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 -34.471259 0.0000000) to (6.8936352 34.471259 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1361811 4.1361811 3.0829274 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -34.471259 0.0000000) to (6.8936352 34.471259 3.0829274) create_atoms CPU = 0.000 seconds 51 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1361811 4.1361811 3.0829274 Created 51 atoms using lattice units in orthogonal box = (0.0000000 -34.471259 0.0000000) to (6.8936352 34.471259 3.0829274) create_atoms CPU = 0.000 seconds 51 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 = 3 21 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 100 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_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 21 1 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) = 4.376 | 4.376 | 4.376 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -632.11915 0 -632.11915 48033.454 83 0 -648.47188 0 -648.47188 8788.0384 Loop time of 3.90828 on 1 procs for 83 steps with 100 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -632.11915191428 -648.471385283199 -648.471883135215 Force two-norm initial, final = 39.108959 0.10062835 Force max component initial, final = 19.886489 0.024089936 Final line search alpha, max atom move = 1.0000000 0.024089936 Iterations, force evaluations = 83 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.905 | 3.905 | 3.905 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019283 | 0.0019283 | 0.0019283 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001382 | | | 0.04 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1625.00 ave 1625 max 1625 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: 6568.00 ave 6568 max 6568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6568 Ave neighs/atom = 65.680000 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 3 21 1 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.376 | 4.376 | 4.376 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -648.47188 0 -648.47188 8788.0384 1465.2061 85 0 -648.47505 0 -648.47505 6335.0602 1466.7886 Loop time of 0.0833768 on 1 procs for 2 steps with 100 atoms 91.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -648.471883135216 -648.474399112514 -648.475045298281 Force two-norm initial, final = 4.6068806 0.14419763 Force max component initial, final = 4.2684690 0.095410753 Final line search alpha, max atom move = 0.0012124547 0.00011568121 Iterations, force evaluations = 2 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083169 | 0.083169 | 0.083169 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 4.0568e-05 | 4.0568e-05 | 4.0568e-05 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001675 | | | 0.20 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1615.00 ave 1615 max 1615 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: 7858.00 ave 7858 max 7858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7858 Ave neighs/atom = 78.580000 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 = 3 21 1 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -648.47505 0 -648.47505 6335.0602 Loop time of 1.857e-06 on 1 procs for 0 steps with 100 atoms 161.6% 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 | | 1.857e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1615.00 ave 1615 max 1615 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: 7822.00 ave 7822 max 7822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7822 Ave neighs/atom = 78.220000 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 = 3 21 1 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) = 4.514 | 4.514 | 4.514 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 -648.47505 -648.47505 6.905187 68.942518 3.0810941 6335.0602 6335.0602 104.39202 18940.959 -40.170825 2.5769141 135.2177 Loop time of 1.734e-06 on 1 procs for 0 steps with 100 atoms 173.0% 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 | | 1.734e-06 | | |100.00 Nlocal: 100.000 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1615.00 ave 1615 max 1615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3911.00 ave 3911 max 3911 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7822.00 ave 7822 max 7822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7822 Ave neighs/atom = 78.220000 Neighbor list builds = 0 Dangerous builds = 0 100 -648.475045298281 eV 2.57691406619655 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04