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 = 3.6111526 3.6111526 3.6111526 Created orthogonal box = (0.0000000 -51.069410 0.0000000) to (25.534705 51.069410 3.6111526) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0855528 4.0855528 3.6111526 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -51.069410 0.0000000) to (25.534705 51.069410 3.6111526) create_atoms CPU = 0.003 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0855528 4.0855528 3.6111526 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -51.069410 0.0000000) to (25.534705 51.069410 3.6111526) create_atoms CPU = 0.002 seconds 402 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 802 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.294 | 5.294 | 5.294 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3050.3554 0 -3050.3554 74583.417 65 0 -3395.0747 0 -3395.0747 9385.3373 Loop time of 12.1414 on 1 procs for 65 steps with 802 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 = -3050.35542387291 -3395.07150458722 -3395.0746629925 Force two-norm initial, final = 519.78031 0.25781084 Force max component initial, final = 180.31013 0.052521595 Final line search alpha, max atom move = 1.0000000 0.052521595 Iterations, force evaluations = 65 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.076 | 12.076 | 12.076 | 0.0 | 99.46 Neigh | 0.040658 | 0.040658 | 0.040658 | 0.0 | 0.33 Comm | 0.012285 | 0.012285 | 0.012285 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0127 | | | 0.10 Nlocal: 802.000 ave 802 max 802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4238.00 ave 4238 max 4238 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: 43264.0 ave 43264 max 43264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43264 Ave neighs/atom = 53.945137 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.294 | 5.294 | 5.294 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3395.0747 0 -3395.0747 9385.3373 9418.1918 71 0 -3395.2633 0 -3395.2633 -101.0982 9471.7995 Loop time of 0.83634 on 1 procs for 6 steps with 802 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 = -3395.0746629925 -3395.26327769199 -3395.26334446475 Force two-norm initial, final = 96.979884 1.2624031 Force max component initial, final = 68.601266 0.93350723 Final line search alpha, max atom move = 0.00081847883 0.00076405591 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83269 | 0.83269 | 0.83269 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072811 | 0.00072811 | 0.00072811 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002923 | | | 0.35 Nlocal: 802.000 ave 802 max 802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4238.00 ave 4238 max 4238 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: 43280.0 ave 43280 max 43280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43280 Ave neighs/atom = 53.965087 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.432 | 5.432 | 5.432 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3395.2633 0 -3395.2633 -101.0982 Loop time of 6.135e-06 on 1 procs for 0 steps with 802 atoms 163.0% 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 | | 6.135e-06 | | |100.00 Nlocal: 802.000 ave 802 max 802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4234.00 ave 4234 max 4234 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: 43256.0 ave 43256 max 43256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43256 Ave neighs/atom = 53.935162 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.432 | 5.432 | 5.432 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 -3395.2633 -3395.2633 25.552084 102.12921 3.6295786 -101.0982 -101.0982 -134.61502 -157.89002 -10.789544 2.2737555 143.27105 Loop time of 6.645e-06 on 1 procs for 0 steps with 802 atoms 240.8% 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 | | 6.645e-06 | | |100.00 Nlocal: 802.000 ave 802 max 802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4234.00 ave 4234 max 4234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21628.0 ave 21628 max 21628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43256.0 ave 43256 max 43256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43256 Ave neighs/atom = 53.935162 Neighbor list builds = 0 Dangerous builds = 0 802 -3395.26334446475 eV 2.27375546761339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13