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 = 3.6150004 3.6150004 3.6150004 Created orthogonal box = (0.0000000 -56.468111 0.0000000) to (28.234055 56.468111 3.6150004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0913870 5.0913870 3.6150004 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.468111 0.0000000) to (28.234055 56.468111 3.6150004) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0913870 5.0913870 3.6150004 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.468111 0.0000000) to (28.234055 56.468111 3.6150004) create_atoms CPU = 0.002 seconds 490 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 36 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 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_762798677854_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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3272.1132 0 -3272.1132 81922.857 60 0 -3433.5462 0 -3433.5462 8244.1236 Loop time of 1.05074 on 1 procs for 60 steps with 978 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 = -3272.11324316948 -3433.54307642865 -3433.54618483608 Force two-norm initial, final = 827.35578 0.15177388 Force max component initial, final = 220.35453 0.027739121 Final line search alpha, max atom move = 1.0000000 0.027739121 Iterations, force evaluations = 60 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0079 | 1.0079 | 1.0079 | 0.0 | 95.92 Neigh | 0.013885 | 0.013885 | 0.013885 | 0.0 | 1.32 Comm | 0.015202 | 0.015202 | 0.015202 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01379 | | | 1.31 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6151.00 ave 6151 max 6151 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: 84000.0 ave 84000 max 84000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84000 Ave neighs/atom = 85.889571 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3433.5462 0 -3433.5462 8244.1236 11526.962 66 0 -3433.806 0 -3433.806 -373.43084 11592.033 Loop time of 0.0766072 on 1 procs for 6 steps with 978 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 = -3433.54618483608 -3433.8047196186 -3433.80598662369 Force two-norm initial, final = 114.42500 5.6557280 Force max component initial, final = 98.440155 5.0537886 Final line search alpha, max atom move = 0.00024739457 0.0012502799 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071891 | 0.071891 | 0.071891 | 0.0 | 93.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010021 | 0.0010021 | 0.0010021 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003714 | | | 4.85 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6154.00 ave 6154 max 6154 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: 84136.0 ave 84136 max 84136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84136 Ave neighs/atom = 86.028630 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.738 | 4.738 | 4.738 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3433.806 0 -3433.806 -373.43084 Loop time of 7.257e-06 on 1 procs for 0 steps with 978 atoms 192.9% 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 | | 7.257e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6154.00 ave 6154 max 6154 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: 84068.0 ave 84068 max 84068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84068 Ave neighs/atom = 85.959100 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.738 | 4.738 | 4.738 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 -3433.806 -3433.806 28.227766 113.5382 3.6169383 -373.43084 -373.43084 -79.163847 -342.25196 -698.87671 2.2788982 136.22346 Loop time of 7.177e-06 on 1 procs for 0 steps with 978 atoms 264.7% 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 | | 7.177e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6154.00 ave 6154 max 6154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42034.0 ave 42034 max 42034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84068.0 ave 84068 max 84068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84068 Ave neighs/atom = 85.959100 Neighbor list builds = 0 Dangerous builds = 0 978 -3433.80598662369 eV 2.27889823902465 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01