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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -37.737594 0.0000000) to (32.681715 37.737594 6.4094117) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8659489 5.8057837 6.4094117 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -37.737594 0.0000000) to (32.681715 37.737594 6.4094117) create_atoms CPU = 0.001 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8659489 5.8057837 6.4094117 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -37.737594 0.0000000) to (32.681715 37.737594 6.4094117) create_atoms CPU = 0.001 seconds 628 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 20 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1246 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4525.2954 0 -4525.2954 78176.682 392 0 -5005.838 0 -5005.838 -73765.722 Loop time of 10.8558 on 1 procs for 392 steps with 1246 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4525.29540407973 -5005.83469668829 -5005.83797564726 Force two-norm initial, final = 597.72959 0.25234261 Force max component initial, final = 165.28134 0.075238252 Final line search alpha, max atom move = 1.0000000 0.075238252 Iterations, force evaluations = 392 762 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.622 | 10.622 | 10.622 | 0.0 | 97.84 Neigh | 0.095273 | 0.095273 | 0.095273 | 0.0 | 0.88 Comm | 0.077406 | 0.077406 | 0.077406 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06148 | | | 0.57 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6321.00 ave 6321 max 6321 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: 195460.0 ave 195460 max 195460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195460 Ave neighs/atom = 156.86998 Neighbor list builds = 7 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 392 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.064 | 5.064 | 5.064 Mbytes Step Temp E_pair E_mol TotEng Press Volume 392 0 -5005.838 0 -5005.838 -73765.722 15809.83 437 0 -5028.3449 0 -5028.3449 -1073.2405 14971.854 Loop time of 0.707263 on 1 procs for 45 steps with 1246 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 = -5005.83797564724 -5028.34001164168 -5028.34494886511 Force two-norm initial, final = 1284.0171 18.692749 Force max component initial, final = 923.44746 13.250968 Final line search alpha, max atom move = 0.00093569416 0.012398853 Iterations, force evaluations = 45 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67309 | 0.67309 | 0.67309 | 0.0 | 95.17 Neigh | 0.013206 | 0.013206 | 0.013206 | 0.0 | 1.87 Comm | 0.0033349 | 0.0033349 | 0.0033349 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01763 | | | 2.49 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6433.00 ave 6433 max 6433 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: 199914.0 ave 199914 max 199914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199914 Ave neighs/atom = 160.44462 Neighbor list builds = 1 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5028.3449 0 -5028.3449 -1073.2405 Loop time of 2.496e-06 on 1 procs for 0 steps with 1246 atoms 200.3% 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 | | 2.496e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6452.00 ave 6452 max 6452 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: 201776.0 ave 201776 max 201776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201776 Ave neighs/atom = 161.93900 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.584 | 5.584 | 5.584 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 -5028.3449 -5028.3449 31.549695 74.405406 6.377874 -1073.2405 -1073.2405 -1040.3972 -1397.9211 -781.40315 2.1848171 3106.0113 Loop time of 3.293e-06 on 1 procs for 0 steps with 1246 atoms 242.9% 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 | | 3.293e-06 | | |100.00 Nlocal: 1246.00 ave 1246 max 1246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6452.00 ave 6452 max 6452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100888.0 ave 100888 max 100888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201776.0 ave 201776 max 201776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201776 Ave neighs/atom = 161.93900 Neighbor list builds = 0 Dangerous builds = 0 1246 -5028.34494886511 eV 2.18481711632014 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12