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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -42.020484 0.0000000) to (25.732186 42.020484 7.7585460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6785792 4.7750549 5.1723640 Created 527 atoms using lattice units in orthogonal box = (0.0000000 -42.020484 0.0000000) to (25.732186 42.020484 7.7585460) create_atoms CPU = 0.001 seconds 527 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6785792 4.7750549 5.1723640 Created 533 atoms using lattice units in orthogonal box = (0.0000000 -42.020484 0.0000000) to (25.732186 42.020484 7.7585460) create_atoms CPU = 0.001 seconds 533 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 22 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1056 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_269937397263_001#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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6963.5585 0 -6963.5585 15671.149 65 0 -7151.7324 0 -7151.7324 11155.972 Loop time of 12.2095 on 1 procs for 65 steps with 1056 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 = -6963.55853560138 -7151.72847603457 -7151.73237181901 Force two-norm initial, final = 70.171383 0.16395151 Force max component initial, final = 10.234924 0.015342189 Final line search alpha, max atom move = 1.0000000 0.015342189 Iterations, force evaluations = 65 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.179 | 12.179 | 12.179 | 0.0 | 99.75 Neigh | 0.019239 | 0.019239 | 0.019239 | 0.0 | 0.16 Comm | 0.0049642 | 0.0049642 | 0.0049642 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00584 | | | 0.05 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5043.00 ave 5043 max 5043 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: 142288.0 ave 142288 max 142288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142288 Ave neighs/atom = 134.74242 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.025 | 5.025 | 5.025 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -7151.7324 0 -7151.7324 11155.972 16778.304 72 0 -7152.4622 0 -7152.4622 -159.94875 16856.78 Loop time of 0.911993 on 1 procs for 7 steps with 1056 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 = -7151.732371819 -7152.45562393922 -7152.46219838487 Force two-norm initial, final = 251.86244 3.0244622 Force max component initial, final = 239.23373 2.1956279 Final line search alpha, max atom move = 6.5766289e-05 0.00014439830 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90985 | 0.90985 | 0.90985 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036309 | 0.00036309 | 0.00036309 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001784 | | | 0.20 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 142236.0 ave 142236 max 142236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142236 Ave neighs/atom = 134.69318 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.163 | 5.163 | 5.163 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7152.4622 0 -7152.4622 -159.94875 Loop time of 2.151e-06 on 1 procs for 0 steps with 1056 atoms 139.5% 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 | | 2.151e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 141924.0 ave 141924 max 141924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141924 Ave neighs/atom = 134.39773 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 7 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.163 | 5.163 | 5.163 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 -7152.4622 -7152.4622 25.707726 84.598829 7.7508012 -159.94875 -159.94875 -123.91841 -147.44958 -208.47825 2.5225743 1006.3886 Loop time of 1.792e-06 on 1 procs for 0 steps with 1056 atoms 167.4% 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 | | 1.792e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70962.0 ave 70962 max 70962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141924.0 ave 141924 max 141924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141924 Ave neighs/atom = 134.39773 Neighbor list builds = 0 Dangerous builds = 0 1056 -7152.46219838487 eV 2.52257428892575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14