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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -38.136789 0.0000000) to (17.976401 38.136789 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2871768 5.2340380 4.3599177 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -38.136789 0.0000000) to (17.976401 38.136789 4.3599177) create_atoms CPU = 0.000 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2871768 5.2340380 4.3599177 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -38.136789 0.0000000) to (17.976401 38.136789 4.3599177) create_atoms CPU = 0.000 seconds 206 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 8 atoms, new total = 404 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.834 | 4.834 | 4.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2485.86 0 -2485.86 65225.428 228 0 -2619.1705 0 -2619.1705 -15645.436 Loop time of 18.516 on 1 procs for 228 steps with 404 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 = -2485.85995707575 -2619.16814065994 -2619.17053277936 Force two-norm initial, final = 352.68790 0.23235773 Force max component initial, final = 118.82924 0.079192016 Final line search alpha, max atom move = 1.0000000 0.079192016 Iterations, force evaluations = 228 438 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.473 | 18.473 | 18.473 | 0.0 | 99.77 Neigh | 0.027498 | 0.027498 | 0.027498 | 0.0 | 0.15 Comm | 0.011005 | 0.011005 | 0.011005 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004219 | | | 0.02 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3313.00 ave 3313 max 3313 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: 29732.0 ave 29732 max 29732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29732 Ave neighs/atom = 73.594059 Neighbor list builds = 4 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 228 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.215 | 5.215 | 5.215 Mbytes Step Temp E_pair E_mol TotEng Press Volume 228 0 -2619.1705 0 -2619.1705 -15645.436 5977.9897 236 0 -2619.4738 0 -2619.4738 -7704.3659 5955.775 Loop time of 0.44945 on 1 procs for 8 steps with 404 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 = -2619.17053277936 -2619.47338168405 -2619.47375728285 Force two-norm initial, final = 83.181306 3.7481245 Force max component initial, final = 80.262519 2.7184128 Final line search alpha, max atom move = 0.010128164 0.027532530 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44874 | 0.44874 | 0.44874 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001728 | 0.0001728 | 0.0001728 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005359 | | | 0.12 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3317.00 ave 3317 max 3317 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: 29704.0 ave 29704 max 29704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29704 Ave neighs/atom = 73.524752 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2619.4738 0 -2619.4738 -7704.3659 Loop time of 1.9e-06 on 1 procs for 0 steps with 404 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3317.00 ave 3317 max 3317 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: 30126.0 ave 30126 max 30126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30126 Ave neighs/atom = 74.569307 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 5.353 | 5.353 | 5.353 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 -2619.4738 -2619.4738 18.031877 76.273577 4.3303523 -7704.3659 -7704.3659 733.54315 -24510.079 663.4385 2.5321059 1135.3314 Loop time of 2.6e-06 on 1 procs for 0 steps with 404 atoms 461.5% 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 | | 2.6e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15063.0 ave 15063 max 15063 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30126.0 ave 30126 max 30126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30126 Ave neighs/atom = 74.569307 Neighbor list builds = 0 Dangerous builds = 0 404 -2619.47375728285 eV 2.53210585963613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19