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 -51.125532 0.0000000) to (10.435955 51.125532 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7436161 4.6477756 5.1383093 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -51.125532 0.0000000) to (10.435955 51.125532 7.7074639) create_atoms CPU = 0.001 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7436161 4.6477756 5.1383093 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.125532 0.0000000) to (10.435955 51.125532 7.7074639) create_atoms CPU = 0.001 seconds 265 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 = 4 36 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 1 atoms, new total = 527 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 = 4 36 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) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3524.3749 0 -3524.3749 26883.824 25 0 -5003.3905 0 -5003.3905 14493.313 Loop time of 3.1734 on 1 procs for 25 steps with 527 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3524.37490517189 -5003.38943421084 -5003.39049773206 Force two-norm initial, final = 34.647252 745.19262 Force max component initial, final = 7.6129941 511.81921 Final line search alpha, max atom move = 3.8160794e-07 0.00019531428 Iterations, force evaluations = 25 231 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1616 | 3.1616 | 3.1616 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0062458 | 0.0062458 | 0.0062458 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005598 | | | 0.18 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2599.00 ave 2599 max 2599 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: 30372.0 ave 30372 max 30372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30372 Ave neighs/atom = 57.631879 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 = 4 36 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.466 | 4.466 | 4.466 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -5003.3905 0 -5003.3905 14493.313 8224.5387 51 0 -5368.1721 0 -5368.1721 -6244.176 8301.2397 Loop time of 2.60145 on 1 procs for 26 steps with 527 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 = -5003.39049773207 -5368.17142491011 -5368.17208844737 Force two-norm initial, final = 756.46583 211.57749 Force max component initial, final = 511.81921 95.493089 Final line search alpha, max atom move = 4.1654737e-08 3.9777395e-06 Iterations, force evaluations = 26 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5741 | 2.5741 | 2.5741 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044852 | 0.0044852 | 0.0044852 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02285 | | | 0.88 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2599.00 ave 2599 max 2599 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: 30396.0 ave 30396 max 30396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30396 Ave neighs/atom = 57.677419 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 = 4 36 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) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5368.1721 0 -5368.1721 -6244.176 Loop time of 2.307e-06 on 1 procs for 0 steps with 527 atoms 173.4% 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 | | 2.307e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2540.00 ave 2540 max 2540 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: 30376.0 ave 30376 max 30376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30376 Ave neighs/atom = 57.639469 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 = 4 36 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) = 4.604 | 4.604 | 4.604 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 -5368.1721 -5368.1721 10.474242 102.4982 7.7322184 -6244.176 -6244.176 -8956.5211 -700.06408 -9075.943 0.0056879444 421.87596 Loop time of 2.314e-06 on 1 procs for 0 steps with 527 atoms 216.1% 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 | | 2.314e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2540.00 ave 2540 max 2540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15188.0 ave 15188 max 15188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30376.0 ave 30376 max 30376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30376 Ave neighs/atom = 57.639469 Neighbor list builds = 0 Dangerous builds = 0 527 -5368.17208844737 eV 0.00568794439048332 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06