Volume 342 0 -4525.1125 0 -4525.1125 -6489.0595 12620.9 374 0 -4536.8179 0 -4536.8179 -1856.8939 12557.149 Loop time of 2.43786 on 1 procs for 32 steps with 1064 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 = -4525.11253833081 -4536.81431058448 -4536.81793905773 Force two-norm initial, final = 609.09551 0.96262400 Force max component initial, final = 490.60739 0.12486777 Final line search alpha, max atom move = 8.2999240e-05 1.0363930e-05 Iterations, force evaluations = 32 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4203 | 2.4203 | 2.4203 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027266 | 0.0027266 | 0.0027266 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01487 | | | 0.61 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4584.00 ave 4584 max 4584 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: 69280.0 ave 69280 max 69280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69280 Ave neighs/atom = 65.112782 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 = 11 28 2 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) = 4.741 | 4.741 | 4.741 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4536.8179 0 -4536.8179 -1856.8939 Loop time of 3.265e-06 on 1 procs for 0 steps with 1064 atoms 122.5% 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 | | 3.265e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4655.00 ave 4655 max 4655 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: 69342.0 ave 69342 max 69342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69342 Ave neighs/atom = 65.171053 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 = 11 28 2 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) = 4.741 | 4.741 | 4.741 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 -4536.8179 -4536.8179 30.271347 83.610198 4.9613522 -1856.8939 -1856.8939 -10.704688 -5570.8096 10.832594 2.4023107 2057.3022 Loop time of 3.195e-06 on 1 procs for 0 steps with 1064 atoms 125.2% 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 | | 3.195e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4655.00 ave 4655 max 4655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34671.0 ave 34671 max 34671 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69342.0 ave 69342 max 69342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69342 Ave neighs/atom = 65.171053 Neighbor list builds = 0 Dangerous builds = 0 1064 -4536.81793905773 eV 2.40231073979399 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:41