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 -29.168385 0.0000000) to (25.260562 29.168385 4.9540038) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5339471 4.4874438 4.9540038 Created 308 atoms using lattice units in orthogonal box = (0.0000000 -29.168385 0.0000000) to (25.260562 29.168385 4.9540038) create_atoms CPU = 0.001 seconds 308 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5339471 4.4874438 4.9540038 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -29.168385 0.0000000) to (25.260562 29.168385 4.9540038) create_atoms CPU = 0.001 seconds 316 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 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 1 atoms, new total = 623 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 22 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) = 4.864 | 4.864 | 4.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2451.5674 0 -2451.5674 55078.37 60 0 -2644.459 0 -2644.459 7077.9996 Loop time of 4.27035 on 1 procs for 60 steps with 623 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 = -2451.56741594935 -2644.45672751125 -2644.45895598691 Force two-norm initial, final = 443.34756 0.20816342 Force max component initial, final = 232.40235 0.039246651 Final line search alpha, max atom move = 1.0000000 0.039246651 Iterations, force evaluations = 60 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2495 | 4.2495 | 4.2495 | 0.0 | 99.51 Neigh | 0.013052 | 0.013052 | 0.013052 | 0.0 | 0.31 Comm | 0.0032737 | 0.0032737 | 0.0032737 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004474 | | | 0.10 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2694.00 ave 2694 max 2694 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: 35804.0 ave 35804 max 35804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35804 Ave neighs/atom = 57.470305 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 22 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.864 | 4.864 | 4.864 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2644.459 0 -2644.459 7077.9996 7300.3172 65 0 -2644.5666 0 -2644.5666 -16.488268 7328.4948 Loop time of 0.331432 on 1 procs for 5 steps with 623 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 = -2644.45895598691 -2644.56637439922 -2644.56657295397 Force two-norm initial, final = 63.588417 0.53880550 Force max component initial, final = 56.928201 0.25367099 Final line search alpha, max atom move = 0.00038382395 9.7365001e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33025 | 0.33025 | 0.33025 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017959 | 0.00017959 | 0.00017959 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009985 | | | 0.30 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2701.00 ave 2701 max 2701 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: 35838.0 ave 35838 max 35838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35838 Ave neighs/atom = 57.524880 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 22 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) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2644.5666 0 -2644.5666 -16.488268 Loop time of 1.89e-06 on 1 procs for 0 steps with 623 atoms 158.7% 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 | | 1.89e-06 | | |100.00 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2701.00 ave 2701 max 2701 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: 35804.0 ave 35804 max 35804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35804 Ave neighs/atom = 57.470305 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 22 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) = 5.002 | 5.002 | 5.002 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 -2644.5666 -2644.5666 25.253818 58.55459 4.9559485 -16.488268 -16.488268 -55.443471 -33.649197 39.627864 2.2583127 591.48853 Loop time of 1.823e-06 on 1 procs for 0 steps with 623 atoms 164.6% 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 | | 1.823e-06 | | |100.00 Nlocal: 623.000 ave 623 max 623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2701.00 ave 2701 max 2701 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17902.0 ave 17902 max 17902 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35804.0 ave 35804 max 35804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35804 Ave neighs/atom = 57.470305 Neighbor list builds = 0 Dangerous builds = 0 623 -2644.56657295397 eV 2.25831269514396 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04