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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -44.586871 0.0000000) to (14.861089 44.586871 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3709085 4.3709085 3.6043435 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.586871 0.0000000) to (14.861089 44.586871 3.6043435) create_atoms CPU = 0.001 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3709085 4.3709085 3.6043435 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.586871 0.0000000) to (14.861089 44.586871 3.6043435) create_atoms CPU = 0.000 seconds 206 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 = 5 30 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 8 atoms, new total = 404 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_492310898779_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 = 5 30 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) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1701.0661 0 -1701.0661 -815.0521 41 0 -1708.5013 0 -1708.5013 -9582.843 Loop time of 1.16428 on 1 procs for 41 steps with 404 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1701.0661408753 -1708.50022312003 -1708.50131930705 Force two-norm initial, final = 13.954295 0.090680466 Force max component initial, final = 3.8785380 0.018884168 Final line search alpha, max atom move = 1.0000000 0.018884168 Iterations, force evaluations = 41 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1599 | 1.1599 | 1.1599 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022476 | 0.0022476 | 0.0022476 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002182 | | | 0.19 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2920.00 ave 2920 max 2920 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: 31176.0 ave 31176 max 31176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31176 Ave neighs/atom = 77.168317 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 = 5 30 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -1708.5013 0 -1708.5013 -9582.843 4776.5442 48 0 -1708.5725 0 -1708.5725 -2440.4427 4754.9996 Loop time of 0.110159 on 1 procs for 7 steps with 404 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1708.50131930705 -1708.57123699174 -1708.57250765836 Force two-norm initial, final = 33.891925 0.55010057 Force max component initial, final = 27.802780 0.51628221 Final line search alpha, max atom move = 0.00028804024 0.00014871005 Iterations, force evaluations = 7 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10912 | 0.10912 | 0.10912 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001889 | 0.0001889 | 0.0001889 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008519 | | | 0.77 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2880.00 ave 2880 max 2880 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: 31288.0 ave 31288 max 31288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31288 Ave neighs/atom = 77.445545 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 = 5 30 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1708.5725 0 -1708.5725 -2440.4427 Loop time of 1.836e-06 on 1 procs for 0 steps with 404 atoms 163.4% 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 | | 1.836e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2880.00 ave 2880 max 2880 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: 31320.0 ave 31320 max 31320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31320 Ave neighs/atom = 77.524752 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 = 5 30 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) = 4.588 | 4.588 | 4.588 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 -1708.5725 -1708.5725 14.770325 89.173743 3.610135 -2440.4427 -2440.4427 -172.8966 -7170.8145 22.383091 2.2846846 183.88464 Loop time of 1.657e-06 on 1 procs for 0 steps with 404 atoms 120.7% 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 | | 1.657e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2880.00 ave 2880 max 2880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15660.0 ave 15660 max 15660 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31320.0 ave 31320 max 31320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31320 Ave neighs/atom = 77.524752 Neighbor list builds = 0 Dangerous builds = 0 404 -1708.57250765836 eV 2.28468456716946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01