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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7938385 4.9203981 5.3397869 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) create_atoms CPU = 0.002 seconds 806 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7938385 4.9203981 5.3397869 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -61.815585 0.0000000) to (35.687464 61.815585 5.3397869) create_atoms CPU = 0.001 seconds 806 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 11 38 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 1608 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.263 | 6.263 | 6.263 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10151.905 0 -10151.905 47050.479 126 0 -10439.182 0 -10439.182 3450.4688 Loop time of 100.178 on 1 procs for 126 steps with 1608 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10151.9052787766 -10439.1728245158 -10439.1820616251 Force two-norm initial, final = 339.52734 0.47959937 Force max component initial, final = 85.868202 0.12616475 Final line search alpha, max atom move = 0.55185515 0.069624669 Iterations, force evaluations = 126 242 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 100.11 | 100.11 | 100.11 | 0.0 | 99.93 Neigh | 0.040029 | 0.040029 | 0.040029 | 0.0 | 0.04 Comm | 0.014931 | 0.014931 | 0.014931 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01576 | | | 0.02 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6969.00 ave 6969 max 6969 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: 119984.0 ave 119984 max 119984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119984 Ave neighs/atom = 74.616915 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -10439.182 0 -10439.182 3450.4688 23559.583 132 0 -10440.022 0 -10440.022 877.74747 23585.714 Loop time of 3.65174 on 1 procs for 6 steps with 1608 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10439.1820616251 -10440.0220831565 -10440.0221275222 Force two-norm initial, final = 282.49945 2.1608371 Force max component initial, final = 252.35610 1.3311213 Final line search alpha, max atom move = 0.0016201788 0.0021566546 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6489 | 3.6489 | 3.6489 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046718 | 0.00046718 | 0.00046718 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002325 | | | 0.06 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6962.00 ave 6962 max 6962 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: 117576.0 ave 117576 max 117576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117576 Ave neighs/atom = 73.119403 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 6.782 | 6.782 | 6.782 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10440.022 0 -10440.022 877.74747 Loop time of 1.959e-06 on 1 procs for 0 steps with 1608 atoms 153.1% 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 | | 1.959e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 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: 117930.0 ave 117930 max 117930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117930 Ave neighs/atom = 73.339552 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 6.782 | 6.782 | 6.782 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 -10440.022 -10440.022 35.555071 123.63117 5.3656149 877.74747 877.74747 80.406132 2461.9759 90.86038 2.505546 2615.2121 Loop time of 1.964e-06 on 1 procs for 0 steps with 1608 atoms 203.7% 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 | | 1.964e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6930.00 ave 6930 max 6930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58965.0 ave 58965 max 58965 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117930.0 ave 117930 max 117930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117930 Ave neighs/atom = 73.339552 Neighbor list builds = 0 Dangerous builds = 0 1608 -10440.0221275222 eV 2.50554597969525 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:45