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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0659487 5.5147802 4.9780318 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) create_atoms CPU = 0.004 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0659487 5.5147802 4.9780318 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445241 0.0000000) to (28.596615 40.445241 4.9780318) create_atoms CPU = 0.003 seconds 532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4609.6403 0 -4609.6403 12500.854 32 0 -4648.0848 0 -4648.0848 -6631.7154 Loop time of 1.33619 on 1 procs for 32 steps with 1048 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 = -4609.64031734477 -4648.08171787859 -4648.08479676348 Force two-norm initial, final = 51.330911 0.17749410 Force max component initial, final = 15.333997 0.014965548 Final line search alpha, max atom move = 1.0000000 0.014965548 Iterations, force evaluations = 32 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2882 | 1.2882 | 1.2882 | 0.0 | 96.41 Neigh | 0.031061 | 0.031061 | 0.031061 | 0.0 | 2.32 Comm | 0.009154 | 0.009154 | 0.009154 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007755 | | | 0.58 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7523.00 ave 7523 max 7523 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: 235152.0 ave 235152 max 235152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235152 Ave neighs/atom = 224.38168 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.430 | 5.430 | 5.430 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -4648.0848 0 -4648.0848 -6631.7154 11515.153 35 0 -4648.123 0 -4648.123 -3933.2574 11497.406 Loop time of 0.154046 on 1 procs for 3 steps with 1048 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 = -4648.08479676347 -4648.12255113625 -4648.12295475391 Force two-norm initial, final = 41.123848 0.20461989 Force max component initial, final = 40.990229 0.022877891 Final line search alpha, max atom move = 0.00021179364 4.8453918e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15015 | 0.15015 | 0.15015 | 0.0 | 97.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092007 | 0.00092007 | 0.00092007 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002978 | | | 1.93 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7568.00 ave 7568 max 7568 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: 235712.0 ave 235712 max 235712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235712 Ave neighs/atom = 224.91603 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4648.123 0 -4648.123 -3933.2574 Loop time of 6.385e-06 on 1 procs for 0 steps with 1048 atoms 156.6% 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 | | 6.385e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7568.00 ave 7568 max 7568 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: 235808.0 ave 235808 max 235808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235808 Ave neighs/atom = 225.00763 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.568 | 5.568 | 5.568 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 -4648.123 -4648.123 28.606437 80.890483 4.9686531 -3933.2574 -3933.2574 -3.1891549 -11794.632 -1.9514668 2.3249414 554.82634 Loop time of 7.919e-06 on 1 procs for 0 steps with 1048 atoms 239.9% 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 | | 7.919e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7568.00 ave 7568 max 7568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117904.0 ave 117904 max 117904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235808.0 ave 235808 max 235808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235808 Ave neighs/atom = 225.00763 Neighbor list builds = 0 Dangerous builds = 0 1048 -4619.58453516671 eV 2.32494141758238 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02