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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -47.906004 0.0000000) to (29.336316 47.906004 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3338757 5.4438641 5.8968214 Created 1037 atoms using lattice units in orthogonal box = (0.0000000 -47.906004 0.0000000) to (29.336316 47.906004 8.8452321) create_atoms CPU = 0.002 seconds 1037 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3338757 5.4438641 5.8968214 Created 1061 atoms using lattice units in orthogonal box = (0.0000000 -47.906004 0.0000000) to (29.336316 47.906004 8.8452321) create_atoms CPU = 0.001 seconds 1061 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2093 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.097 | 8.097 | 8.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8555.8262 0 -8555.8262 8711.3653 161 0 -8673.1974 0 -8673.1974 -11601.114 Loop time of 9.28463 on 1 procs for 161 steps with 2093 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 = -8555.82617219466 -8673.18904313936 -8673.19744029991 Force two-norm initial, final = 69.477049 0.42050076 Force max component initial, final = 9.1836733 0.11600954 Final line search alpha, max atom move = 0.94606753 0.10975286 Iterations, force evaluations = 161 293 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0087 | 9.0087 | 9.0087 | 0.0 | 97.03 Neigh | 0.18389 | 0.18389 | 0.18389 | 0.0 | 1.98 Comm | 0.053214 | 0.053214 | 0.053214 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03888 | | | 0.42 Nlocal: 2093.00 ave 2093 max 2093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12361.0 ave 12361 max 12361 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: 793138.0 ave 793138 max 793138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793138 Ave neighs/atom = 378.94792 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 161 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.097 | 8.097 | 8.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 161 0 -8673.1974 0 -8673.1974 -11601.114 24861.925 166 0 -8673.8925 0 -8673.8925 -37.468048 24692.081 Loop time of 0.249212 on 1 procs for 5 steps with 2093 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 = -8673.19744029989 -8673.89154553344 -8673.89253663005 Force two-norm initial, final = 319.67226 2.7892100 Force max component initial, final = 222.62805 1.7292768 Final line search alpha, max atom move = 0.00011383547 0.00019685303 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24427 | 0.24427 | 0.24427 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083542 | 0.00083542 | 0.00083542 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004102 | | | 1.65 Nlocal: 2093.00 ave 2093 max 2093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12379.0 ave 12379 max 12379 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: 793754.0 ave 793754 max 793754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 793754 Ave neighs/atom = 379.24224 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.235 | 8.235 | 8.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8673.8925 0 -8673.8925 -37.468048 Loop time of 2.241e-06 on 1 procs for 0 steps with 2093 atoms 223.1% 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 | | 2.241e-06 | | |100.00 Nlocal: 2093.00 ave 2093 max 2093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12405.0 ave 12405 max 12405 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: 794834.0 ave 794834 max 794834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 794834 Ave neighs/atom = 379.75824 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 8.235 | 8.235 | 8.235 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 -8673.8925 -8673.8925 29.264466 95.458913 8.8389487 -37.468048 -37.468048 97.854082 -98.131654 -112.12657 2.2570516 597.89355 Loop time of 3.189e-06 on 1 procs for 0 steps with 2093 atoms 250.9% 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 | | 3.189e-06 | | |100.00 Nlocal: 2093.00 ave 2093 max 2093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12405.0 ave 12405 max 12405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 397417.0 ave 397417 max 397417 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 794834.0 ave 794834 max 794834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 794834 Ave neighs/atom = 379.75824 Neighbor list builds = 0 Dangerous builds = 0 2093 -8673.89253663005 eV 2.25705163463477 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10