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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -41.595076 0.0000000) to (29.412161 41.595076 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4563880 5.6720559 5.1200000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.595076 0.0000000) to (29.412161 41.595076 5.1200000) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4563880 5.6720559 5.1200000 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.595076 0.0000000) to (29.412161 41.595076 5.1200000) create_atoms CPU = 0.003 seconds 532 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 = 10 28 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_390178379548_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 = 10 28 2 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) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3482.9093 0 -3482.9093 60933.366 50 0 -3736.7212 0 -3736.7212 14163.431 Loop time of 4.59479 on 1 procs for 50 steps with 1060 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 = -3482.90930792245 -3736.71868478436 -3736.72123455785 Force two-norm initial, final = 258.31288 0.15669513 Force max component initial, final = 58.606420 0.035491981 Final line search alpha, max atom move = 1.0000000 0.035491981 Iterations, force evaluations = 50 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5715 | 4.5715 | 4.5715 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010693 | 0.010693 | 0.010693 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0126 | | | 0.27 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4503.00 ave 4503 max 4503 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: 82712.0 ave 82712 max 82712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82712 Ave neighs/atom = 78.030189 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 = 10 28 2 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.599 | 4.599 | 4.599 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -3736.7212 0 -3736.7212 14163.431 12527.627 63 0 -3737.8854 0 -3737.8854 218.77368 12647.628 Loop time of 0.673236 on 1 procs for 13 steps with 1060 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 = -3736.72123455786 -3737.88468359114 -3737.88542493778 Force two-norm initial, final = 230.85611 3.4751870 Force max component initial, final = 212.02851 2.6019303 Final line search alpha, max atom move = 0.00031144945 0.00081036978 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66535 | 0.66535 | 0.66535 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014904 | 0.0014904 | 0.0014904 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006393 | | | 0.95 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4473.00 ave 4473 max 4473 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: 81928.0 ave 81928 max 81928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81928 Ave neighs/atom = 77.290566 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 = 10 29 2 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) = 4.737 | 4.737 | 4.737 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.8854 0 -3737.8854 218.77368 Loop time of 6.715e-06 on 1 procs for 0 steps with 1060 atoms 178.7% 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 | | 6.715e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4473.00 ave 4473 max 4473 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: 81904.0 ave 81904 max 81904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81904 Ave neighs/atom = 77.267925 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 = 10 29 2 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) = 4.737 | 4.737 | 4.737 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 -3737.8854 -3737.8854 29.378868 84.161765 5.1151596 218.77368 218.77368 46.625005 333.45701 276.23903 2.3264313 501.54601 Loop time of 7.587e-06 on 1 procs for 0 steps with 1060 atoms 224.1% 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 | | 7.587e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4473.00 ave 4473 max 4473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40952.0 ave 40952 max 40952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81904.0 ave 81904 max 81904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81904 Ave neighs/atom = 77.267925 Neighbor list builds = 0 Dangerous builds = 0 1060 -3737.88542493778 eV 2.32643125912226 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05