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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -54.138878 0.0000000) to (44.204209 54.138878 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498340 5.1913993 5.9740873 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -54.138878 0.0000000) to (44.204209 54.138878 8.9611309) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498340 5.1913993 5.9740873 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -54.138878 0.0000000) to (44.204209 54.138878 8.9611309) create_atoms CPU = 0.002 seconds 1758 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3508 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.565 | 6.565 | 6.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13373.356 0 -13373.356 54038.704 1049 0 -14163.159 0 -14163.159 -46788.297 Loop time of 51.415 on 1 procs for 1049 steps with 3508 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 = -13373.3563359162 -14163.145088821 -14163.1592010322 Force two-norm initial, final = 793.54523 0.38051724 Force max component initial, final = 118.33907 0.067116077 Final line search alpha, max atom move = 0.60679192 0.040725493 Iterations, force evaluations = 1049 2078 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.29 | 50.29 | 50.29 | 0.0 | 97.81 Neigh | 0.52332 | 0.52332 | 0.52332 | 0.0 | 1.02 Comm | 0.2453 | 0.2453 | 0.2453 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3563 | | | 0.69 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10401.0 ave 10401 max 10401 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: 485460.0 ave 485460 max 485460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 485460 Ave neighs/atom = 138.38655 Neighbor list builds = 16 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1049 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.567 | 6.567 | 6.567 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1049 0 -14163.159 0 -14163.159 -46788.297 42890.953 1092 0 -14218.872 0 -14218.872 -585.82484 41615.084 Loop time of 1.22968 on 1 procs for 43 steps with 3508 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14163.1592010322 -14218.8631269276 -14218.8718540523 Force two-norm initial, final = 2687.1608 32.886245 Force max component initial, final = 2125.0596 27.444345 Final line search alpha, max atom move = 0.00063451846 0.017413943 Iterations, force evaluations = 43 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0927 | 1.0927 | 1.0927 | 0.0 | 88.86 Neigh | 0.10139 | 0.10139 | 0.10139 | 0.0 | 8.25 Comm | 0.004895 | 0.004895 | 0.004895 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03073 | | | 2.50 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10373.0 ave 10373 max 10373 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: 495292.0 ave 495292 max 495292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495292 Ave neighs/atom = 141.18928 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.084 | 7.084 | 7.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14218.872 0 -14218.872 -585.82484 Loop time of 2.17e-06 on 1 procs for 0 steps with 3508 atoms 184.3% 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 | | 2.17e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10301.0 ave 10301 max 10301 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: 496164.0 ave 496164 max 496164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496164 Ave neighs/atom = 141.43786 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.084 | 7.084 | 7.084 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 -14218.872 -14218.872 43.244303 104.59748 9.2002716 -585.82484 -585.82484 -85.36522 -1020.6913 -651.41799 2.2260917 6626.3945 Loop time of 2.873e-06 on 1 procs for 0 steps with 3508 atoms 348.1% 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 | | 2.873e-06 | | |100.00 Nlocal: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10301.0 ave 10301 max 10301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 248082.0 ave 248082 max 248082 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 496164.0 ave 496164 max 496164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496164 Ave neighs/atom = 141.43786 Neighbor list builds = 0 Dangerous builds = 0 3508 -14218.8718540522 eV 2.22609166740743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:53