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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -71.541063 0.0000000) to (41.301914 71.541063 7.0147812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3541405 6.4199883 7.0147812 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.541063 0.0000000) to (41.301914 71.541063 7.0147812) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3541405 6.4199883 7.0147812 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.541063 0.0000000) to (41.301914 71.541063 7.0147812) create_atoms CPU = 0.008 seconds 1249 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 ghost atom cutoff = 6 binsize = 3, bins = 14 48 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2472 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.247 | 5.247 | 5.247 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8242.8582 0 -8242.8582 1353.6321 31 0 -8265.7466 0 -8265.7466 -3031.5007 Loop time of 4.57315 on 1 procs for 31 steps with 2472 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 = -8242.85823175604 -8265.73980621929 -8265.74661121813 Force two-norm initial, final = 24.471444 0.73383844 Force max component initial, final = 4.6063538 0.12453703 Final line search alpha, max atom move = 0.28331316 0.035282979 Iterations, force evaluations = 31 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.525 | 4.525 | 4.525 | 0.0 | 98.95 Neigh | 0.024827 | 0.024827 | 0.024827 | 0.0 | 0.54 Comm | 0.0092483 | 0.0092483 | 0.0092483 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01407 | | | 0.31 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6774.00 ave 6774 max 6774 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: 132584.0 ave 132584 max 132584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132584 Ave neighs/atom = 53.634304 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 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.247 | 5.247 | 5.247 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -8265.7466 0 -8265.7466 -3031.5007 41454.31 34 0 -8265.8544 0 -8265.8544 -868.68961 41317.463 Loop time of 0.531493 on 1 procs for 3 steps with 2472 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8265.74661121815 -8265.85433697701 -8265.85443270953 Force two-norm initial, final = 91.599489 0.91334119 Force max component initial, final = 68.889314 0.35439492 Final line search alpha, max atom move = 0.00098478344 0.00034900224 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52602 | 0.52602 | 0.52602 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009409 | 0.0009409 | 0.0009409 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004537 | | | 0.85 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6772.00 ave 6772 max 6772 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: 132746.0 ave 132746 max 132746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132746 Ave neighs/atom = 53.699838 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 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.385 | 5.385 | 5.385 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8265.8544 0 -8265.8544 -868.68961 Loop time of 6.685e-06 on 1 procs for 0 steps with 2472 atoms 179.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6772.00 ave 6772 max 6772 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: 132760.0 ave 132760 max 132760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132760 Ave neighs/atom = 53.705502 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 ghost atom cutoff = 6 binsize = 3, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.385 | 5.385 | 5.385 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 -8265.8544 -8265.8544 41.242026 143.08213 7.001777 -868.68961 -868.68961 -13.722524 -2603.8378 11.491474 2.5046621 1091.2528 Loop time of 9.883e-06 on 1 procs for 0 steps with 2472 atoms 253.0% 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 | | 9.883e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6772.00 ave 6772 max 6772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66380.0 ave 66380 max 66380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132760.0 ave 132760 max 132760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132760 Ave neighs/atom = 53.705502 Neighbor list builds = 0 Dangerous builds = 0 2472 -8265.85443270953 eV 2.50466211011179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05