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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7363449 5.1518137 6.0968188 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) create_atoms CPU = 0.004 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7363449 5.1518137 6.0968188 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -67.341565 0.0000000) to (38.879671 67.341565 6.0968188) create_atoms CPU = 0.003 seconds 1466 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 32 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_592013496703_005#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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12509.753 0 -12509.753 31542.171 107 0 -12985.14 0 -12985.14 4939.8481 Loop time of 6.56442 on 1 procs for 107 steps with 2926 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 = -12509.7534821442 -12985.1280853911 -12985.1402038106 Force two-norm initial, final = 461.84118 0.40551073 Force max component initial, final = 107.69892 0.10943910 Final line search alpha, max atom move = 0.68691153 0.075174977 Iterations, force evaluations = 107 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3306 | 6.3306 | 6.3306 | 0.0 | 96.44 Neigh | 0.16028 | 0.16028 | 0.16028 | 0.0 | 2.44 Comm | 0.04064 | 0.04064 | 0.04064 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03294 | | | 0.50 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15940.0 ave 15940 max 15940 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: 655012.0 ave 655012 max 655012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 655012 Ave neighs/atom = 223.85919 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.32 | 11.32 | 11.32 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -12985.14 0 -12985.14 4939.8481 31925.6 110 0 -12985.327 0 -12985.327 5.4587367 32013.835 Loop time of 0.196083 on 1 procs for 3 steps with 2926 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 = -12985.1402038106 -12985.3189019914 -12985.3267697301 Force two-norm initial, final = 182.21255 2.4034877 Force max component initial, final = 150.72895 1.9006067 Final line search alpha, max atom move = 4.3594598e-05 8.2856185e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1914 | 0.1914 | 0.1914 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079995 | 0.00079995 | 0.00079995 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003885 | | | 1.98 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15950.0 ave 15950 max 15950 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: 654948.0 ave 654948 max 654948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654948 Ave neighs/atom = 223.83732 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 10.83 | 10.83 | 10.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12985.327 0 -12985.327 5.4587367 Loop time of 2.175e-06 on 1 procs for 0 steps with 2926 atoms 183.9% 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 | | 2.175e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15950.0 ave 15950 max 15950 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: 654700.0 ave 654700 max 654700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654700 Ave neighs/atom = 223.75256 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 10 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 10.83 | 10.83 | 10.83 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 -12985.327 -12985.327 38.884504 134.98033 6.0994497 5.4587367 5.4587367 -69.911827 -8.8714887 95.159526 2.2402673 924.62495 Loop time of 2.782e-06 on 1 procs for 0 steps with 2926 atoms 287.6% 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 | | 2.782e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15950.0 ave 15950 max 15950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327350.0 ave 327350 max 327350 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 654700.0 ave 654700 max 654700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654700 Ave neighs/atom = 223.75256 Neighbor list builds = 0 Dangerous builds = 0 2926 -12985.3267697301 eV 2.24026730781822 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07