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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -47.979005 0.0000000) to (33.926280 47.979005 5.1737092) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3118660 6.1368495 5.1737092 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -47.979005 0.0000000) to (33.926280 47.979005 5.1737092) create_atoms CPU = 0.002 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3118660 6.1368495 5.1737092 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -47.979005 0.0000000) to (33.926280 47.979005 5.1737092) create_atoms CPU = 0.002 seconds 690 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 26 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1370 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.083 | 5.083 | 5.083 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5402.2715 0 -5402.2715 12810.622 673 0 -5564.4043 0 -5564.4043 -68573.608 Loop time of 15.3266 on 1 procs for 673 steps with 1370 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 = -5402.27149374532 -5564.39923338765 -5564.40427164452 Force two-norm initial, final = 106.17486 0.22620275 Force max component initial, final = 18.537134 0.018887678 Final line search alpha, max atom move = 1.0000000 0.018887678 Iterations, force evaluations = 673 1283 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.87 | 14.87 | 14.87 | 0.0 | 97.02 Neigh | 0.25562 | 0.25562 | 0.25562 | 0.0 | 1.67 Comm | 0.10607 | 0.10607 | 0.10607 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09446 | | | 0.62 Nlocal: 1370.00 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7679.00 ave 7679 max 7679 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: 212708.0 ave 212708 max 212708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212708 Ave neighs/atom = 155.26131 Neighbor list builds = 17 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 673 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.480 | 5.480 | 5.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 673 0 -5564.4043 0 -5564.4043 -68573.608 16843.002 717 0 -5594.6308 0 -5594.6308 58.543999 16032.032 Loop time of 0.512995 on 1 procs for 44 steps with 1370 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 = -5564.40427164453 -5594.62970803452 -5594.63079897245 Force two-norm initial, final = 1353.1162 4.5926275 Force max component initial, final = 1139.5570 3.1316299 Final line search alpha, max atom move = 0.00046510330 0.0014565314 Iterations, force evaluations = 44 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49354 | 0.49354 | 0.49354 | 0.0 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028788 | 0.0028788 | 0.0028788 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01658 | | | 3.23 Nlocal: 1370.00 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7695.00 ave 7695 max 7695 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: 212816.0 ave 212816 max 212816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212816 Ave neighs/atom = 155.34015 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.620 | 5.620 | 5.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5594.6308 0 -5594.6308 58.543999 Loop time of 2.119e-06 on 1 procs for 0 steps with 1370 atoms 188.8% 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 | | 2.119e-06 | | |100.00 Nlocal: 1370.00 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7950.00 ave 7950 max 7950 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: 223220.0 ave 223220 max 223220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223220 Ave neighs/atom = 162.93431 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.620 | 5.620 | 5.620 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 -5594.6308 -5594.6308 33.708066 96.057751 4.9513352 58.543999 58.543999 310.94946 -143.72119 8.4037215 2.2791101 4426.4419 Loop time of 3.049e-06 on 1 procs for 0 steps with 1370 atoms 196.8% 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 | | 3.049e-06 | | |100.00 Nlocal: 1370.00 ave 1370 max 1370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7950.00 ave 7950 max 7950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111610.0 ave 111610 max 111610 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223220.0 ave 223220 max 223220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223220 Ave neighs/atom = 162.93431 Neighbor list builds = 0 Dangerous builds = 0 1370 -5594.63079897245 eV 2.27911014592202 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16