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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -77.137433 0.0000000) to (44.535318 77.137433 6.9836950) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5707846 5.9012244 6.9836950 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -77.137433 0.0000000) to (44.535318 77.137433 6.9836950) create_atoms CPU = 0.004 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5707846 5.9012244 6.9836950 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.137433 0.0000000) to (44.535318 77.137433 6.9836950) create_atoms CPU = 0.003 seconds 1466 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 36 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2924 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_019873715786_000#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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9690.5525 0 -9690.5525 5665.4895 40 0 -9802.4128 0 -9802.4128 2215.6743 Loop time of 1.94995 on 1 procs for 40 steps with 2924 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 = -9690.55251496904 -9802.40439841259 -9802.41282345908 Force two-norm initial, final = 58.792166 0.24257727 Force max component initial, final = 8.5525591 0.037753617 Final line search alpha, max atom move = 1.0000000 0.037753617 Iterations, force evaluations = 40 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8649 | 1.8649 | 1.8649 | 0.0 | 95.64 Neigh | 0.061651 | 0.061651 | 0.061651 | 0.0 | 3.16 Comm | 0.011625 | 0.011625 | 0.011625 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01181 | | | 0.61 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12118.0 ave 12118 max 12118 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: 509476.0 ave 509476 max 509476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509476 Ave neighs/atom = 174.23940 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.994 | 6.994 | 6.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -9802.4128 0 -9802.4128 2215.6743 47982.735 45 0 -9802.6436 0 -9802.6436 -2.8567427 48107.406 Loop time of 0.193769 on 1 procs for 5 steps with 2924 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 = -9802.41282345893 -9802.64331015911 -9802.64357535601 Force two-norm initial, final = 139.39700 0.70976709 Force max component initial, final = 129.57783 0.56498978 Final line search alpha, max atom move = 0.00018810171 0.00010627554 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18912 | 0.18912 | 0.18912 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073375 | 0.00073375 | 0.00073375 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003919 | | | 2.02 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12115.0 ave 12115 max 12115 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: 509540.0 ave 509540 max 509540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509540 Ave neighs/atom = 174.26129 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.132 | 7.132 | 7.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9802.6436 0 -9802.6436 -2.8567427 Loop time of 1.854e-06 on 1 procs for 0 steps with 2924 atoms 161.8% 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 | | 1.854e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12109.0 ave 12109 max 12109 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: 509128.0 ave 509128 max 509128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509128 Ave neighs/atom = 174.12038 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.132 | 7.132 | 7.132 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 -9802.6436 -9802.6436 44.526576 154.8774 6.9759696 -2.8567427 -2.8567427 -18.812814 -0.33591757 10.578504 2.5577234 1196.0528 Loop time of 2.373e-06 on 1 procs for 0 steps with 2924 atoms 252.8% 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 | | 2.373e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12109.0 ave 12109 max 12109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 254564.0 ave 254564 max 254564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 509128.0 ave 509128 max 509128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509128 Ave neighs/atom = 174.12038 Neighbor list builds = 0 Dangerous builds = 0 2924 -9802.64357535601 eV 2.55772338691472 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02