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 = 3.6336621 3.6336621 3.6336621 Created orthogonal box = (0.0000000 -65.808419 0.0000000) to (23.266790 65.808419 5.1387742) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2423094 5.6177919 5.1387742 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.808419 0.0000000) to (23.266790 65.808419 5.1387742) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2423094 5.6177919 5.1387742 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.808419 0.0000000) to (23.266790 65.808419 5.1387742) create_atoms CPU = 0.001 seconds 658 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 47 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1314 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_529419924683_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.673 | 4.673 | 4.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5314.579 0 -5314.579 10828.813 64 0 -5382.5755 0 -5382.5755 5598.2809 Loop time of 61.6378 on 1 procs for 64 steps with 1314 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 = -5314.57903873784 -5382.57085652137 -5382.57546847605 Force two-norm initial, final = 47.809301 0.17717003 Force max component initial, final = 10.435906 0.038536655 Final line search alpha, max atom move = 1.0000000 0.038536655 Iterations, force evaluations = 64 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 61.603 | 61.603 | 61.603 | 0.0 | 99.94 Neigh | 0.012001 | 0.012001 | 0.012001 | 0.0 | 0.02 Comm | 0.010652 | 0.010652 | 0.010652 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01185 | | | 0.02 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5578.00 ave 5578 max 5578 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: 75032.0 ave 75032 max 75032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75032 Ave neighs/atom = 57.101979 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.673 | 4.673 | 4.673 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -5382.5755 0 -5382.5755 5598.2809 15736.475 68 0 -5382.741 0 -5382.741 -292.67514 15799.919 Loop time of 2.00624 on 1 procs for 4 steps with 1314 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 = -5382.57546847605 -5382.73901546505 -5382.74097606643 Force two-norm initial, final = 103.91365 6.2534882 Force max component initial, final = 74.029730 5.2538972 Final line search alpha, max atom move = 0.00011532623 0.00060591215 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0046 | 2.0046 | 2.0046 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026878 | 0.00026878 | 0.00026878 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001366 | | | 0.07 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5600.00 ave 5600 max 5600 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: 74316.0 ave 74316 max 74316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74316 Ave neighs/atom = 56.557078 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.811 | 4.811 | 4.811 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5382.741 0 -5382.741 -292.67514 Loop time of 2.218e-06 on 1 procs for 0 steps with 1314 atoms 180.3% 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 | | 2.218e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5600.00 ave 5600 max 5600 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: 73680.0 ave 73680 max 73680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73680 Ave neighs/atom = 56.073059 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 9 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.811 | 4.811 | 4.811 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 -5382.741 -5382.741 23.32028 131.96589 5.1340418 -292.67514 -292.67514 -344.16305 -1.5863058 -532.27607 2.4227918 422.46437 Loop time of 2.1e-06 on 1 procs for 0 steps with 1314 atoms 238.1% 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 | | 2.1e-06 | | |100.00 Nlocal: 1314.00 ave 1314 max 1314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5600.00 ave 5600 max 5600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36840.0 ave 36840 max 36840 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73680.0 ave 73680 max 73680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73680 Ave neighs/atom = 56.073059 Neighbor list builds = 0 Dangerous builds = 0 1314 -3365.442160275 eV 2.42279183636094 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:05