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 = 3.6147282 3.6147282 3.6147282 Created orthogonal box = (0.0000000 -39.597363 0.0000000) to (8.0827779 39.597363 8.8542395) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8496667 5.2796484 5.9028264 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.597363 0.0000000) to (8.0827779 39.597363 8.8542395) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8496667 5.2796484 5.9028264 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.597363 0.0000000) to (8.0827779 39.597363 8.8542395) create_atoms CPU = 0.001 seconds 242 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 2 19 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1625.2009 0 -1625.2009 40678.562 44 0 -1684.164 0 -1684.164 9029.2674 Loop time of 0.49269 on 1 procs for 44 steps with 480 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 = -1625.20090979897 -1684.16267540685 -1684.16402467402 Force two-norm initial, final = 124.97126 0.13271058 Force max component initial, final = 38.235136 0.035186649 Final line search alpha, max atom move = 1.0000000 0.035186649 Iterations, force evaluations = 44 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48665 | 0.48665 | 0.48665 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0034879 | 0.0034879 | 0.0034879 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002549 | | | 0.52 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4974.00 ave 4974 max 4974 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: 107884.0 ave 107884 max 107884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107884 Ave neighs/atom = 224.75833 Neighbor list builds = 0 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1684.164 0 -1684.164 9029.2674 5667.7172 53 0 -1684.3595 0 -1684.3595 181.66105 5703.1756 Loop time of 0.0620693 on 1 procs for 9 steps with 480 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 = -1684.16402467402 -1684.35806205591 -1684.3595367256 Force two-norm initial, final = 61.091704 1.1634070 Force max component initial, final = 52.792095 0.73692675 Final line search alpha, max atom move = 0.00053698448 0.00039571823 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059998 | 0.059998 | 0.059998 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038541 | 0.00038541 | 0.00038541 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001686 | | | 2.72 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4817.00 ave 4817 max 4817 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: 107280.0 ave 107280 max 107280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107280 Ave neighs/atom = 223.50000 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1684.3595 0 -1684.3595 181.66105 Loop time of 1.516e-06 on 1 procs for 0 steps with 480 atoms 197.9% 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 | | 1.516e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 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: 107056.0 ave 107056 max 107056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107056 Ave neighs/atom = 223.03333 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 5.123 | 5.123 | 5.123 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 -1684.3595 -1684.3595 8.0729533 79.878253 8.8441428 181.66105 181.66105 146.458 191.73855 206.78661 2.279847 292.97012 Loop time of 2.068e-06 on 1 procs for 0 steps with 480 atoms 193.4% 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 | | 2.068e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53528.0 ave 53528 max 53528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107056.0 ave 107056 max 107056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107056 Ave neighs/atom = 223.03333 Neighbor list builds = 0 Dangerous builds = 0 480 -1684.3595367256 eV 2.27984704154396 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00