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 = 2.8675702 2.8675702 2.8675702 Created orthogonal box = (0.0000000 -34.888364 0.0000000) to (17.442748 34.888364 2.8675702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2999794 3.2999794 2.8675702 Created 149 atoms using lattice units in orthogonal box = (0.0000000 -34.888364 0.0000000) to (17.442748 34.888364 2.8675702) create_atoms CPU = 0.000 seconds 149 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2999794 3.2999794 2.8675702 Created 149 atoms using lattice units in orthogonal box = (0.0000000 -34.888364 0.0000000) to (17.442748 34.888364 2.8675702) create_atoms CPU = 0.000 seconds 149 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 = 5 20 1 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 = 294 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_427873955970_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 = 5 20 1 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) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1224.9287 0 -1224.9287 27339.055 53 0 -1252.8884 0 -1252.8884 -4324.13 Loop time of 2.94303 on 1 procs for 53 steps with 294 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 = -1224.92869161564 -1252.88764593289 -1252.88841459728 Force two-norm initial, final = 96.462241 0.077458321 Force max component initial, final = 36.532542 0.012933175 Final line search alpha, max atom move = 1.0000000 0.012933175 Iterations, force evaluations = 53 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9331 | 2.9331 | 2.9331 | 0.0 | 99.66 Neigh | 0.0047192 | 0.0047192 | 0.0047192 | 0.0 | 0.16 Comm | 0.0031079 | 0.0031079 | 0.0031079 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002149 | | | 0.07 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3343.00 ave 3343 max 3343 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: 34640.0 ave 34640 max 34640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34640 Ave neighs/atom = 117.82313 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 = 5 20 1 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.431 | 4.431 | 4.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1252.8884 0 -1252.8884 -4324.13 3490.1137 56 0 -1252.9119 0 -1252.9119 1298.9125 3478.2901 Loop time of 0.191031 on 1 procs for 3 steps with 294 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 = -1252.88841459728 -1252.91177711874 -1252.91194360128 Force two-norm initial, final = 19.196961 0.090620490 Force max component initial, final = 14.667680 0.017510356 Final line search alpha, max atom move = 0.0016116698 2.8220912e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19037 | 0.19037 | 0.19037 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013744 | 0.00013744 | 0.00013744 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005269 | | | 0.28 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3212.00 ave 3212 max 3212 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: 33912.0 ave 33912 max 33912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33912 Ave neighs/atom = 115.34694 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 = 5 20 1 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) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1252.9119 0 -1252.9119 1298.9125 Loop time of 1.545e-06 on 1 procs for 0 steps with 294 atoms 194.2% 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 | | 1.545e-06 | | |100.00 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3212.00 ave 3212 max 3212 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: 34266.0 ave 34266 max 34266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34266 Ave neighs/atom = 116.55102 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 = 5 20 1 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) = 4.569 | 4.569 | 4.569 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 -1252.9119 -1252.9119 17.404961 69.776729 2.8640602 1298.9125 1298.9125 2.046898 3898.7024 -4.0116846 2.3335118 127.88945 Loop time of 1.673e-06 on 1 procs for 0 steps with 294 atoms 179.3% 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 | | 1.673e-06 | | |100.00 Nlocal: 294.000 ave 294 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3212.00 ave 3212 max 3212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17133.0 ave 17133 max 17133 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34266.0 ave 34266 max 34266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34266 Ave neighs/atom = 116.55102 Neighbor list builds = 0 Dangerous builds = 0 294 -1252.91194360128 eV 2.33351184038462 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03