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 = 3.1599882 3.1599882 3.1599882 Created orthogonal box = (0.0000000 -47.714776 0.0000000) to (33.739441 47.714776 4.4688982) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3272802 4.6040573 4.4688982 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.714776 0.0000000) to (33.739441 47.714776 4.4688982) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3272802 4.6040573 4.4688982 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.714776 0.0000000) to (33.739441 47.714776 4.4688982) create_atoms CPU = 0.001 seconds 458 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 11 29 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 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_698578166685_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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20004.69 0 -20004.69 16537.148 47 0 -20303.711 0 -20303.711 9836.4248 Loop time of 25.8207 on 1 procs for 47 steps with 908 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -20004.6903265111 -20303.6979565337 -20303.711461933 Force two-norm initial, final = 302.94394 0.42713362 Force max component initial, final = 75.864461 0.067689546 Final line search alpha, max atom move = 1.0000000 0.067689546 Iterations, force evaluations = 47 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.8 | 25.8 | 25.8 | 0.0 | 99.92 Neigh | 0.0098833 | 0.0098833 | 0.0098833 | 0.0 | 0.04 Comm | 0.0053514 | 0.0053514 | 0.0053514 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005669 | | | 0.02 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4123.00 ave 4123 max 4123 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: 58328.0 ave 58328 max 58328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58328 Ave neighs/atom = 64.237885 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -20303.711 0 -20303.711 9836.4248 14388.689 52 0 -20304.066 0 -20304.066 -183.33341 14443.878 Loop time of 1.93169 on 1 procs for 5 steps with 908 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 = -20303.711461933 -20304.0638262951 -20304.0662808761 Force two-norm initial, final = 180.28616 2.9395358 Force max component initial, final = 162.44966 2.0129548 Final line search alpha, max atom move = 0.00010879342 0.00021899624 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9302 | 1.9302 | 1.9302 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023513 | 0.00023513 | 0.00023513 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001227 | | | 0.06 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4138.00 ave 4138 max 4138 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: 58284.0 ave 58284 max 58284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58284 Ave neighs/atom = 64.189427 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20304.066 0 -20304.066 -183.33341 Loop time of 1.711e-06 on 1 procs for 0 steps with 908 atoms 233.8% 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 | | 1.711e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4138.00 ave 4138 max 4138 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: 58248.0 ave 58248 max 58248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58248 Ave neighs/atom = 64.149780 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 = 6.615858 ghost atom cutoff = 6.615858 binsize = 3.307929, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.615858 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) = 4.692 | 4.692 | 4.692 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 -20304.066 -20304.066 33.76075 95.847545 4.4636562 -183.33341 -183.33341 -168.89971 -158.07692 -223.02361 2.4344289 713.9039 Loop time of 1.553e-06 on 1 procs for 0 steps with 908 atoms 193.2% 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 | | 1.553e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4138.00 ave 4138 max 4138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29124.0 ave 29124 max 29124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58248.0 ave 58248 max 58248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58248 Ave neighs/atom = 64.149780 Neighbor list builds = 0 Dangerous builds = 0 908 -4617.6436577929 eV 2.43442889398691 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:29