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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -38.426064 0.0000000) to (19.213032 38.426064 2.4599767) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4646451 3.4646451 2.4599767 Created 244 atoms using lattice units in orthogonal box = (0.0000000 -38.426064 0.0000000) to (19.213032 38.426064 2.4599767) create_atoms CPU = 0.002 seconds 244 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4646451 3.4646451 2.4599767 Created 245 atoms using lattice units in orthogonal box = (0.0000000 -38.426064 0.0000000) to (19.213032 38.426064 2.4599767) create_atoms CPU = 0.001 seconds 245 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 21 1 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 485 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5074.1923 0 -5074.1923 799826.25 110 0 -6133.2298 0 -6133.2298 8119.4068 Loop time of 18.2089 on 1 procs for 110 steps with 485 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 = -5074.1923118476 -6133.22372771626 -6133.22977144928 Force two-norm initial, final = 5189.3929 0.70906514 Force max component initial, final = 2435.4972 0.10720725 Final line search alpha, max atom move = 0.34580079 0.037072351 Iterations, force evaluations = 110 207 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.144 | 18.144 | 18.144 | 0.0 | 99.65 Neigh | 0.014349 | 0.014349 | 0.014349 | 0.0 | 0.08 Comm | 0.031404 | 0.031404 | 0.031404 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0188 | | | 0.10 Nlocal: 485.000 ave 485 max 485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6683.00 ave 6683 max 6683 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: 122784.0 ave 122784 max 122784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122784 Ave neighs/atom = 253.16289 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -6133.2298 0 -6133.2298 8119.4068 3632.3091 142 0 -6136.4499 0 -6136.4499 2612.1314 3638.3498 Loop time of 2.91588 on 1 procs for 32 steps with 485 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 = -6133.22977144929 -6136.44463107365 -6136.44992395143 Force two-norm initial, final = 172.86930 14.291943 Force max component initial, final = 119.51041 13.369613 Final line search alpha, max atom move = 9.6094447e-05 0.0012847456 Iterations, force evaluations = 32 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8817 | 2.8817 | 2.8817 | 0.0 | 98.83 Neigh | 0.014153 | 0.014153 | 0.014153 | 0.0 | 0.49 Comm | 0.0050307 | 0.0050307 | 0.0050307 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01501 | | | 0.51 Nlocal: 485.000 ave 485 max 485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 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: 121942.0 ave 121942 max 121942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121942 Ave neighs/atom = 251.42680 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.057 | 5.057 | 5.057 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6136.4499 0 -6136.4499 2612.1314 Loop time of 6.044e-06 on 1 procs for 0 steps with 485 atoms 165.5% 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 | | 6.044e-06 | | |100.00 Nlocal: 485.000 ave 485 max 485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 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: 121860.0 ave 121860 max 121860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121860 Ave neighs/atom = 251.25773 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.057 | 5.057 | 5.057 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 -6136.4499 -6136.4499 19.498592 78.108066 2.3889404 2612.1314 2612.1314 1133.2662 985.72144 5717.4064 2.0362369 164.73387 Loop time of 7.196e-06 on 1 procs for 0 steps with 485 atoms 250.1% 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 | | 7.196e-06 | | |100.00 Nlocal: 485.000 ave 485 max 485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6634.00 ave 6634 max 6634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60930.0 ave 60930 max 60930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121860.0 ave 121860 max 121860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121860 Ave neighs/atom = 251.25773 Neighbor list builds = 0 Dangerous builds = 0 485 -6136.44992395143 eV 2.03623685401235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21