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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.053422 0.0000000) to (14.513332 41.053422 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9760778 6.0367502 4.9780318 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.053422 0.0000000) to (14.513332 41.053422 4.9780318) create_atoms CPU = 0.003 seconds 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9760778 6.0367502 4.9780318 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.053422 0.0000000) to (14.513332 41.053422 4.9780318) create_atoms CPU = 0.002 seconds 274 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 540 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_103383163946_000#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2379.4217 0 -2379.4217 10551.935 64 0 -2394.6745 0 -2394.6745 -5137.3497 Loop time of 1.7319 on 1 procs for 64 steps with 540 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 = -2379.42169296283 -2394.67255810283 -2394.67453188355 Force two-norm initial, final = 33.822861 0.14690616 Force max component initial, final = 9.9210954 0.027867929 Final line search alpha, max atom move = 1.0000000 0.027867929 Iterations, force evaluations = 64 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6876 | 1.6876 | 1.6876 | 0.0 | 97.44 Neigh | 0.016172 | 0.016172 | 0.016172 | 0.0 | 0.93 Comm | 0.016288 | 0.016288 | 0.016288 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01181 | | | 0.68 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5499.00 ave 5499 max 5499 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: 120972.0 ave 120972 max 120972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120972 Ave neighs/atom = 224.02222 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.934 | 4.934 | 4.934 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -2394.6745 0 -2394.6745 -5137.3497 5932.041 67 0 -2394.6926 0 -2394.6926 -2148.9862 5922.0259 Loop time of 0.0829529 on 1 procs for 3 steps with 540 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2394.67453188354 -2394.692287207 -2394.69260739485 Force two-norm initial, final = 22.162568 0.15293606 Force max component initial, final = 21.106407 0.027937934 Final line search alpha, max atom move = 0.00035171052 9.8260653e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.080267 | 0.080267 | 0.080267 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067081 | 0.00067081 | 0.00067081 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002016 | | | 2.43 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5499.00 ave 5499 max 5499 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: 121076.0 ave 121076 max 121076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121076 Ave neighs/atom = 224.21481 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2394.6926 0 -2394.6926 -2148.9862 Loop time of 6.526e-06 on 1 procs for 0 steps with 540 atoms 153.2% 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 | | 6.526e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5499.00 ave 5499 max 5499 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: 121080.0 ave 121080 max 121080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121080 Ave neighs/atom = 224.22222 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.072 | 5.072 | 5.072 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 -2394.6926 -2394.6926 14.488411 82.106843 4.9781754 -2148.9862 -2148.9862 -2.9034368 -6439.0314 -5.0238192 2.3284789 260.04658 Loop time of 7.478e-06 on 1 procs for 0 steps with 540 atoms 227.3% 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 | | 7.478e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5499.00 ave 5499 max 5499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60540.0 ave 60540 max 60540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121080.0 ave 121080 max 121080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121080 Ave neighs/atom = 224.22222 Neighbor list builds = 0 Dangerous builds = 0 540 -2379.98769653885 eV 2.32847892644848 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02