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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -37.771091 0.0000000) to (12.590364 37.771091 3.4919386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8424475 4.8424475 3.4919386 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -37.771091 0.0000000) to (12.590364 37.771091 3.4919386) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8424475 4.8424475 3.4919386 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -37.771091 0.0000000) to (12.590364 37.771091 3.4919386) create_atoms CPU = 0.001 seconds 158 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 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, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_108408461881_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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1316.8048 0 -1316.8048 60594.159 19 0 -1378.7402 0 -1378.7402 13438.737 Loop time of 0.350416 on 1 procs for 19 steps with 312 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 = -1316.80476030246 -1378.73933970344 -1378.74021155243 Force two-norm initial, final = 177.39800 0.13054848 Force max component initial, final = 62.508391 0.034584334 Final line search alpha, max atom move = 1.0000000 0.034584334 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34405 | 0.34405 | 0.34405 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003709 | 0.003709 | 0.003709 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002656 | | | 0.76 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3603.00 ave 3603 max 3603 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: 41592.0 ave 41592 max 41592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41592 Ave neighs/atom = 133.30769 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -1378.7402 0 -1378.7402 13438.737 3321.1951 27 0 -1378.9445 0 -1378.9445 146.98806 3345.2748 Loop time of 0.123198 on 1 procs for 8 steps with 312 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 = -1378.74021155243 -1378.94441784183 -1378.94445757226 Force two-norm initial, final = 59.172218 0.58834485 Force max component initial, final = 52.837008 0.37195127 Final line search alpha, max atom move = 0.0024982355 0.00092922186 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11818 | 0.11818 | 0.11818 | 0.0 | 95.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013119 | 0.0013119 | 0.0013119 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003705 | | | 3.01 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3558.00 ave 3558 max 3558 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: 41528.0 ave 41528 max 41528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41528 Ave neighs/atom = 133.10256 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1378.9445 0 -1378.9445 146.98806 Loop time of 7.046e-06 on 1 procs for 0 steps with 312 atoms 170.3% 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 | | 7.046e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3558.00 ave 3558 max 3558 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: 41384.0 ave 41384 max 41384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41384 Ave neighs/atom = 132.64103 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.581 | 4.581 | 4.581 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 -1378.9445 -1378.9445 12.569666 76.06622 3.4987767 146.98806 146.98806 177.84844 156.52207 106.59367 2.240197 146.04909 Loop time of 6.705e-06 on 1 procs for 0 steps with 312 atoms 268.5% 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 | | 6.705e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3558.00 ave 3558 max 3558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20692.0 ave 20692 max 20692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41384.0 ave 41384 max 41384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41384 Ave neighs/atom = 132.64103 Neighbor list builds = 0 Dangerous builds = 0 312 -1378.94445757226 eV 2.24019699219425 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00