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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -46.562511 0.0000000) to (10.974889 46.562511 5.1736123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0971606 5.1736123 5.1736123 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -46.562511 0.0000000) to (10.974889 46.562511 5.1736123) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0971606 5.1736123 5.1736123 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -46.562511 0.0000000) to (10.974889 46.562511 5.1736123) create_atoms CPU = 0.001 seconds 218 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 ghost atom cutoff = 8 binsize = 4, bins = 3 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 434 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1326.7758 0 -1326.7758 184897.53 506 0 -1753.6533 0 -1753.6533 -57719.975 Loop time of 4.40725 on 1 procs for 506 steps with 434 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1326.77582878138 -1753.6516183345 -1753.65329509537 Force two-norm initial, final = 495.79787 0.11526382 Force max component initial, final = 205.81780 0.013031286 Final line search alpha, max atom move = 1.0000000 0.013031286 Iterations, force evaluations = 506 962 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2863 | 4.2863 | 4.2863 | 0.0 | 97.26 Neigh | 0.050179 | 0.050179 | 0.050179 | 0.0 | 1.14 Comm | 0.04394 | 0.04394 | 0.04394 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0268 | | | 0.61 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4669.00 ave 4669 max 4669 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: 74928.0 ave 74928 max 74928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74928 Ave neighs/atom = 172.64516 Neighbor list builds = 9 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 ghost atom cutoff = 8 binsize = 4, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 506 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 506 0 -1753.6533 0 -1753.6533 -57719.975 5287.6221 542 0 -1758.6961 0 -1758.6961 -475.2396 5100.1627 Loop time of 0.182277 on 1 procs for 36 steps with 434 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 = -1753.65329509537 -1758.69477801085 -1758.69608598864 Force two-norm initial, final = 354.50804 3.5897334 Force max component initial, final = 291.66957 2.4892449 Final line search alpha, max atom move = 0.00029119276 0.00072485007 Iterations, force evaluations = 36 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16827 | 0.16827 | 0.16827 | 0.0 | 92.32 Neigh | 0.0054433 | 0.0054433 | 0.0054433 | 0.0 | 2.99 Comm | 0.0016272 | 0.0016272 | 0.0016272 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006935 | | | 3.80 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4769.00 ave 4769 max 4769 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: 77092.0 ave 77092 max 77092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77092 Ave neighs/atom = 177.63134 Neighbor list builds = 1 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 ghost atom cutoff = 8 binsize = 4, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.660 | 4.660 | 4.660 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1758.6961 0 -1758.6961 -475.2396 Loop time of 1.792e-06 on 1 procs for 0 steps with 434 atoms 167.4% 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 | | 1.792e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4769.00 ave 4769 max 4769 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: 77396.0 ave 77396 max 77396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77396 Ave neighs/atom = 178.33180 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 ghost atom cutoff = 8 binsize = 4, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.660 | 4.660 | 4.660 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 -1758.6961 -1758.6961 10.652535 92.239061 5.1905833 -475.2396 -475.2396 -657.16037 -774.53748 5.9790389 2.2976479 1232.5267 Loop time of 2.066e-06 on 1 procs for 0 steps with 434 atoms 242.0% 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 | | 2.066e-06 | | |100.00 Nlocal: 434.000 ave 434 max 434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4769.00 ave 4769 max 4769 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38698.0 ave 38698 max 38698 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77396.0 ave 77396 max 77396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77396 Ave neighs/atom = 178.33180 Neighbor list builds = 0 Dangerous builds = 0 434 -1758.69608598864 eV 2.29764793653178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04