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 = 2.8169555 2.8169555 2.8169555 Created orthogonal box = (0.0000000 -56.479783 0.0000000) to (32.608618 56.479783 4.8791101) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3802621 4.4959031 4.8791101 Created 804 atoms using lattice units in orthogonal box = (0.0000000 -56.479783 0.0000000) to (32.608618 56.479783 4.8791101) create_atoms CPU = 0.006 seconds 804 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3802621 4.4959031 4.8791101 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -56.479783 0.0000000) to (32.608618 56.479783 4.8791101) create_atoms CPU = 0.005 seconds 806 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1604 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.569 | 5.569 | 5.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5572.8907 0 -5572.8907 151079.92 271 0 -6426.2867 0 -6426.2867 73011.381 Loop time of 18.4999 on 1 procs for 271 steps with 1604 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5572.89065284556 -6426.28208618189 -6426.28673649529 Force two-norm initial, final = 1291.8864 0.27664099 Force max component initial, final = 406.66678 0.080594002 Final line search alpha, max atom move = 0.81896618 0.066003763 Iterations, force evaluations = 271 519 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.112 | 18.112 | 18.112 | 0.0 | 97.90 Neigh | 0.16461 | 0.16461 | 0.16461 | 0.0 | 0.89 Comm | 0.12667 | 0.12667 | 0.12667 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09664 | | | 0.52 Nlocal: 1604.00 ave 1604 max 1604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10098.0 ave 10098 max 10098 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: 295344.0 ave 295344 max 295344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295344 Ave neighs/atom = 184.12968 Neighbor list builds = 4 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 271 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.949 | 5.949 | 5.949 Mbytes Step Temp E_pair E_mol TotEng Press Volume 271 0 -6426.2867 0 -6426.2867 73011.381 17971.984 313 0 -6445.9862 0 -6445.9862 -199.82016 18602.928 Loop time of 1.86441 on 1 procs for 42 steps with 1604 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6426.2867364953 -6445.98240228277 -6445.9861676851 Force two-norm initial, final = 1463.3126 7.5622887 Force max component initial, final = 1008.6719 4.2722521 Final line search alpha, max atom move = 0.00011691026 0.00049947011 Iterations, force evaluations = 42 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7706 | 1.7706 | 1.7706 | 0.0 | 94.97 Neigh | 0.039095 | 0.039095 | 0.039095 | 0.0 | 2.10 Comm | 0.012364 | 0.012364 | 0.012364 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04233 | | | 2.27 Nlocal: 1604.00 ave 1604 max 1604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 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: 291250.0 ave 291250 max 291250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291250 Ave neighs/atom = 181.57731 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.705 | 5.705 | 5.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6445.9862 0 -6445.9862 -199.82016 Loop time of 6.365e-06 on 1 procs for 0 steps with 1604 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1604.00 ave 1604 max 1604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9968.00 ave 9968 max 9968 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: 288548.0 ave 288548 max 288548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288548 Ave neighs/atom = 179.89277 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 ghost atom cutoff = 8 binsize = 4, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.705 | 5.705 | 5.705 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 -6445.9862 -6445.9862 33.383547 114.48349 4.8675001 -199.82016 -199.82016 14.218391 -246.60687 -367.07201 2.2679055 8536.6281 Loop time of 6.736e-06 on 1 procs for 0 steps with 1604 atoms 311.8% 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 | | 6.736e-06 | | |100.00 Nlocal: 1604.00 ave 1604 max 1604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9968.00 ave 9968 max 9968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144274.0 ave 144274 max 144274 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288548.0 ave 288548 max 288548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288548 Ave neighs/atom = 179.89277 Neighbor list builds = 0 Dangerous builds = 0 1604 -6445.9861676851 eV 2.26790553097435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21