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 = 3.6148132 3.6148132 3.6148132 Created orthogonal box = (0.0000000 -44.712770 0.0000000) to (14.904257 44.712770 3.6148132) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3836049 4.3836049 3.6148132 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.712770 0.0000000) to (14.904257 44.712770 3.6148132) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3836049 4.3836049 3.6148132 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.712770 0.0000000) to (14.904257 44.712770 3.6148132) create_atoms CPU = 0.000 seconds 206 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 17 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 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_380822813353_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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1405.3804 0 -1405.3804 21388.808 51 0 -1438.5535 0 -1438.5535 5243.4508 Loop time of 1.28239 on 1 procs for 51 steps with 408 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 = -1405.38039719277 -1438.55214060155 -1438.55353695443 Force two-norm initial, final = 82.045165 0.10214334 Force max component initial, final = 27.731878 0.022980267 Final line search alpha, max atom move = 1.0000000 0.022980267 Iterations, force evaluations = 51 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2588 | 1.2588 | 1.2588 | 0.0 | 98.16 Neigh | 0.010897 | 0.010897 | 0.010897 | 0.0 | 0.85 Comm | 0.0086398 | 0.0086398 | 0.0086398 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004057 | | | 0.32 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8412.00 ave 8412 max 8412 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: 187520.0 ave 187520 max 187520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187520 Ave neighs/atom = 459.60784 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -1438.5535 0 -1438.5535 5243.4508 4817.8998 56 0 -1438.6007 0 -1438.6007 -3.6815479 4836.7072 Loop time of 0.0994009 on 1 procs for 5 steps with 408 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 = -1438.55353695443 -1438.60008199656 -1438.60074130305 Force two-norm initial, final = 28.629990 0.28539857 Force max component initial, final = 22.454207 0.18997322 Final line search alpha, max atom move = 0.00021997362 4.1789096e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096874 | 0.096874 | 0.096874 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051382 | 0.00051382 | 0.00051382 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002013 | | | 2.02 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8412.00 ave 8412 max 8412 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: 187536.0 ave 187536 max 187536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187536 Ave neighs/atom = 459.64706 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1438.6007 0 -1438.6007 -3.6815479 Loop time of 1.878e-06 on 1 procs for 0 steps with 408 atoms 159.7% 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 | | 1.878e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8342.00 ave 8342 max 8342 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: 187260.0 ave 187260 max 187260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187260 Ave neighs/atom = 458.97059 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.037500000000001 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) = 5.095 | 5.095 | 5.095 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 -1438.6007 -1438.6007 14.8909 89.814202 3.6164615 -3.6815479 -3.6815479 44.591931 7.3214248 -62.958 2.2925056 188.26506 Loop time of 2.667e-06 on 1 procs for 0 steps with 408 atoms 187.5% 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 | | 2.667e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8342.00 ave 8342 max 8342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93630.0 ave 93630 max 93630 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187260.0 ave 187260 max 187260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187260 Ave neighs/atom = 458.97059 Neighbor list builds = 0 Dangerous builds = 0 408 -1438.60074130305 eV 2.2925055721626 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01