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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -39.358316 0.0000000) to (19.279834 39.358316 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1412891 4.7225756 5.7481359 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358316 0.0000000) to (19.279834 39.358316 8.6222039) create_atoms CPU = 0.003 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1412891 4.7225756 5.7481359 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358316 0.0000000) to (19.279834 39.358316 8.6222039) create_atoms CPU = 0.002 seconds 612 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 = 7 27 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 48 atoms, new total = 1176 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_444394830472_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 = 7 27 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) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5185.2159 0 -5185.2159 -4238.5334 15 0 -5186.0968 0 -5186.0968 -3873.2547 Loop time of 1.20936 on 1 procs for 15 steps with 1176 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5185.21589750524 -5186.09240143545 -5186.09681529279 Force two-norm initial, final = 3.7531974 0.20692751 Force max component initial, final = 0.40999810 0.0092209589 Final line search alpha, max atom move = 1.0000000 0.0092209589 Iterations, force evaluations = 15 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2023 | 1.2023 | 1.2023 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029847 | 0.0029847 | 0.0029847 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004062 | | | 0.34 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 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: 90432.0 ave 90432 max 90432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90432 Ave neighs/atom = 76.897959 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 27 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -5186.0968 0 -5186.0968 -3873.2547 13085.433 17 0 -5186.1349 0 -5186.1349 -64.062509 13056.872 Loop time of 0.156477 on 1 procs for 2 steps with 1176 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5186.0968152928 -5186.13415571053 -5186.13493661523 Force two-norm initial, final = 49.795563 1.9835516 Force max component initial, final = 37.127603 1.9038804 Final line search alpha, max atom move = 0.00015785340 0.00030053400 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15466 | 0.15466 | 0.15466 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035385 | 0.00035385 | 0.00035385 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001466 | | | 0.94 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 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: 90384.0 ave 90384 max 90384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90384 Ave neighs/atom = 76.857143 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 = 7 27 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) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5186.1349 0 -5186.1349 -64.062509 Loop time of 6.646e-06 on 1 procs for 0 steps with 1176 atoms 165.5% 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 | | 6.646e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 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: 90384.0 ave 90384 max 90384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90384 Ave neighs/atom = 76.857143 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 = 7 27 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) = 4.724 | 4.724 | 4.724 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 -5186.1349 -5186.1349 19.256124 78.716633 8.6139779 -64.062509 -64.062509 -62.244193 -363.34091 233.39758 2.4327041 994.84927 Loop time of 7.066e-06 on 1 procs for 0 steps with 1176 atoms 254.7% 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 | | 7.066e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4072.00 ave 4072 max 4072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45192.0 ave 45192 max 45192 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90384.0 ave 90384 max 90384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90384 Ave neighs/atom = 76.857143 Neighbor list builds = 0 Dangerous builds = 0 1176 -5186.13493661523 eV 2.43270413413415 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01