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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -40.246517 0.0000000) to (9.4861951 40.246517 4.0449272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3119069 4.8783658 4.0449272 Created 132 atoms using lattice units in orthogonal box = (0.0000000 -40.246517 0.0000000) to (9.4861951 40.246517 4.0449272) create_atoms CPU = 0.001 seconds 132 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3119069 4.8783658 4.0449272 Created 134 atoms using lattice units in orthogonal box = (0.0000000 -40.246517 0.0000000) to (9.4861951 40.246517 4.0449272) create_atoms CPU = 0.001 seconds 134 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 = 4 31 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 2 atoms, new total = 264 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 = 4 31 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) = 4.796 | 4.796 | 4.796 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1108.3577 0 -1108.3577 18393.732 35 0 -1125.4496 0 -1125.4496 2802.0731 Loop time of 1.21151 on 1 procs for 35 steps with 264 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1108.35772074118 -1125.44851629986 -1125.44961611605 Force two-norm initial, final = 37.633806 0.10913646 Force max component initial, final = 9.8097153 0.015493606 Final line search alpha, max atom move = 1.0000000 0.015493606 Iterations, force evaluations = 35 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2083 | 1.2083 | 1.2083 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016057 | 0.0016057 | 0.0016057 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001596 | | | 0.13 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2280.00 ave 2280 max 2280 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: 15220.0 ave 15220 max 15220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15220 Ave neighs/atom = 57.651515 Neighbor list builds = 0 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 = 4 31 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.796 | 4.796 | 4.796 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1125.4496 0 -1125.4496 2802.0731 3088.5957 40 0 -1125.5072 0 -1125.5072 74.921172 3092.9552 Loop time of 0.123497 on 1 procs for 5 steps with 264 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 = -1125.44961611605 -1125.50643139771 -1125.50722891317 Force two-norm initial, final = 24.350322 0.63778579 Force max component initial, final = 23.732045 0.58582193 Final line search alpha, max atom move = 0.00052168643 0.00030561536 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12266 | 0.12266 | 0.12266 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015273 | 0.00015273 | 0.00015273 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006858 | | | 0.56 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 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: 15196.0 ave 15196 max 15196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15196 Ave neighs/atom = 57.560606 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 = 4 31 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) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1125.5072 0 -1125.5072 74.921172 Loop time of 2.023e-06 on 1 procs for 0 steps with 264 atoms 197.7% 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 | | 2.023e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 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: 15180.0 ave 15180 max 15180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15180 Ave neighs/atom = 57.500000 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 = 4 31 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) = 4.934 | 4.934 | 4.934 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 -1125.5072 -1125.5072 9.4661517 80.847528 4.0414148 74.921172 74.921172 -25.639646 -52.793957 303.19712 2.3447388 176.14329 Loop time of 1.712e-06 on 1 procs for 0 steps with 264 atoms 175.2% 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 | | 1.712e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7590.00 ave 7590 max 7590 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15180.0 ave 15180 max 15180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15180 Ave neighs/atom = 57.500000 Neighbor list builds = 0 Dangerous builds = 0 264 -1125.50722891317 eV 2.34473883068785 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01