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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -49.325080 0.0000000) to (13.424586 49.325080 8.7884547) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7533941 5.4805644 5.8589698 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.325080 0.0000000) to (13.424586 49.325080 8.7884547) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7533941 5.4805644 5.8589698 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.325080 0.0000000) to (13.424586 49.325080 8.7884547) create_atoms CPU = 0.001 seconds 507 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 4 24 3 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3192.5597 0 -3192.5597 68574.556 78 0 -3537.5327 0 -3537.5327 6816.4529 Loop time of 3.23231 on 1 procs for 78 steps with 1008 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 = -3192.55967478134 -3537.5294935508 -3537.53269141626 Force two-norm initial, final = 556.09696 0.17795596 Force max component initial, final = 99.195157 0.044356676 Final line search alpha, max atom move = 1.0000000 0.044356676 Iterations, force evaluations = 78 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1993 | 3.1993 | 3.1993 | 0.0 | 98.98 Neigh | 0.012853 | 0.012853 | 0.012853 | 0.0 | 0.40 Comm | 0.010537 | 0.010537 | 0.010537 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009657 | | | 0.30 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6504.00 ave 6504 max 6504 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: 201370.0 ave 201370 max 201370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201370 Ave neighs/atom = 199.77183 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 4 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.474 | 5.474 | 5.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -3537.5327 0 -3537.5327 6816.4529 11638.881 83 0 -3537.7199 0 -3537.7199 -261.85037 11696.631 Loop time of 0.151801 on 1 procs for 5 steps with 1008 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 = -3537.53269141626 -3537.71814589099 -3537.71988151924 Force two-norm initial, final = 92.753192 3.4496898 Force max component initial, final = 74.481321 2.3100669 Final line search alpha, max atom move = 0.00018541902 0.00042833034 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14953 | 0.14953 | 0.14953 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038658 | 0.00038658 | 0.00038658 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001882 | | | 1.24 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689.00 ave 6689 max 6689 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: 200972.0 ave 200972 max 200972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200972 Ave neighs/atom = 199.37698 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.612 | 5.612 | 5.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3537.7199 0 -3537.7199 -261.85037 Loop time of 2.211e-06 on 1 procs for 0 steps with 1008 atoms 180.9% 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 | | 2.211e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6665.00 ave 6665 max 6665 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: 200778.0 ave 200778 max 200778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200778 Ave neighs/atom = 199.18452 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 5.612 | 5.612 | 5.612 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 -3537.7199 -3537.7199 13.44373 99.096585 8.7797535 -261.85037 -261.85037 -316.87866 -155.44988 -313.22256 2.3114693 407.93871 Loop time of 2.682e-06 on 1 procs for 0 steps with 1008 atoms 261.0% 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 | | 2.682e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6665.00 ave 6665 max 6665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100389.0 ave 100389 max 100389 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200778.0 ave 200778 max 200778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200778 Ave neighs/atom = 199.18452 Neighbor list builds = 0 Dangerous builds = 0 1008 -3537.71988151924 eV 2.31146933708085 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03