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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -31.781834 0.0000000) to (22.470926 31.781834 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9654575 4.9848922 4.4499063 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -31.781834 0.0000000) to (22.470926 31.781834 4.4499063) create_atoms CPU = 0.002 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9654575 4.9848922 4.4499063 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -31.781834 0.0000000) to (22.470926 31.781834 4.4499063) create_atoms CPU = 0.001 seconds 206 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 22 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2706.6972 0 -2706.6972 2184.4989 50 0 -2729.0045 0 -2729.0045 -11678.89 Loop time of 2.20374 on 1 procs for 50 steps with 404 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 = -2706.69723939867 -2729.0028827132 -2729.00449974418 Force two-norm initial, final = 20.432166 0.11410104 Force max component initial, final = 5.1212487 0.013357433 Final line search alpha, max atom move = 1.0000000 0.013357433 Iterations, force evaluations = 50 96 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1869 | 2.1869 | 2.1869 | 0.0 | 99.24 Neigh | 0.0042482 | 0.0042482 | 0.0042482 | 0.0 | 0.19 Comm | 0.0060649 | 0.0060649 | 0.0060649 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006497 | | | 0.29 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 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: 23084.0 ave 23084 max 23084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23084 Ave neighs/atom = 57.138614 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.432 | 4.432 | 4.432 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2729.0045 0 -2729.0045 -11678.89 6355.9546 53 0 -2729.0677 0 -2729.0677 -3475.4875 6335.7306 Loop time of 0.137167 on 1 procs for 3 steps with 404 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 = -2729.00449974419 -2729.06715109888 -2729.06769387012 Force two-norm initial, final = 53.487382 0.12987963 Force max component initial, final = 43.626306 0.021073016 Final line search alpha, max atom move = 0.00037588444 7.9210187e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13562 | 0.13562 | 0.13562 | 0.0 | 98.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033819 | 0.00033819 | 0.00033819 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001212 | | | 0.88 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 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: 23068.0 ave 23068 max 23068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23068 Ave neighs/atom = 57.099010 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.570 | 4.570 | 4.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2729.0677 0 -2729.0677 -3475.4875 Loop time of 6.455e-06 on 1 procs for 0 steps with 404 atoms 154.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 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: 23068.0 ave 23068 max 23068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23068 Ave neighs/atom = 57.099010 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.570 | 4.570 | 4.570 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 -2729.0677 -2729.0677 22.422172 63.563669 4.4453921 -3475.4875 -3475.4875 1.4235113 -10427.387 -0.49885844 2.4409075 408.32073 Loop time of 2.3415e-05 on 1 procs for 0 steps with 404 atoms 140.9% 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 | | 2.342e-05 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2492.00 ave 2492 max 2492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11534.0 ave 11534 max 11534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23068.0 ave 23068 max 23068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23068 Ave neighs/atom = 57.099010 Neighbor list builds = 0 Dangerous builds = 0 404 -2729.06769387012 eV 2.44090749466455 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02