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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -63.350820 0.0000000) to (44.793306 63.350820 4.9770340) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0830415 5.8654908 4.9770340 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.350820 0.0000000) to (44.793306 63.350820 4.9770340) create_atoms CPU = 0.003 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0830415 5.8654908 4.9770340 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -63.350820 0.0000000) to (44.793306 63.350820 4.9770340) create_atoms CPU = 0.003 seconds 1299 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 = 12 34 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 25 atoms, new total = 2573 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 34 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) = 6.536 | 6.536 | 6.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11364.503 0 -11364.503 10391.549 56 0 -11417.36 0 -11417.36 -6242.0772 Loop time of 2.37158 on 1 procs for 56 steps with 2573 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11364.5031910298 -11417.3498199944 -11417.360334012 Force two-norm initial, final = 113.99038 0.38790377 Force max component initial, final = 35.864070 0.069541836 Final line search alpha, max atom move = 1.0000000 0.069541836 Iterations, force evaluations = 56 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3418 | 2.3418 | 2.3418 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015405 | 0.015405 | 0.015405 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01439 | | | 0.61 Nlocal: 2573.00 ave 2573 max 2573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12823.0 ave 12823 max 12823 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: 448286.0 ave 448286 max 448286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448286 Ave neighs/atom = 174.22697 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 34 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.536 | 6.536 | 6.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -11417.36 0 -11417.36 -6242.0772 28246.585 58 0 -11417.427 0 -11417.427 -2918.5751 28193.612 Loop time of 0.111789 on 1 procs for 2 steps with 2573 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 = -11417.3603340121 -11417.4268514996 -11417.4268668087 Force two-norm initial, final = 100.35129 0.42301033 Force max component initial, final = 72.463864 0.12071090 Final line search alpha, max atom move = 0.0014520695 0.00017528062 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10886 | 0.10886 | 0.10886 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055272 | 0.00055272 | 0.00055272 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002375 | | | 2.12 Nlocal: 2573.00 ave 2573 max 2573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12839.0 ave 12839 max 12839 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: 448436.0 ave 448436 max 448436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448436 Ave neighs/atom = 174.28527 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 = 12 34 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) = 6.674 | 6.674 | 6.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11417.427 0 -11417.427 -2918.5751 Loop time of 1.99e-06 on 1 procs for 0 steps with 2573 atoms 150.8% 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 | | 1.99e-06 | | |100.00 Nlocal: 2573.00 ave 2573 max 2573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12839.0 ave 12839 max 12839 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: 448616.0 ave 448616 max 448616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448616 Ave neighs/atom = 174.35523 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 = 12 34 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) = 6.674 | 6.674 | 6.674 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 -11417.427 -11417.427 44.751258 126.70164 4.9723678 -2918.5751 -2918.5751 -6.0670314 -8756.5115 6.8532844 2.1916593 859.0587 Loop time of 1.911e-06 on 1 procs for 0 steps with 2573 atoms 209.3% 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 | | 1.911e-06 | | |100.00 Nlocal: 2573.00 ave 2573 max 2573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12839.0 ave 12839 max 12839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224308.0 ave 224308 max 224308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 448616.0 ave 448616 max 448616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 448616 Ave neighs/atom = 174.35523 Neighbor list builds = 0 Dangerous builds = 0 2573 -11417.4268668087 eV 2.1916593174708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03