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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -43.052085 0.0000000) to (43.052085 43.052085 4.0499994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7148785 5.7148785 4.0499994 Created 451 atoms using lattice units in orthogonal box = (0.0000000 -43.052085 0.0000000) to (43.052085 43.052085 4.0499994) create_atoms CPU = 0.003 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7148785 5.7148785 4.0499994 Created 453 atoms using lattice units in orthogonal box = (0.0000000 -43.052085 0.0000000) to (43.052085 43.052085 4.0499994) create_atoms CPU = 0.002 seconds 453 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 20 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 904 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_117656786760_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.983 | 4.983 | 4.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2985.4161 0 -2985.4161 7435.7564 62 0 -3031.618 0 -3031.618 2817.1703 Loop time of 2.18941 on 1 procs for 62 steps with 904 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 = -2985.4160582759 -3031.61535332889 -3031.61797437172 Force two-norm initial, final = 24.144403 0.11961592 Force max component initial, final = 3.4783659 0.0091781541 Final line search alpha, max atom move = 1.0000000 0.0091781541 Iterations, force evaluations = 62 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1111 | 2.1111 | 2.1111 | 0.0 | 96.43 Neigh | 0.043605 | 0.043605 | 0.043605 | 0.0 | 1.99 Comm | 0.020156 | 0.020156 | 0.020156 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0145 | | | 0.66 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 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: 156578.0 ave 156578 max 156578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156578 Ave neighs/atom = 173.20575 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3031.618 0 -3031.618 2817.1703 15013.202 68 0 -3031.7379 0 -3031.7379 -52.567192 15067.87 Loop time of 0.162648 on 1 procs for 6 steps with 904 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 = -3031.61797437171 -3031.73738079909 -3031.73790978877 Force two-norm initial, final = 54.050662 0.87994642 Force max component initial, final = 49.872363 0.61651843 Final line search alpha, max atom move = 0.00048696583 0.00030022341 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1572 | 0.1572 | 0.1572 | 0.0 | 96.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012854 | 0.0012854 | 0.0012854 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004162 | | | 2.56 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 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: 156844.0 ave 156844 max 156844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156844 Ave neighs/atom = 173.50000 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3031.7379 0 -3031.7379 -52.567192 Loop time of 5.854e-06 on 1 procs for 0 steps with 904 atoms 187.9% 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 | | 5.854e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 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: 156362.0 ave 156362 max 156362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156362 Ave neighs/atom = 172.96681 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.120 | 5.120 | 5.120 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 -3031.7379 -3031.7379 43.03487 86.566482 4.044656 -52.567192 -52.567192 -44.23384 -47.999416 -65.46832 2.5608335 197.41946 Loop time of 7.116e-06 on 1 procs for 0 steps with 904 atoms 281.1% 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 | | 7.116e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78181.0 ave 78181 max 78181 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156362.0 ave 156362 max 156362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156362 Ave neighs/atom = 172.96681 Neighbor list builds = 0 Dangerous builds = 0 904 -2976.38262861552 eV 2.5608335130911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03