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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -37.477133 0.0000000) to (17.666890 37.477133 4.0530626) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7193453 4.6024550 4.0530626 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -37.477133 0.0000000) to (17.666890 37.477133 4.0530626) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7193453 4.6024550 4.0530626 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.477133 0.0000000) to (17.666890 37.477133 4.0530626) create_atoms CPU = 0.000 seconds 229 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 5 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 452 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_650279905230_005#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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1807.0297 0 -1807.0297 67020.433 60 0 -1926.4022 0 -1926.4022 -4190.9284 Loop time of 0.410599 on 1 procs for 60 steps with 452 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 = -1807.02972759897 -1926.40039390974 -1926.40223587423 Force two-norm initial, final = 357.71204 0.15374286 Force max component initial, final = 123.92202 0.028774214 Final line search alpha, max atom move = 1.0000000 0.028774214 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39925 | 0.39925 | 0.39925 | 0.0 | 97.24 Neigh | 0.0043443 | 0.0043443 | 0.0043443 | 0.0 | 1.06 Comm | 0.0040953 | 0.0040953 | 0.0040953 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002907 | | | 0.71 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4578.00 ave 4578 max 4578 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: 74220.0 ave 74220 max 74220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74220 Ave neighs/atom = 164.20354 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 5 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1926.4022 0 -1926.4022 -4190.9284 5367.1011 63 0 -1926.4258 0 -1926.4258 -42.097219 5353.3675 Loop time of 0.0246987 on 1 procs for 3 steps with 452 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 = -1926.40223587423 -1926.42463597461 -1926.42579099499 Force two-norm initial, final = 25.305989 1.2138622 Force max component initial, final = 19.263953 1.0861870 Final line search alpha, max atom move = 0.00020778013 0.00022568807 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023471 | 0.023471 | 0.023471 | 0.0 | 95.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022945 | 0.00022945 | 0.00022945 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009982 | | | 4.04 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4513.00 ave 4513 max 4513 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: 74320.0 ave 74320 max 74320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74320 Ave neighs/atom = 164.42478 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1926.4258 0 -1926.4258 -42.097219 Loop time of 1.926e-06 on 1 procs for 0 steps with 452 atoms 155.8% 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 | | 1.926e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 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: 74356.0 ave 74356 max 74356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74356 Ave neighs/atom = 164.50442 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 5 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.619 | 4.619 | 4.619 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 -1926.4258 -1926.4258 17.672252 74.810813 4.0492145 -42.097219 -42.097219 57.698772 140.77917 -324.7696 2.281674 342.77154 Loop time of 1.89e-06 on 1 procs for 0 steps with 452 atoms 211.6% 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 | | 1.89e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4548.00 ave 4548 max 4548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37178.0 ave 37178 max 37178 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74356.0 ave 74356 max 74356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74356 Ave neighs/atom = 164.50442 Neighbor list builds = 0 Dangerous builds = 0 452 -1926.42568322979 eV 2.28167401564429 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00