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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -35.135851 0.0000000) to (4.0571386 35.135851 4.9689597) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0571386 4.6847802 4.9689597 Created 60 atoms using lattice units in orthogonal box = (0.0000000 -35.135851 0.0000000) to (4.0571386 35.135851 4.9689597) create_atoms CPU = 0.001 seconds 60 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0571386 4.6847802 4.9689597 Created 62 atoms using lattice units in orthogonal box = (0.0000000 -35.135851 0.0000000) to (4.0571386 35.135851 4.9689597) create_atoms CPU = 0.000 seconds 62 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 1 14 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 120 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 1 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -495.65049 0 -495.65049 0.0035977353 1 0 -495.65049 0 -495.65049 0.0035977353 Loop time of 0.0057836 on 1 procs for 1 steps with 120 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 = -495.650489587539 -495.650489587539 -495.650489587539 Force two-norm initial, final = 1.1329989e-07 3.5973336e-08 Force max component initial, final = 4.6115934e-08 1.5621554e-08 Final line search alpha, max atom move = 1.0000000 1.5621554e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0056046 | 0.0056046 | 0.0056046 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010724 | 0.00010724 | 0.00010724 | 0.0 | 1.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.177e-05 | | | 1.24 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 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: 46320.0 ave 46320 max 46320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46320 Ave neighs/atom = 386.00000 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 1 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -495.65049 0 -495.65049 0.0035977354 1416.6605 2 0 -495.65049 0 -495.65049 -1.5096293e-06 1416.6605 Loop time of 0.00604564 on 1 procs for 1 steps with 120 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 = -495.650489587538 -495.650489587538 -495.650489587487 Force two-norm initial, final = 5.5121258e-06 8.1791196e-08 Force max component initial, final = 3.2611185e-06 6.1298834e-08 Final line search alpha, max atom move = 1.0000000 6.1298834e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0056542 | 0.0056542 | 0.0056542 | 0.0 | 93.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001051 | 0.0001051 | 0.0001051 | 0.0 | 1.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002863 | | | 4.74 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 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: 46320.0 ave 46320 max 46320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46320 Ave neighs/atom = 386.00000 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -495.65049 0 -495.65049 -1.5097149e-06 Loop time of 1.658e-06 on 1 procs for 0 steps with 120 atoms 120.6% 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 | | 1.658e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 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: 46320.0 ave 46320 max 46320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46320 Ave neighs/atom = 386.00000 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 1 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 4.647 | 4.647 | 4.647 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 -495.65049 -495.65049 4.0571386 70.271702 4.9689597 -1.5097149e-06 -1.5097149e-06 3.4262439e-05 -6.9326173e-05 3.053459e-05 2.4844799 8.2066895e-17 Loop time of 1.598e-06 on 1 procs for 0 steps with 120 atoms 62.6% 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 | | 1.598e-06 | | |100.00 Nlocal: 120.000 ave 120 max 120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5042.00 ave 5042 max 5042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23160.0 ave 23160 max 23160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46320.0 ave 46320 max 46320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46320 Ave neighs/atom = 386.00000 Neighbor list builds = 0 Dangerous builds = 0 120 -495.650489587487 eV 2.48447986315138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00