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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -57.607803 0.0000000) to (35.277431 57.607803 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6899082 5.5749487 5.9736509 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -57.607803 0.0000000) to (35.277431 57.607803 8.9604763) create_atoms CPU = 0.002 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6899082 5.5749487 5.9736509 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.607803 0.0000000) to (35.277431 57.607803 8.9604763) create_atoms CPU = 0.002 seconds 1491 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.504 | 6.504 | 6.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10838.646 0 -10838.646 68790.773 733 0 -11740.898 0 -11740.898 -63002.061 Loop time of 28.8855 on 1 procs for 733 steps with 2976 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10838.6464920367 -11740.8868610196 -11740.8977468853 Force two-norm initial, final = 972.42455 0.36416726 Force max component initial, final = 154.93544 0.050276962 Final line search alpha, max atom move = 0.66317649 0.033342499 Iterations, force evaluations = 733 1434 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.013 | 28.013 | 28.013 | 0.0 | 96.98 Neigh | 0.54178 | 0.54178 | 0.54178 | 0.0 | 1.88 Comm | 0.13942 | 0.13942 | 0.13942 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1917 | | | 0.66 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9476.00 ave 9476 max 9476 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: 413970.0 ave 413970 max 413970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413970 Ave neighs/atom = 139.10282 Neighbor list builds = 19 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 733 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.502 | 6.502 | 6.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 733 0 -11740.898 0 -11740.898 -63002.061 36419.951 782 0 -11821.71 0 -11821.71 -10.443764 35048.423 Loop time of 1.17837 on 1 procs for 49 steps with 2976 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11740.8977468852 -11821.6992876721 -11821.7095329587 Force two-norm initial, final = 3063.5105 7.8380839 Force max component initial, final = 2253.3278 2.2335397 Final line search alpha, max atom move = 5.2216381e-05 0.00011662736 Iterations, force evaluations = 49 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0278 | 1.0278 | 1.0278 | 0.0 | 87.23 Neigh | 0.11489 | 0.11489 | 0.11489 | 0.0 | 9.75 Comm | 0.005283 | 0.005283 | 0.005283 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03036 | | | 2.58 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9406.00 ave 9406 max 9406 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: 423536.0 ave 423536 max 423536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423536 Ave neighs/atom = 142.31720 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.639 | 6.639 | 6.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11821.71 0 -11821.71 -10.443764 Loop time of 2.362e-06 on 1 procs for 0 steps with 2976 atoms 169.3% 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 | | 2.362e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9399.00 ave 9399 max 9399 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: 423682.0 ave 423682 max 423682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423682 Ave neighs/atom = 142.36626 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.639 | 6.639 | 6.639 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 -11821.71 -11821.71 33.986696 111.21614 9.2723909 -10.443764 -10.443764 32.797154 41.528047 -105.65649 2.2980448 5590.9273 Loop time of 3.276e-06 on 1 procs for 0 steps with 2976 atoms 244.2% 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 | | 3.276e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9399.00 ave 9399 max 9399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 211841.0 ave 211841 max 211841 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 423682.0 ave 423682 max 423682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 423682 Ave neighs/atom = 142.36626 Neighbor list builds = 0 Dangerous builds = 0 2976 -11400.8387801929 eV 2.29804484836215 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30