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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -42.773407 0.0000000) to (52.386511 42.773407 8.8549365) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9870298 5.4994380 5.9032910 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -42.773407 0.0000000) to (52.386511 42.773407 8.8549365) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9870298 5.4994380 5.9032910 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -42.773407 0.0000000) to (52.386511 42.773407 8.8549365) create_atoms CPU = 0.002 seconds 1686 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 3342 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.513 | 6.513 | 6.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11308.731 0 -11308.731 34196.37 86 0 -11763.686 0 -11763.686 -865.51542 Loop time of 28.4103 on 1 procs for 86 steps with 3342 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11308.7313633081 -11763.674997525 -11763.6864702371 Force two-norm initial, final = 295.42249 0.39161505 Force max component initial, final = 28.173291 0.091973686 Final line search alpha, max atom move = 1.0000000 0.091973686 Iterations, force evaluations = 86 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.299 | 28.299 | 28.299 | 0.0 | 99.61 Neigh | 0.064678 | 0.064678 | 0.064678 | 0.0 | 0.23 Comm | 0.01828 | 0.01828 | 0.01828 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02806 | | | 0.10 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9400.00 ave 9400 max 9400 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: 440666.0 ave 440666 max 440666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440666 Ave neighs/atom = 131.85697 Neighbor list builds = 2 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.513 | 6.513 | 6.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -11763.686 0 -11763.686 -865.51542 39683.389 88 0 -11763.728 0 -11763.728 -1.9091768 39658.867 Loop time of 0.945963 on 1 procs for 2 steps with 3342 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 = -11763.6864702371 -11763.7180705411 -11763.7283724061 Force two-norm initial, final = 61.309718 1.2920354 Force max component initial, final = 56.134217 1.0465904 Final line search alpha, max atom move = 2.8261781e-05 2.9578509e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94315 | 0.94315 | 0.94315 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004018 | 0.0004018 | 0.0004018 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002413 | | | 0.26 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9386.00 ave 9386 max 9386 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: 440628.0 ave 440628 max 440628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440628 Ave neighs/atom = 131.84560 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.650 | 6.650 | 6.650 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11763.728 0 -11763.728 -1.9091768 Loop time of 2.391e-06 on 1 procs for 0 steps with 3342 atoms 209.1% 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 | | 2.391e-06 | | |100.00 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376.00 ave 9376 max 9376 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: 440684.0 ave 440684 max 440684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440684 Ave neighs/atom = 131.86236 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.650 | 6.650 | 6.650 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 -11763.728 -11763.728 52.322192 85.529184 8.8621694 -1.9091768 -1.9091768 19.607871 -42.272438 16.937036 2.229487 1984.0041 Loop time of 2.462e-06 on 1 procs for 0 steps with 3342 atoms 284.3% 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 | | 2.462e-06 | | |100.00 Nlocal: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376.00 ave 9376 max 9376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 220342.0 ave 220342 max 220342 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 440684.0 ave 440684 max 440684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440684 Ave neighs/atom = 131.86236 Neighbor list builds = 0 Dangerous builds = 0 3342 -11763.7283724061 eV 2.22948699264683 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30