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 = 3.6149390 3.6149390 3.6149390 Created orthogonal box = (0.0000000 -44.273780 0.0000000) to (6.2612581 44.273780 5.1122958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2612581 5.9031707 5.1122958 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -44.273780 0.0000000) to (6.2612581 44.273780 5.1122958) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2612581 5.9031707 5.1122958 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.273780 0.0000000) to (6.2612581 44.273780 5.1122958) create_atoms CPU = 0.000 seconds 122 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 22 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 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_547744193826_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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -826.99439 0 -826.99439 29221.587 89 0 -847.48823 0 -847.48823 10281.909 Loop time of 0.484754 on 1 procs for 89 steps with 240 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -826.994393965152 -847.48738956434 -847.488233730692 Force two-norm initial, final = 46.638689 0.090169169 Force max component initial, final = 17.323320 0.018018726 Final line search alpha, max atom move = 1.0000000 0.018018726 Iterations, force evaluations = 89 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47293 | 0.47293 | 0.47293 | 0.0 | 97.56 Neigh | 0.0030626 | 0.0030626 | 0.0030626 | 0.0 | 0.63 Comm | 0.0058753 | 0.0058753 | 0.0058753 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002886 | | | 0.60 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4244.00 ave 4244 max 4244 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: 48512.0 ave 48512 max 48512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48512 Ave neighs/atom = 202.13333 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -847.48823 0 -847.48823 10281.909 2834.3546 95 0 -847.57104 0 -847.57104 13.743853 2855.2747 Loop time of 0.0262059 on 1 procs for 6 steps with 240 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 = -847.488233730692 -847.570853422978 -847.571039446435 Force two-norm initial, final = 32.634204 0.18351684 Force max component initial, final = 22.109234 0.076574102 Final line search alpha, max atom move = 0.00091105636 6.9763323e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.024863 | 0.024863 | 0.024863 | 0.0 | 94.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002996 | 0.0002996 | 0.0002996 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001043 | | | 3.98 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 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: 48228.0 ave 48228 max 48228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48228 Ave neighs/atom = 200.95000 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.634 | 4.634 | 4.634 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -847.57104 0 -847.57104 13.743853 Loop time of 1.541e-06 on 1 procs for 0 steps with 240 atoms 129.8% 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 | | 1.541e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 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: 48084.0 ave 48084 max 48084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48084 Ave neighs/atom = 200.35000 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 = 8.3953371 ghost atom cutoff = 8.3953371 binsize = 4.1976686, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337104797363 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) = 4.634 | 4.634 | 4.634 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 -847.57104 -847.57104 6.2845086 88.933274 5.1087223 13.743853 13.743853 -39.840392 38.134061 42.93789 2.4621065 161.6109 Loop time of 1.576e-06 on 1 procs for 0 steps with 240 atoms 126.9% 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 | | 1.576e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4485.00 ave 4485 max 4485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24042.0 ave 24042 max 24042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48084.0 ave 48084 max 48084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48084 Ave neighs/atom = 200.35000 Neighbor list builds = 0 Dangerous builds = 0 240 -847.571039446435 eV 2.4621064891595 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00