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 = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -33.733474 0.0000000) to (41.314899 33.733474 6.9834925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7217028 4.3371609 4.6556617 Created 838 atoms using lattice units in orthogonal box = (0.0000000 -33.733474 0.0000000) to (41.314899 33.733474 6.9834925) create_atoms CPU = 0.001 seconds 838 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7217028 4.3371609 4.6556617 Created 844 atoms using lattice units in orthogonal box = (0.0000000 -33.733474 0.0000000) to (41.314899 33.733474 6.9834925) create_atoms CPU = 0.001 seconds 844 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 20 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1678 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_262519520678_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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.531 | 5.531 | 5.531 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3220.9043 0 -3220.9043 401969.43 82 0 -7145.8818 0 -7145.8818 7375.4103 Loop time of 12.9586 on 1 procs for 82 steps with 1678 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 = -3220.90433809322 -7145.87553636243 -7145.88182327044 Force two-norm initial, final = 4591.4472 0.32429163 Force max component initial, final = 758.68037 0.084934355 Final line search alpha, max atom move = 1.0000000 0.084934355 Iterations, force evaluations = 82 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.903 | 12.903 | 12.903 | 0.0 | 99.57 Neigh | 0.028433 | 0.028433 | 0.028433 | 0.0 | 0.22 Comm | 0.012348 | 0.012348 | 0.012348 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01446 | | | 0.11 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6630.00 ave 6630 max 6630 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: 219174.0 ave 219174 max 219174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219174 Ave neighs/atom = 130.61621 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.528 | 5.528 | 5.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -7145.8818 0 -7145.8818 7375.4103 19465.718 88 0 -7146.3209 0 -7146.3209 -4.6246932 19547.722 Loop time of 0.756219 on 1 procs for 6 steps with 1678 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 = -7145.88182327044 -7146.3205284955 -7146.32085930118 Force two-norm initial, final = 189.52124 0.57584466 Force max component initial, final = 171.71930 0.27690620 Final line search alpha, max atom move = 0.00018995382 5.2599391e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75306 | 0.75306 | 0.75306 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044181 | 0.00044181 | 0.00044181 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002717 | | | 0.36 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6469.00 ave 6469 max 6469 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: 219004.0 ave 219004 max 219004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219004 Ave neighs/atom = 130.51490 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.666 | 5.666 | 5.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7146.3209 0 -7146.3209 -4.6246932 Loop time of 2.144e-06 on 1 procs for 0 steps with 1678 atoms 186.6% 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 | | 2.144e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466.00 ave 6466 max 6466 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: 216494.0 ave 216494 max 216494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216494 Ave neighs/atom = 129.01907 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 ghost atom cutoff = 7 binsize = 3.5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.666 | 5.666 | 5.666 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 -7146.3209 -7146.3209 41.351357 67.79964 6.972347 -4.6246932 -4.6246932 -22.715901 2.246316 6.5955053 2.2976882 1970.5201 Loop time of 2.142e-06 on 1 procs for 0 steps with 1678 atoms 233.4% 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 | | 2.142e-06 | | |100.00 Nlocal: 1678.00 ave 1678 max 1678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466.00 ave 6466 max 6466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108247.0 ave 108247 max 108247 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 216494.0 ave 216494 max 216494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 216494 Ave neighs/atom = 129.01907 Neighbor list builds = 0 Dangerous builds = 0 1678 -7146.32085930118 eV 2.29768820553286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14