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 = 4.0497635 4.0497635 4.0497635 Created orthogonal box = (0.0000000 -49.928838 0.0000000) to (17.652510 49.928838 5.7272305) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5035563 5.2556672 5.7272305 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -49.928838 0.0000000) to (17.652510 49.928838 5.7272305) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5035563 5.2556672 5.7272305 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -49.928838 0.0000000) to (17.652510 49.928838 5.7272305) create_atoms CPU = 0.001 seconds 306 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 604 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_942551040047_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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1928.2676 0 -1928.2676 18733.121 77 0 -2000.0596 0 -2000.0596 -1893.6021 Loop time of 0.813132 on 1 procs for 77 steps with 604 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 = -1928.26757018351 -2000.05798467974 -2000.05963913532 Force two-norm initial, final = 156.92573 0.073120866 Force max component initial, final = 52.183921 0.0072304621 Final line search alpha, max atom move = 1.0000000 0.0072304621 Iterations, force evaluations = 77 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79132 | 0.79132 | 0.79132 | 0.0 | 97.32 Neigh | 0.011782 | 0.011782 | 0.011782 | 0.0 | 1.45 Comm | 0.0059147 | 0.0059147 | 0.0059147 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004117 | | | 0.51 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 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: 103304.0 ave 103304 max 103304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103304 Ave neighs/atom = 171.03311 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.931 | 4.931 | 4.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -2000.0596 0 -2000.0596 -1893.6021 10095.611 81 0 -2000.0849 0 -2000.0849 45.193056 10069.772 Loop time of 0.0413854 on 1 procs for 4 steps with 604 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2000.05963913532 -2000.08454280039 -2000.08485629262 Force two-norm initial, final = 22.189244 0.90713342 Force max component initial, final = 18.347970 0.72963594 Final line search alpha, max atom move = 0.00071657304 0.00052283744 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039936 | 0.039936 | 0.039936 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029831 | 0.00029831 | 0.00029831 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001151 | | | 2.78 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 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: 102924.0 ave 102924 max 102924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102924 Ave neighs/atom = 170.40397 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2000.0849 0 -2000.0849 45.193056 Loop time of 1.533e-06 on 1 procs for 0 steps with 604 atoms 130.5% 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 | | 1.533e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 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: 103168.0 ave 103168 max 103168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103168 Ave neighs/atom = 170.80795 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.070 | 5.070 | 5.070 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 -2000.0849 -2000.0849 17.604748 99.848754 5.7285825 45.193056 45.193056 68.777877 116.0802 -49.278904 2.7335992 537.96903 Loop time of 1.577e-06 on 1 procs for 0 steps with 604 atoms 190.2% 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 | | 1.577e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5036.00 ave 5036 max 5036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51584.0 ave 51584 max 51584 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 103168.0 ave 103168 max 103168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103168 Ave neighs/atom = 170.80795 Neighbor list builds = 0 Dangerous builds = 0 604 -2000.08485629262 eV 2.73359924421555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01