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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -62.145929 0.0000000) to (35.877938 62.145929 6.0935647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5196827 5.5768830 6.0935647 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.145929 0.0000000) to (35.877938 62.145929 6.0935647) create_atoms CPU = 0.003 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5196827 5.5768830 6.0935647 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.145929 0.0000000) to (35.877938 62.145929 6.0935647) create_atoms CPU = 0.002 seconds 1250 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2482 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.337 | 7.337 | 7.337 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10780.22 0 -10780.22 15867.935 26 0 -10847.216 0 -10847.216 -2807.1434 Loop time of 1.7333 on 1 procs for 26 steps with 2482 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10780.2199894432 -10847.2060429363 -10847.216232471 Force two-norm initial, final = 142.28999 0.30450373 Force max component initial, final = 21.290791 0.059154949 Final line search alpha, max atom move = 0.37303458 0.022066842 Iterations, force evaluations = 26 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6846 | 1.6846 | 1.6846 | 0.0 | 97.19 Neigh | 0.03411 | 0.03411 | 0.03411 | 0.0 | 1.97 Comm | 0.0076561 | 0.0076561 | 0.0076561 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006956 | | | 0.40 Nlocal: 2482.00 ave 2482 max 2482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 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: 612148.0 ave 612148 max 612148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612148 Ave neighs/atom = 246.63497 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.337 | 7.337 | 7.337 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -10847.216 0 -10847.216 -2807.1434 27173.25 27 0 -10847.227 0 -10847.227 -1456.818 27152.042 Loop time of 0.109785 on 1 procs for 1 steps with 2482 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 = -10847.2162324711 -10847.2162324711 -10847.2270144761 Force two-norm initial, final = 38.806795 2.6671561 Force max component initial, final = 29.750851 1.9772311 Final line search alpha, max atom move = 3.3612484e-05 6.6459650e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1081 | 0.1081 | 0.1081 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032406 | 0.00032406 | 0.00032406 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00136 | | | 1.24 Nlocal: 2482.00 ave 2482 max 2482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 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: 612328.0 ave 612328 max 612328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612328 Ave neighs/atom = 246.70749 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.475 | 7.475 | 7.475 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10847.227 0 -10847.227 -1456.818 Loop time of 2.17e-06 on 1 procs for 0 steps with 2482 atoms 184.3% 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 | | 2.17e-06 | | |100.00 Nlocal: 2482.00 ave 2482 max 2482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 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: 612380.0 ave 612380 max 612380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612380 Ave neighs/atom = 246.72844 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 9 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 7.475 | 7.475 | 7.475 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 -10847.227 -10847.227 35.862696 124.29186 6.0913968 -1456.818 -1456.818 -104.02747 -4383.0566 116.63013 2.1839858 893.64407 Loop time of 2.466e-06 on 1 procs for 0 steps with 2482 atoms 283.9% 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 | | 2.466e-06 | | |100.00 Nlocal: 2482.00 ave 2482 max 2482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12931.0 ave 12931 max 12931 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 306190.0 ave 306190 max 306190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 612380.0 ave 612380 max 612380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 612380 Ave neighs/atom = 246.72844 Neighbor list builds = 0 Dangerous builds = 0 2482 -10847.2270144761 eV 2.18398576078015 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02