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 -72.576688 0.0000000) to (51.319468 72.576688 5.7021631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9693105 6.7200637 5.7021631 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -72.576688 0.0000000) to (51.319468 72.576688 5.7021631) create_atoms CPU = 0.016 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9693105 6.7200637 5.7021631 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -72.576688 0.0000000) to (51.319468 72.576688 5.7021631) create_atoms CPU = 0.015 seconds 1300 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 = 12 34 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 8 atoms, new total = 2588 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 = 12 34 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) = 10.42 | 10.42 | 10.42 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8528.9219 0 -8528.9219 5608.0344 132 0 -8680.9449 0 -8680.9449 2485.4781 Loop time of 12.414 on 1 procs for 132 steps with 2588 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8528.92187299959 -8680.93690037888 -8680.94486903135 Force two-norm initial, final = 53.381190 0.21334037 Force max component initial, final = 7.7031678 0.020758013 Final line search alpha, max atom move = 1.0000000 0.020758013 Iterations, force evaluations = 132 240 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.013 | 12.013 | 12.013 | 0.0 | 96.77 Neigh | 0.2486 | 0.2486 | 0.2486 | 0.0 | 2.00 Comm | 0.079139 | 0.079139 | 0.079139 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07323 | | | 0.59 Nlocal: 2588.00 ave 2588 max 2588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12900.0 ave 12900 max 12900 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: 450184.0 ave 450184 max 450184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450184 Ave neighs/atom = 173.95054 Neighbor list builds = 4 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 = 12 34 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 : 132 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.42 | 10.42 | 10.42 Mbytes Step Temp E_pair E_mol TotEng Press Volume 132 0 -8680.9449 0 -8680.9449 2485.4781 42476.52 137 0 -8681.2743 0 -8681.2743 -141.60462 42608.323 Loop time of 0.350749 on 1 procs for 5 steps with 2588 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 = -8680.94486903134 -8681.26620844764 -8681.27429242211 Force two-norm initial, final = 149.27539 6.6366284 Force max component initial, final = 138.89462 4.3139459 Final line search alpha, max atom move = 6.5140219e-05 0.00028101138 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34195 | 0.34195 | 0.34195 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019312 | 0.0019312 | 0.0019312 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006865 | | | 1.96 Nlocal: 2588.00 ave 2588 max 2588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12876.0 ave 12876 max 12876 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: 450128.0 ave 450128 max 450128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450128 Ave neighs/atom = 173.92890 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 = 12 34 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) = 9.931 | 9.931 | 9.931 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8681.2743 0 -8681.2743 -141.60462 Loop time of 7.868e-06 on 1 procs for 0 steps with 2588 atoms 165.2% 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 | | 7.868e-06 | | |100.00 Nlocal: 2588.00 ave 2588 max 2588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12900.0 ave 12900 max 12900 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: 449560.0 ave 449560 max 449560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449560 Ave neighs/atom = 173.70943 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 = 12 34 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) = 9.931 | 9.931 | 9.931 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 -8681.2743 -8681.2743 51.211466 145.84651 5.7046788 -141.60462 -141.60462 -157.58213 -104.94533 -162.28641 2.6825857 1290.4287 Loop time of 6.495e-06 on 1 procs for 0 steps with 2588 atoms 292.5% 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 | | 6.495e-06 | | |100.00 Nlocal: 2588.00 ave 2588 max 2588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12900.0 ave 12900 max 12900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224780.0 ave 224780 max 224780 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 449560.0 ave 449560 max 449560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449560 Ave neighs/atom = 173.70943 Neighbor list builds = 0 Dangerous builds = 0 2588 -8681.27429242211 eV 2.68258574465644 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13