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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -74.682099 0.0000000) to (37.339024 74.682099 4.0499858) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7106743 5.7106743 4.0499858 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -74.682099 0.0000000) to (37.339024 74.682099 4.0499858) create_atoms CPU = 0.003 seconds 681 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7106743 5.7106743 4.0499858 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -74.682099 0.0000000) to (37.339024 74.682099 4.0499858) create_atoms CPU = 0.002 seconds 681 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 ghost atom cutoff = 6 binsize = 3, bins = 13 50 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 11 atoms, new total = 1351 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_022920256108_001#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 ghost atom cutoff = 6 binsize = 3, bins = 13 50 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.653 | 4.653 | 4.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4506.348 0 -4506.348 1579.0969 40 0 -4524.1002 0 -4524.1002 -3215.1943 Loop time of 3.16021 on 1 procs for 40 steps with 1351 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4506.34804646866 -4524.09627820457 -4524.10017509801 Force two-norm initial, final = 19.054938 0.17003393 Force max component initial, final = 6.2805224 0.019012677 Final line search alpha, max atom move = 1.0000000 0.019012677 Iterations, force evaluations = 40 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1408 | 3.1408 | 3.1408 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.008657 | 0.008657 | 0.008657 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01075 | | | 0.34 Nlocal: 1351.00 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5379.00 ave 5379 max 5379 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: 72540.0 ave 72540 max 72540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72540 Ave neighs/atom = 53.693560 Neighbor list builds = 0 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 ghost atom cutoff = 6 binsize = 3, bins = 13 50 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.653 | 4.653 | 4.653 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4524.1002 0 -4524.1002 -3215.1943 22587.23 45 0 -4524.1907 0 -4524.1907 -840.07133 22503.964 Loop time of 0.347368 on 1 procs for 5 steps with 1351 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4524.10017509801 -4524.1898699803 -4524.19066427063 Force two-norm initial, final = 52.126347 1.6927145 Force max component initial, final = 46.418330 1.6680995 Final line search alpha, max atom move = 0.00019350491 0.00032278544 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34292 | 0.34292 | 0.34292 | 0.0 | 98.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00094538 | 0.00094538 | 0.00094538 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003499 | | | 1.01 Nlocal: 1351.00 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5376.00 ave 5376 max 5376 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: 72852.0 ave 72852 max 72852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72852 Ave neighs/atom = 53.924500 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 ghost atom cutoff = 6 binsize = 3, bins = 13 50 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.791 | 4.791 | 4.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4524.1907 0 -4524.1907 -840.07133 Loop time of 6.515e-06 on 1 procs for 0 steps with 1351 atoms 184.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 1351.00 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5376.00 ave 5376 max 5376 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: 72864.0 ave 72864 max 72864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72864 Ave neighs/atom = 53.933383 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 ghost atom cutoff = 6 binsize = 3, bins = 13 50 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.791 | 4.791 | 4.791 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 -4524.1907 -4524.1907 37.352309 149.3642 4.0336207 -840.07133 -840.07133 118.8031 -2622.9281 -16.089034 2.5437021 180.62944 Loop time of 7.868e-06 on 1 procs for 0 steps with 1351 atoms 228.8% 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 | | 7.868e-06 | | |100.00 Nlocal: 1351.00 ave 1351 max 1351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5376.00 ave 5376 max 5376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36432.0 ave 36432 max 36432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72864.0 ave 72864 max 72864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72864 Ave neighs/atom = 53.933383 Neighbor list builds = 0 Dangerous builds = 0 1351 -4524.19066427063 eV 2.54370211942264 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04