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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -40.646848 0.0000000) to (9.5805539 40.646848 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3547972 4.9268906 4.0851619 Created 132 atoms using lattice units in orthogonal box = (0.0000000 -40.646848 0.0000000) to (9.5805539 40.646848 4.0851619) create_atoms CPU = 0.001 seconds 132 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3547972 4.9268906 4.0851619 Created 134 atoms using lattice units in orthogonal box = (0.0000000 -40.646848 0.0000000) to (9.5805539 40.646848 4.0851619) create_atoms CPU = 0.000 seconds 134 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 31 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 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 264 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.794 | 4.794 | 4.794 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1079.9387 0 -1079.9387 20506.966 36 0 -1098.4164 0 -1098.4164 2099.8417 Loop time of 1.17488 on 1 procs for 36 steps with 264 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1079.93868633865 -1098.41538329402 -1098.41643315527 Force two-norm initial, final = 41.595551 0.11107702 Force max component initial, final = 10.879058 0.015773198 Final line search alpha, max atom move = 1.0000000 0.015773198 Iterations, force evaluations = 36 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1724 | 1.1724 | 1.1724 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013086 | 0.0013086 | 0.0013086 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001197 | | | 0.10 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2228.00 ave 2228 max 2228 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: 15192.0 ave 15192 max 15192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15192 Ave neighs/atom = 57.545455 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.794 | 4.794 | 4.794 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -1098.4164 0 -1098.4164 2099.8417 3181.6819 41 0 -1098.4709 0 -1098.4709 -15.713635 3184.8406 Loop time of 0.214755 on 1 procs for 5 steps with 264 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 = -1098.41643315527 -1098.47083224624 -1098.4709416669 Force two-norm initial, final = 24.640790 0.25439139 Force max component initial, final = 23.334378 0.078273352 Final line search alpha, max atom move = 0.0017211312 0.00013471870 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21357 | 0.21357 | 0.21357 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024768 | 0.00024768 | 0.00024768 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009373 | | | 0.44 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 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: 15172.0 ave 15172 max 15172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15172 Ave neighs/atom = 57.469697 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1098.4709 0 -1098.4709 -15.713635 Loop time of 3.54e-06 on 1 procs for 0 steps with 264 atoms 141.2% 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 | | 3.54e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 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: 15172.0 ave 15172 max 15172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15172 Ave neighs/atom = 57.469697 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 4.932 | 4.932 | 4.932 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 -1098.4709 -1098.4709 9.5654672 81.617902 4.0793981 -15.713635 -15.713635 10.465188 -18.285198 -39.320896 2.368447 176.11214 Loop time of 3.772e-06 on 1 procs for 0 steps with 264 atoms 159.1% 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 | | 3.772e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2272.00 ave 2272 max 2272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7586.00 ave 7586 max 7586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15172.0 ave 15172 max 15172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15172 Ave neighs/atom = 57.469697 Neighbor list builds = 0 Dangerous builds = 0 264 -1098.4709416669 eV 2.36844702631361 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01