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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -57.599912 0.0000000) to (40.729289 57.599912 4.9758746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0789983 5.5880512 4.9758746 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -57.599912 0.0000000) to (40.729289 57.599912 4.9758746) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0789983 5.5880512 4.9758746 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -57.599912 0.0000000) to (40.729289 57.599912 4.9758746) create_atoms CPU = 0.003 seconds 1080 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 ghost atom cutoff = 8 binsize = 4, bins = 11 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2144 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.446 | 6.446 | 6.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8126.3082 0 -8126.3082 139912.17 100 0 -9296.6032 0 -9296.6032 3325.8935 Loop time of 3.82161 on 1 procs for 100 steps with 2144 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 = -8126.30819083944 -9296.59524162952 -9296.60319956852 Force two-norm initial, final = 1780.6354 0.27598030 Force max component initial, final = 241.56787 0.012657060 Final line search alpha, max atom move = 1.0000000 0.012657060 Iterations, force evaluations = 100 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7327 | 3.7327 | 3.7327 | 0.0 | 97.67 Neigh | 0.044126 | 0.044126 | 0.044126 | 0.0 | 1.15 Comm | 0.024484 | 0.024484 | 0.024484 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02033 | | | 0.53 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12268.0 ave 12268 max 12268 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: 425776.0 ave 425776 max 425776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 425776 Ave neighs/atom = 198.58955 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 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -9296.6032 0 -9296.6032 3325.8935 23346.838 102 0 -9296.6558 0 -9296.6558 7.620295 23388.407 Loop time of 0.106816 on 1 procs for 2 steps with 2144 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 = -9296.60319956862 -9296.6525399941 -9296.65577684712 Force two-norm initial, final = 87.505879 1.5151008 Force max component initial, final = 65.594432 1.3104526 Final line search alpha, max atom move = 8.1736845e-05 0.00010711226 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.104 | 0.104 | 0.104 | 0.0 | 97.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051535 | 0.00051535 | 0.00051535 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002302 | | | 2.16 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12281.0 ave 12281 max 12281 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: 426272.0 ave 426272 max 426272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426272 Ave neighs/atom = 198.82090 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 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.584 | 6.584 | 6.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9296.6558 0 -9296.6558 7.620295 Loop time of 1.946e-06 on 1 procs for 0 steps with 2144 atoms 154.2% 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 | | 1.946e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12281.0 ave 12281 max 12281 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: 426144.0 ave 426144 max 426144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426144 Ave neighs/atom = 198.76119 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 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.584 | 6.584 | 6.584 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 -9296.6558 -9296.6558 40.774074 115.27411 4.9760503 7.620295 7.620295 -39.965288 89.827848 -27.001675 2.3076982 1009.9316 Loop time of 2.658e-06 on 1 procs for 0 steps with 2144 atoms 263.4% 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 | | 2.658e-06 | | |100.00 Nlocal: 2144.00 ave 2144 max 2144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12281.0 ave 12281 max 12281 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 213072.0 ave 213072 max 213072 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 426144.0 ave 426144 max 426144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426144 Ave neighs/atom = 198.76119 Neighbor list builds = 0 Dangerous builds = 0 2144 -9296.65577684712 eV 2.30769816181807 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04