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 = 3.6150007 3.6150007 3.6150007 Created orthogonal box = (0.0000000 -65.470447 0.0000000) to (23.147299 65.470447 5.1123830) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2102508 5.5889406 5.1123830 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.470447 0.0000000) to (23.147299 65.470447 5.1123830) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2102508 5.5889406 5.1123830 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.470447 0.0000000) to (23.147299 65.470447 5.1123830) create_atoms CPU = 0.002 seconds 658 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 8 41 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 6.428375000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_642748370624_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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4411.5128 0 -4411.5128 63755.055 72 0 -4605.8074 0 -4605.8074 5871.4822 Loop time of 0.715185 on 1 procs for 72 steps with 1312 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 = -4411.51284246544 -4605.80305869865 -4605.80736744556 Force two-norm initial, final = 1118.4028 0.17342459 Force max component initial, final = 346.63213 0.029142595 Final line search alpha, max atom move = 1.0000000 0.029142595 Iterations, force evaluations = 72 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6845 | 0.6845 | 0.6845 | 0.0 | 95.71 Neigh | 0.016801 | 0.016801 | 0.016801 | 0.0 | 2.35 Comm | 0.0069287 | 0.0069287 | 0.0069287 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006953 | | | 0.97 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6493.00 ave 6493 max 6493 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: 112880.0 ave 112880 max 112880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112880 Ave neighs/atom = 86.036585 Neighbor list builds = 2 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 8 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -4605.8074 0 -4605.8074 5871.4822 15495.265 76 0 -4605.9675 0 -4605.9675 -294.972 15555.164 Loop time of 0.0334571 on 1 procs for 4 steps with 1312 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 = -4605.80736744556 -4605.96576116215 -4605.96747933906 Force two-norm initial, final = 106.39066 6.0163658 Force max component initial, final = 77.125511 5.0976327 Final line search alpha, max atom move = 0.00012259941 0.00062496677 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031661 | 0.031661 | 0.031661 | 0.0 | 94.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003219 | 0.0003219 | 0.0003219 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001474 | | | 4.41 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6521.00 ave 6521 max 6521 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: 113088.0 ave 113088 max 113088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113088 Ave neighs/atom = 86.195122 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 5.210 | 5.210 | 5.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4605.9675 0 -4605.9675 -294.972 Loop time of 1.736e-06 on 1 procs for 0 steps with 1312 atoms 172.8% 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 | | 1.736e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6521.00 ave 6521 max 6521 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: 113048.0 ave 113048 max 113048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113048 Ave neighs/atom = 86.164634 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 = 6.428375 ghost atom cutoff = 6.428375 binsize = 3.2141875, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.428375000000001 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) = 5.210 | 5.210 | 5.210 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 -4605.9675 -4605.9675 23.191666 131.30724 5.1080361 -294.972 -294.972 -327.0965 -33.211542 -524.60797 2.3383497 479.05761 Loop time of 3.177e-06 on 1 procs for 0 steps with 1312 atoms 220.3% 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 | | 3.177e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6521.00 ave 6521 max 6521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56524.0 ave 56524 max 56524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113048.0 ave 113048 max 113048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113048 Ave neighs/atom = 86.164634 Neighbor list builds = 0 Dangerous builds = 0 1312 -4605.96747933906 eV 2.33834968848172 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01