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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -43.258034 0.0000000) to (11.773346 43.258034 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0457195 4.8064482 5.1383093 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -43.258034 0.0000000) to (11.773346 43.258034 7.7074639) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0457195 4.8064482 5.1383093 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -43.258034 0.0000000) to (11.773346 43.258034 7.7074639) create_atoms CPU = 0.001 seconds 254 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 506 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3370.9031 0 -3370.9031 41357.043 35 0 -5225.0126 0 -5225.0126 32744.246 Loop time of 4.18714 on 1 procs for 35 steps with 506 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3370.9030656353 -5225.01216512132 -5225.01256139068 Force two-norm initial, final = 27.953034 154.24237 Force max component initial, final = 6.8283633 73.164179 Final line search alpha, max atom move = 4.4652636e-08 3.2669735e-06 Iterations, force evaluations = 35 349 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1728 | 4.1728 | 4.1728 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0076771 | 0.0076771 | 0.0076771 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006617 | | | 0.16 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 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: 29248.0 ave 29248 max 29248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29248 Ave neighs/atom = 57.802372 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -5225.0126 0 -5225.0126 32744.246 7850.696 36 0 -5225.0131 0 -5225.0131 32369.759 7850.7518 Loop time of 0.0338358 on 1 procs for 1 steps with 506 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 = -5225.0125613907 -5225.0125613907 -5225.01308589529 Force two-norm initial, final = 322.90497 785.22785 Force max component initial, final = 204.31233 348.44464 Final line search alpha, max atom move = 4.8944671e-06 0.0017054508 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033553 | 0.033553 | 0.033553 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 5.6526e-05 | 5.6526e-05 | 5.6526e-05 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002264 | | | 0.67 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 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: 29176.0 ave 29176 max 29176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29176 Ave neighs/atom = 57.660079 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5225.0131 0 -5225.0131 32369.759 Loop time of 1.586e-06 on 1 procs for 0 steps with 506 atoms 189.2% 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 | | 1.586e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 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: 29176.0 ave 29176 max 29176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29176 Ave neighs/atom = 57.660079 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.579 | 4.579 | 4.579 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 -5225.0131 -5225.0131 11.773367 86.516329 7.7074812 32369.759 32369.759 25477.651 40740.237 30891.388 0.0056885148 524.55179 Loop time of 1.731e-06 on 1 procs for 0 steps with 506 atoms 231.1% 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 | | 1.731e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2354.00 ave 2354 max 2354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14588.0 ave 14588 max 14588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29176.0 ave 29176 max 29176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29176 Ave neighs/atom = 57.660079 Neighbor list builds = 0 Dangerous builds = 0 506 -5225.01308589529 eV 0.00568851475344509 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04