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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -61.615724 0.0000000) to (30.807862 61.615724 4.0452705) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3117004 5.3117004 4.0452705 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -61.615724 0.0000000) to (30.807862 61.615724 4.0452705) create_atoms CPU = 0.001 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3117004 5.3117004 4.0452705 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -61.615724 0.0000000) to (30.807862 61.615724 4.0452705) create_atoms CPU = 0.001 seconds 466 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 26 1 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 930 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3037.589 0 -3037.589 31397.895 97 0 -3162.6822 0 -3162.6822 6294.9344 Loop time of 2.28807 on 1 procs for 97 steps with 930 atoms 94.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3037.58896090436 -3162.67913922833 -3162.68224437369 Force two-norm initial, final = 139.26391 0.12443480 Force max component initial, final = 31.568038 0.019235134 Final line search alpha, max atom move = 1.0000000 0.019235134 Iterations, force evaluations = 97 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1994 | 2.1994 | 2.1994 | 0.0 | 96.13 Neigh | 0.04535 | 0.04535 | 0.04535 | 0.0 | 1.98 Comm | 0.031037 | 0.031037 | 0.031037 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01223 | | | 0.53 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8586.00 ave 8586 max 8586 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: 201564.0 ave 201564 max 201564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201564 Ave neighs/atom = 216.73548 Neighbor list builds = 3 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -3162.6822 0 -3162.6822 6294.9344 15357.859 108 0 -3163.1858 0 -3163.1858 22.398057 15473.986 Loop time of 0.164578 on 1 procs for 11 steps with 930 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 = -3162.68224437367 -3163.18372968655 -3163.18575162776 Force two-norm initial, final = 119.87141 0.52909883 Force max component initial, final = 108.26941 0.43679221 Final line search alpha, max atom move = 0.00027640850 0.00012073308 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14734 | 0.14734 | 0.14734 | 0.0 | 89.53 Neigh | 0.011576 | 0.011576 | 0.011576 | 0.0 | 7.03 Comm | 0.0011005 | 0.0011005 | 0.0011005 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00456 | | | 2.77 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8558.00 ave 8558 max 8558 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: 204260.0 ave 204260 max 204260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 204260 Ave neighs/atom = 219.63441 Neighbor list builds = 1 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.550 | 5.550 | 5.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3163.1858 0 -3163.1858 22.398057 Loop time of 2.237e-06 on 1 procs for 0 steps with 930 atoms 178.8% 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 | | 2.237e-06 | | |100.00 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8540.00 ave 8540 max 8540 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: 203540.0 ave 203540 max 203540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203540 Ave neighs/atom = 218.86022 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.550 | 5.550 | 5.550 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 -3163.1858 -3163.1858 30.775912 124.55049 4.0368798 22.398057 22.398057 45.178564 15.701083 6.3145247 2.4696598 502.10385 Loop time of 2.135e-06 on 1 procs for 0 steps with 930 atoms 187.4% 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 | | 2.135e-06 | | |100.00 Nlocal: 930.000 ave 930 max 930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8540.00 ave 8540 max 8540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101770.0 ave 101770 max 101770 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203540.0 ave 203540 max 203540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203540 Ave neighs/atom = 218.86022 Neighbor list builds = 0 Dangerous builds = 0 930 -3163.18575162775 eV 2.46965975683177 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02